WO2015184283A1 - Tethered ribosomes and methods of making and using thereof - Google Patents

Abstract

An engineered ribosome that includes a tethered subunit arrangement is disclosed, wherein the engineered ribosome supports translation of a sequence defined polymer. Methods for making and using the engineered ribsosome are also disclosed, including a method for preparing a sequence defined polymer using the engineered ribosome and a method for preparing a sequence defined polymer using the engineered ribosome in a two-protein translation system.

Description

TETHERED RIBOSOMES AND METHODS OF MAKING AND USING THEREOF

CROSS-REFERENCE TO RELATED APPLICATIONS

[001] This application claims the priority benefit of U.S. Provisional Application No. 62/004,863, filed 29 May 2014, the disclosure of which is incorporated herein by reference in their entirety.

SEQUENCE LISTING

[002] This application contains, as a separate part of the disclosure, a Sequence Listing in computer readable form (filename: 0101-0101-02_SeqList.txt; Created: 26 May 2015; 48,032 bytes), which is incorporated by reference in its entirety.

FIELD OF INVENTION

[003] This invention pertains to engineered ribosomes and methods of making and using thereof, including the use of engineered ribosomes to prepare a sequence defined polymer and enable two protein translation systems in cells.

BACKGROUND

[004] The ribosome is a ribonucleoprotein machine responsible for protein synthesis. In all kingdoms of life it is composed of two subunits, each built on its own ribosomal RNA (rRNA) scaffold. The independent but coordinated functions of the subunits, including their ability to associate at initiation, rotate during elongation, and dissociate after protein release, are an established paradigm of protein synthesis. Furthermore, the bipartite nature of the ribosome is presumed essential for biogenesis since dedicated assembly factors keep immature ribosomal subunits apart and prevent them from translation initiation [Karbstein 2013]. Free exchange of the subunits limits the development of specialized orthogonal genetic systems that could be evolved for novel functions without interfering with native translation.

[005] The ribosome is an extraordinary complex machine. This large particle, in which

RNA is the main structural and functional component, is invariably comprised of two subunits that coordinate distinct but complementary functions: the small subunit decodes the mRNA, while the large subunit catalyzes peptide -bond formation and provides the exit tunnel for the polypeptide. The association of the subunits is tightly regulated throughout the cycle of translation. First, several assembly factors prevent the two subunits from associating during maturation of the ribonucleoproteins. Later on, the initiation of translation is also strictly controlled such that initiation factors, mRNA and fMet-tRNA⁰^⁶¹ sequentially join the small subunit to form a pre-initiation complex before recruiting the large subunit. During elongation, the subunits ratchet relative to each other with an angle of about 6 degrees. Upon termination, the newly synthesized protein is released from the ribosome and the subunits dissociate during an active process called ribosome recycling to prepare for additional rounds of translation. Thus, the requirement for programmed subunit association and dissociation at specific stages of translation likely explains why the ribosome has been maintained as two subunits during the course of evolution. Although initiation at the leaderless mRNAs was suggested to be carried out by the 70S ribosome with pre-associated subunits, no experimental evidence exists showing that the full cycle of protein synthesis could be accomplished by the ribosome with inseparable subunits.

[006] The random exchange of ribosomal subunits between recurrent acts of protein biosynthesis presents an obstacle for making fully orthogonal ribosomes, a task with important implications for both fundamental science and bioengineering. Previously, it was possible to redirect a subpopulation of the small ribosomal subunits from translating indigenous mRNA to translation of a specific mRNA by placing an alternative Shine-Dalgarno (SD) sequence in a reporter mRNA and introducing the complementary changes in the anti-SD region in 16S rRNA [Hui 1987; Rackham 2005], which enabled selection of mutant 30S subunits with new decoding properties [Wang 2007] . However, because large subunits freely exchange between native and orthogonal small subunits, creating a fully orthogonal ribosome has been impossible thereby limiting the engineering of the 50S subunit, including the peptidyl transferase center (PTC) and the nascent peptide exit tunnel, for specialized new properties.

[007] The engineering of a tethered ribosome, in which the subunits are linked to each other, could open new venues preparing orthogonal translation systems, evolving the ribosome for the incorporation of unnatural amino acids in synthetic biology, and molecularly

characterizing dominant lethal mutations. SUMMARY OF THE INVENTION

[008] Disclosed herein are engineered ribosomes, the engineered ribosomes comprising a small subunit, a large subunit, and a linking moiety, wherein the linking moiety tethers the small subunit with the large subunit and wherein the engineered ribosome is capable of supporting translation of a sequence defined polymer.

[009] In certain embodiments, the small subunit comprises rRNA, the large subunit comprises rRNA, and the linking moiety tethers the rRNA of the small subunit with the rRNA of the large subunit. In certain embodiments, the large subunit comprises a permuted variant of a 23 S rRNA. In certain embodiments, the small subunit comprises a permuted variant of a 16S rRNA. In certain embodiments, the small subunit comprises a modified anti-Shine-Dalgarno sequence to permit translation of templates having a complementary Shine-Dalgarno sequence difference from an endogenous cellular mRNAs.

[0010] In certain embodiments, the linking moiety covalently bonds a helix of the large subunit to a helix of the small subunit. In certain embodiments, the linking moiety covalently bonds helix 10, helix 38, helix 42, helix 54, helix 58, helix 63, helix 78, or helix 101 of the permuted variant of the 23 S rRNA. In certain embodiments, the linking moiety covalently bonds helix 11, helix 26, helix 33, or helix 44 of the permuted variant of the 16S rRNA.

[0011] In certain embodiments, the large subunit comprises a LI polynucleotide domain, a L2 polynucleotide domain, and a C polynucleotide domain, wherein the LI domain is followed, in order, by the C domain and the L2 domain, from 5' to 3'. In certain embodiments, the polynucleotide consisting essentially of the L2 domain followed by the LI domain, from 5' to 3', is substantially identical to 23 S rRNA. In certain embodiments, the polynucleotide consisting essentially of the L2 domain followed by the LI domain, from 5' to 3', is at least 95% identical to a 23 S rRNA. In certain embodiments, the C domain comprises a polynucleotide having a length ranging from 1-200 nucleotides. In certain embodiments, the C domain comprises a GAGA polynucleotide.

[0012] In certain embodiments, the small subunit comprises a SI polynucleotide domain and a S2 polynucleotide domain, wherein the S 1 domain is followed, in order, by the S2 domain, from 5 ' to 3 ' . In certain embodiments, the polynucleotide consisting essentially of the S 1 domain followed by the S2 domain, from 5' to 3', is substantially identical to a 16S rRNA. In certain embodiments, the polynucleotide consisting essentially of the SI domain followed by the S2 domain, from 5' to 3', is at least 95% identical to a 16S rRNA.

[0013] In certain embodiments, the linking moiety comprises a Tl polynucleotide domain and a T2 polynucleotide domain. In certain embodiments, the Tl domain links the SI domain and the LI domain and wherein the SI domain is followed, in order, by the Tl domain and the

LI domain, from 5' to 3'. In certain embodiments, the Tl domain comprises a polynucleotide having a length ranging from 5 to 200 nucleotides. In certain embodiments, the Tl domain comprises a polynucleotide having a length ranging from 7 to 20 nucleotides. In certain embodiments, the Tl domain comprises a polyadenine polynucleotide. In certain embodiments, the Tl domain comprises a polyadenine polynucleotide having a length of 7 to 12 adenine nucleotides. In certain embodiments, the T2 domain links the S2 domain and the L2 domain and wherein the L2 domain is followed, in order, by the T2 domain and the S2 domain, from 5 ' to 3 ' .

In certain embodiments, the T2 domain comprises a polynucleotide having a length ranging from 5 to 200 nucleotides. In certain embodiments, the T2 domain comprises a polynucleotide having a length ranging from 7 to 20 nucleotides. In certain embodiments, the T2 domain comprises a polyadenine polynucleotide. In certain embodiments, the T2 domain comprises a polyadenine polynucleotide having a length of 7 to 12 adenine nucleotides.

[0014] In certain embodiments, the engineered ribosome comprises the SI domain followed, in order, by the Tl domain, the LI domain, the C domain, the L2 domain, the T2 domain, and the S2 domain, from 5' to 3'. In certain embodiments, the engineered ribosome comprises a polynucleotide consisting essentially of the SI domain is followed, in order, by the Tl domain, the LI domain, the C domain, the L2 domain, the T2 domain, and the S2 domain, from 5' to 3'.

[0015] In certain embodiments, the engineered ribosome comprises a mutation. In certain embodiments, the mutation is a change-of- function mutation. In certain embodiments, the change-of-function mutation is a gain-of-function mutation. In certain embodiments, the gain-of- function mutation is in a peptidyl transferase center. In certain embodiments, the gain-of- function mutation is in an A-site of the peptidyl transferase center. In certain embodiments, the gain-ofFunction mutation is in the exit tunnel of the engineered ribosome. In certain

embodiments, the engineered ribosome has an antibiotic resistance mutation.

[0016] Disclosed herein are polynucleotides, the polynucleotides encoding the rRNA of the engineered ribosome. In certain embodiments, the polynucleotide is a vector. In certain embodiments, the polynucleotide further comprises a gene to be expressed by the engineered ribosome. In certain embodiments, the gene is a reporter gene. In certain embodiments, the reporter gene is a green fluorescent protein gene. In certain embodiments, the engineered ribosome comprises a modified anti-Shine-Dalgarno sequence and the gene comprises a complementary Shine-Dalgarno sequence to the engineered ribosome. In certain embodiments, the gene comprises a codon and the codon encodes for an unnatural amino acid.

[0017] Disclosed herein are methods for preparing an engineered ribosome, the method comprising expressing a polynucleotide encoding the rRNA of the engineered ribosome. In certain embodiments, method further comprising selecting a mutant. In certain embodiments, the selection step comprises a negative selection step, a positive selection step, or both a negative and a positive selection step.

[0018] Disclosed here are cells, the cells comprising (i) a polynucleotide polynucleotides encoding the rRNA of the engineered ribosome, (ii) the engineered ribosome, or both (i) and (ii).

[0019] In another aspect of the invention, disclosed herein are cells, the cells comprising a first protein translation mechanism and a second protein translation mechanism, wherein the first protein translation mechanism comprises a ribosome, wherein the ribosome lacks a linking moiety between the large subunit and the small subunit and wherein the second protein translation mechanism comprises the engineered ribosome.

[0020] Disclosed herein are methods for preparing a sequence-defined polymer, the methods comprising (a) providing the engineered ribosome and (b) providing an mRNA or DNA template encoding the sequence-defined polymer. In certain embodiments, the sequence-defined polymer is prepared in vitro. In certain embodiments, the method further comprising providing a ribosome-depleted cellular extract or purified translation system. In certain embodiments, the ribosome-depleted cellular extract comprises an SI 50 extract prepared from mid- to late- exponential growth phase cell cultures or cultures having an O.D.600 ~ 3.0 at time of harvest.

[0021] In certain embodiments, the sequence defined polymer is prepared in vivo. In certain embodiments, the sequence defined polymer is prepared in the cell of any of claims 45 or 46. In certain embodiments, the mRNA or DNA encodes or a modified Shine-Dalgarno sequence and the engineered ribosome comprises an anti-Shine-Dalgarno sequence complementary to the modified Shine-Dalgarno sequence.

[0022] In certain embodiments, the sequence-defined polymer comprises an amino acid. In certain embodiments, the amino acid is a natural amino acid. In certain embodiments, the amino acid is an unnatural amino acid.

BRIEF DESCRIPTION OF THE DRAWINGS

[0023] Non-limiting embodiments of the present invention will be described by way of example with reference to the accompanying figures, which are schematic and are not intended to be drawn to scale. In the figures, each identical or nearly identical component illustrated is typically represented by a single numeral. For purposes of clarity, not every component is labeled in every figure, nor is every component of each embodiment of the invention shown where illustration is not necessary to allow those of ordinary skill in the art to understand the invention.

[0024] FIG. 1A illustrates the secondary structure of a large subunit rRNA and a small subunit rRNA.

[0025] FIG. IB illustrates a gene encoding a large subunit rRNA and a small subunit rRNA.

[0026] FIG. 2A illustrates a tethered ribosome having a large subunit, a small subunit, and a linking moiety.

[0027] FIG. 2B illustrates a gene encoding the tethered ribosome of FIG. 2A.

[0028] FIG. 3 illustrates the permutation of a ribosome subunit.

[0029] FIG. 4A illustrates a plasmid having a gene encoding for rRNA. [0030] FIG. 4B illustrates a plasmid having a gene encoding for the rRNA of a tethered ribosome.

[0031] FIG. 5A shows agarose gel electrophoresis of total RNA prepared from SQ171 cells expressing wild-type ribosomes or Ribo-T.

[0032] FIG. 5B shows the agarose electrophoresis analysis of RNA extracted from the corresponding sucrose gradient peaks for the wild-type ribosomes (WT).

[0033] FIG. 5C shows the agarose electrophoresis analysis of RNA extracted from the corresponding sucrose gradient peaks for the Ribo-T.

[0034] FIG. 5D shows a sucrose gradient fractionation of polysomes prepared from cells expressing wild-type ribosomes (FIG. 5B) or Ribo-T (FIG. 5C)

[0035] FIG. 6 shows growth curves for cells expressing wild-type or tethered ribosomes and for fast-growing mutant cells expressing tethered ribosomes.

[0036] FIG. 7 shows a 2D electrophoresis analysis of cellular proteins expressed by tethered ribosomes.

[0037] FIG. 8A shows polyacrylamide gel electrophoresis of rRNA prepared from the isolated wild-type ribosomes or a tethered ribosome.

[0038] FIG. 8B shows the relative abundance of small and large subunit proteins in Ribo-T incomparison with wild-type ribosome as determined by mass-spectrometry.

[0039] FIG. 9A shows a sucrose gradient analysis of wild-type ribosomes.

[0040] FIG. 9B shows a sucrose gradient analysis of tethered ribosomes.

[0041] FIG. 10A shows SDS gel electrophoresis analysis of the DHFR protein synthesized in the Δ ribosome PURExpress system supplemented with purified wt ribosomes (WT) or Ribo- T (T).

[0042] FIG. 10B shows the time course of expression of the sf-GFP protein in the Δ ribosome PURExpress system supplemented with purified wild-type ribosomes or a tethered ribosomes.

[0043] FIG. 11A shows in vivo translation of the orthogonal sf-gfp reporter.

[0044] FIG. 11B shows in vitro translation of the orthogonal sf-gfp reporter by wild-type ribosomes and tethered ribosomes carrying A2058G mutation in the large subunit.

[0045] FIG. 11C shows in vitro translation of the orthogonal sf-gfp reporter by wild-type ribosomes and tethered ribosomes carrying G693 A mutation in the small subunit.

[0046] FIG. 12 shows an orthogonal secM-LacZa reporter gene. [0047] FIG. 13A shows E. coli cells transformed with an orthogonal secM-lacZa gene and a library of tethered ribosomes with different nucleotide combinations at the 2451 and 2452 positions of the large tethered subunit.

[0048] FIG. 13B shows E. coli cells transformed with a secM-lacZa gene with different nucleotide combinations at the 2451 and 2452 positions.

[0049] FIG. 13C shows enhancement of the bypass of the SecM stalling sequence.

[0050] FIG 14 shows o-sfGFP expression with a tethered ribosome.

[0051] FIG 15 shows unnatural amino acid incorporation into o-sfGFP with a tethered ribosome. DETAILED DESCRIPTION

[0052] Ribosomes with tethered and thus inseparable subunits ("Ribo-T") that are capable of successfully carrying out protein synthesis are disclosed. Ribo-T may be prepared by engineering a ribosome comprising a small subunit, a large subunit, and a linking moiety that tethers the small subunit with the large subunit. The engineered ribosome may comprise a hybrid rRNA comprising a small subunit rRNA sequence, a large subunit rRNA sequence, and RNA linkers that may covalently link the small subunit rRNA sequence and the large subunit rRNA sequence into a single entity. The engineered ribosome may be prepared by expressing a polynucleotide encoding the rRNA of the engineered ribosome. The engineered ribosome may also be evolved by positively or negatively selecting mutations. Strikingly, Ribo-T is not only functional in vitro, but is able to support cell growth even in the absence of wild-type ("wt") ribosomes. As a result, Ribo-T has many uses. For example, Ribo-T may be used to prepare sequence-defined polymers, such as naturally occurring proteins or unnaturally occurring amino-acid polymers; create fully orthogonal ribosome-mRNA systems in vitro or in vivo; explore poorly understood functions of the ribosome; and engineer ribosomes with new functions.

Tethered Ribosome

[0053] The engineered ribosome comprises a small subunit, a large subunit, and a linking moiety, wherein the linking moiety tethers the small subunit with the large subunit. The engineered ribosome is capable of supporting translation of a sequence-defined polymer.

[0054] In contrast to a naturally occurring ribosome, the engineered ribosome has a large and a small subunit that are not separable. FIG. 1 depicts a portion of a wild-type ribosome having a small subunit and a large subunit that are separable. FIG 1A illustrates the secondary structure of a large subunit rRNA 101 and a small subunit rRNA 102 that together form a portion of a functional ribosome. FIG. IB illustrates an rRNA gene 200 comprising the operon encoding the large subunit rRNA 202 and the operon encoding the small subunit rRNA 201. In the wild-type rRNA, the large and small subunit rRNAs are excised from the primary transcript and processed to mature individual subunits.

[0055] An embodiment of the engineered tethered ribosome is illustrated in FIG. 2. FIG. 2 A illustrates the secondary structure of a portion of rRNA the engineered ribosome 300. The engineered ribosome comprises a large subunit 301, a small subunit 302, and a linking moiety 303 that tethers the small subunit 302 with the large subunit 301. In the present example, the linking moiety 303 tethers the rRNA of the small subunit 302 with the rRNA of the large subunit 301. The engineered ribosome may also comprise a connector 304, that closes the ends of a native large subunit rRNA. FIG. 2B illustrates an example of an rRNA gene 400 and the operon encoding to the engineered ribosome 300.

Large Subunit

[0056] The large subunit 301 comprises a subunit capable of joining amino acids to form a polypeptide chain. The large subunit 301 may comprise a first large subunit domain ("LI polynucleotide domain" or "LI domain"), a second large subunit domain ("L2 polynucleotide domain" or "L2 domain"), and a connector domain ("C polynucleotide domain" or "C domain") 304, wherein the LI domain is followed, in order, by the C domain and the L2 domain, from 5' to 3'.

[0057] FIG. 2B illustrates an example of an rRNA gene 400 that encodes the engineered ribosome 300, and provides an alternative representation for understanding the engineered ribosome. The encoding polynucleotide 400 may comprise difference sequences that encode for the various domains of the engineered ribosome 300. As illustrated in FIG. 2B, the

polynucleotide encoding the large subunit rRNA 301 comprises the polynucleotide encoding the LI domain 402, the polynucleotide encoding the C domain 406, and the polynucleotide encoding the L2 domain 403.

[0058] The large subunit rRNA 301 may be a permuted variant of a separable large subunit rRNA. In certain embodiments, the permuted variant is a circularly permuted variant of a separable large subunit rRNA. The separable large subunit may be any functional large subunit. In certain embodiments, the separable large subunit may be a 23 S rRNA. In certain

embodiments, the separable large subunit is a wild-type large subunit rRNA. In specific embodiments, the separable large subunit is a wild-type 23 S rRNA.

[0059] If the large subunit 301 is a permuted variant of a large subunit rRNA, then the polynucleotide consisting essentially of the L2 domain followed by the LI domain, from 5' to 3', may be substantially identical to a large subunit rRNA. In certain embodiments, the polynucleotide consisting essentially of the L2 domain followed by the LI domain, from 5' to 3', is at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical to the large subunit rRNA.

[0060] In certain embodiments where the large subunit 301 is a permuted variant of a separable large subunit rRNA, the large subunit 301 may further comprise a C domain 304 that connects the native 5' and 3' ends of the separable large subunit rRNA. The C domain may comprise a polynucleotide having a length ranging from 1-200 nucleotides. In certain

embodiments, the C domain 304 comprises a polynucleotide having a length ranging from 1-150 nucleotides 1-100 nucleotides, 1-90 nucleotides, from 1-80 nucleotides, 1-70 nucleotides, 1-60 nucleotides, 1-50 nucleotides, 1-40 nucleotides, 1-30 nucleotides, 1-20 nucleotides, 1-10 nucleotides, 1-9 nucleotides, 1-8 nucleotides, 1-7 nucleotides, 1-6 nucleotides, 1-5 nucleotides, 1-4 nucleotides, 1-3 nucleotides, or 1-2 nucleotides. In certain embodiments, the C domain comprises a GAGA polynucleotide.

Small Subunit

[0061] The small subunit 302 is capable of binding mRNA. The small subunit 302 comprises a first small subunit domain ("SI polynucleotide domain" or "SI domain") and a second small subunit domain ("S2 polynucleotide domain" or "S2 domain"), wherein the SI domain is followed, in order, by S2 domain, from 5 ' to 3 ' . Referring again to FIG. 2B, the polynucleotide encoding the small subunit rRNA 302 comprises the polynucleotide encoding the SI domain 401 and the polynucleotide encoding the S2 domain 404.

[0062] The small subunit rRNA 302 may be a permuted variant of a separable small subunit rRNA. In certain embodiments, the permuted variant is a circularly permuted variant of a separable small subunit rRNA. The separable small subunit may be any functional small subunit. In certain embodiments, the separable small subunit may be a 16S rRNA. In certain

embodiments, the separable small subunit is a wild-type small subunit rRNA. In specific embodiments, the separable small subunit is a wild-type 23 S rRNA.

[0063] If the small subunit 302 is a permuted variant of a small subunit rRNA, then the polynucleotide consisting essentially of the SI domain followed by the S2 domain, from 5' to 3', may be substantially identical to a small subunit rRNA. In certain embodiments, the

polynucleotide consisting essentially of the SI domain followed by the S2 domain, from 5' to 3', is at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical to the small subunit rRNA. [0064] The small subunit may further comprise a modified-anti-Shine-Dalgarno sequence. The modified anti-Shine-Dalgarno sequence allows for translation of templates having a complementary Shine-Dalgarno sequence different from an endogenous cellular mR A.

Linking Moiety

[0065] Referring again to FIG. IB, the linking moiety 303 tethers the small subunit 302 with the large subunit 301. In certain embodiments that linking moiety covalently bonds a helix of the large subunit 301 to a helix of the small subunit 302.

[0066] The linking moiety may also comprise a first tether domain ("Tl polynucleotide domain" or "Tl domain") and a second tether domain ("T2 polynucleotide domain" or "T2 domain"). Referring again to FIG. 2B, the polynucleotide encoding the linking moiety 303 comprises the polynucleotide encoding the Tl domain 405 and the polynucleotide encoding the T2 domain 407.

[0067] The Tl domain links that SI domain and the LI domain, wherein the SI domain is followed, in order, by the Tl domain and the LI domain, from 5' to 3'. The Tl domain may comprise a polynucleotide having a length ranging from 5-200 nucleotide, 5-150 nucleotides, 5- 100 nucleotides, 5-90 nucleotide, 5-80 nucleotides, 5-70 nucleotides, 5-60 nucleotides, 5-50 nucleotides, 5-40 nucleotides, 5-30 nucleotides, or 5-20 nucleotides, including polynucleotides having 5 nucleotides, 6 nucleotides, 7 nucleotides, 8 nucleotides, 9 nucleotides, 10 nucleotides, 11 nucleotides, 12 nucleotides, 13 nucleotides, 14 nucleotides, 15 nucleotides, 16 nucleotides, 17 nucleotides, 18 nucleotides, 19 nucleotides, or 20 nucleotides. In certain embodiments, Tl comprises polyadenine. In certain embodiments, Tl comprises polyuridine. In certain

embodiments, Tl comprises an unstructured polynucleotide. In certain embodiments, Tl comprises nucleotides that base-pairs with the T2 domain.

[0068] The T2 domain links that L2 domain and the S2 domain, wherein the L2 domain is followed, in order, by the T2 domain and the S2 domain, from 5 ' to 3 ' . The T2 domain may comprise a polynucleotide having a length ranging from 5-200 nucleotides, 5-150 nucleotides, 5-

100 nucleotides, 5-90 nucleotide, 5-80 nucleotides, 5-70 nucleotides, 5-60 nucleotides, 5-50 nucleotides, 5-40 nucleotides, 5-30 nucleotides, or 5-20 nucleotides, including polynucleotides having 5 nucleotides, 6 nucleotides, 7 nucleotides, 8 nucleotides, 9 nucleotides, 10 nucleotides, 11 nucleotides, 12 nucleotides, 13 nucleotides, 14 nucleotides, 15 nucleotides, 16 nucleotides, 17 nucleotides, 18 nucleotides, 19 nucleotides, or 20 nucleotides. In certain embodiments, Tl comprises polyadenine. In certain embodiments, T2 comprises polyuridine. In certain

embodiments, T12comprises an unstructured polynucleotide. In certain embodiments, T2 comprises nucleotides that base-pairs with the Tl domain. [0069] In embodiments having a Tl domain and a T2 domain, the Tl domain and the T2 domain may have the same number of polynucleotides. In other embodiments, the Tl domain and the T2 domain may have a different number of polynucleotides.

[0070] In certain embodiments, the engineered ribosome may comprise a SI domain followed, in order, by a Tl domain, a LI domain, a C domain, a L2 domain, a T2 domain, and a S2 domain, from 5 ' to 3 ' . In specific embodiments, the engineered ribosome may consist essentially of a SI domain followed, in order, by a Tl domain, a LI domain, a C domain, a L2 domain, a T2 domain, and a S2 domain, from 5 ' to 3 ' .

Mutations

[0071] In certain embodiments, the engineered ribosome may comprise one or more mutations. In specific embodiments the mutation is a change-of- function mutation. A change-of- function mutation may be a gain-of-function mutation or a loss-of-function mutation. A gain-of- function mutation may be any mutation that confers a new function. A loss-of-function mutation may be any mutation that results in the loss of a function possessed by the parent.

[0072] In certain embodiments, the change-of-function mutation may be in the peptidyl transferase center of the ribosome. In specific embodiments, the change-of-function mutation may be in an A-site of the peptidyl transferase center. In other embodiments, the change-of- function mutation may be in the exit tunnel of the engineered ribosome.

[0073] In certain embodiments the change-of-function mutation may be an antibiotic resistance mutation. The antibiotic resistance mutation may be either in the large subunit or the small subunit. In certain embodiments antibiotic resistance mutation may render the engineered ribosome resistant to an aminoglycoside, a tetracycline, a pactamycin, a streptomycin, an edein, or any other antibiotic that targets the small ribosomal subunit. In certain embodiments antibiotic resistance mutation may render the engineered ribosome resistant to a macrolide, a

chloramphenicol, a lincosamide, an oxazolidinone, a pleuromutilin, a streptogramin, or any other antibiotic that targets the large ribosomal subunit.

Designing the Tethered Ribosome

[0074] A successful chimeric construct that tethers a large subunit and a small subunit must i) properly interact with the ribosomal proteins and biogenesis factors for functional ribosome assembly; ii) avoid ribonuclease degradation; and iii) have a linker(s) sufficiently short to ensure subunit cis-association, yet long enough for minimal inhibition of subunit movement required for translation initiation, elongation, and peptide release. The native ends of the large subunit and the small subunit are unsuitable given the design constraints outlined above. For example, in a native prokaryotic ribosome, for example, the ends of 16S and 23S rRNA are too far apart (>170 A) to be connected with a nuclease resistant R A linker. As a result, alternative designs are needed if functioning engineered ribosome are to be realized.

[0075] One approach for designing a tethered ribosome is to permute a large subunit to generate new 5 ' and 3' termini. In certain embodiments, a circular permutation (CP) approach is employed because the native ends on the large subunit are proximal to each other. The CP approach has been pioneered in vitro by Polacek and coworkers [Erlacher 2005], and a subsequent pilot study showed that three 23 S rR A circularly permuted variants could assemble into a functional subunit in vivo [Kitahara 2009]. This approach is illustrated in FIG. 3. In

FIG.3, a native large subunit ribosome 510 comprises a second large subunit domain (L2 domain) 513 followed by a first large subunit domain (LI domain), from 5 ' to 3'. The native ends of a large subunit ribosome 510 (which is a simplified representation of the large subunit rRNA 101 represented in FIG. 1A) are connected through a connector domain (C domain) 511 and new termini are prepared at 512. The permuted subunit prepared by this approach comprises the first large subunit domain (LI domain), followed, in order, by the connector domain (C domain) and the second large subunit domain (L2 domain), from 5' to 3'. FIG. 3 also illustrates a portion of a gene 500 that encodes for the small subunit 501 and the new permuted large subunit comprising the LI domain 502, followed, in order, by the C domain 506 and the L2 domain 503, from 5' to 3'.

[0076] Continuing the approach outlined above, new termini for the small subunit need to be prepared so that the new termini for the small unit can be joined with the new termini of the large subunit by the linking moiety, as shown in FIGS. 2 A, B.

[0077] The approach outlined above can be used to generate collections of circularly permuted mutants with new termini. The new termini may be prepared at any location in the native subunit. Although some new termini result in permuted mutants may not be viable, the process disclosed herein is capable of generating and testing collections of permuted mutants.

[0078] In some embodiments, the location of the new termini of a small subunit or large subunit may be selected based on the secondary structure of a subunit, the proximity to the other subunit, the ribosome viability, or any combination thereof.

[0079] The secondary structure of either or both of the large subunit and the small subunit may be used to determine the location for new termini. In certain embodiments, the new termini are prepared in a helix of a native subunit. In some specific embodiments the new termini are prepared in hairpin of a native subunit.

[0080] The proximity to the other subunit may be used to select the location of the new termini in either or both of the large subunit or the small subunit. In certain embodiments, the new termini are located in the subunit solvent side of the native subunit. In some other embodiments the new termini are located close to the subunit interface rim. In certain specific embodiments the new termini are located in the subunit solvent side and close to the subunit interface rim.

[0081] Ribosome viability may be used to select the location of the new termini in either or both of the large subunit or the small subunit. For example, polynucleotide sequences or secondary structures that are in either or both of the large subunit or the small subunit that are not highly conserved in populations may be used to select the location for new termini.

[0082] In certain embodiments where the engineered ribosome is a 23 S construct, the linking moiety may covalently bond helix 10, helix 38, helix 42, helix 54, helix 58, helix 63, helix 78, or helix 101 of a permuted variant of the 23 S rRNA. In certain embodiments where the engineered ribosome is a 16S rRNA construct, the linking moiety may covalently bond helix 11, helix 26, helix 33, or helix 44 of a permuted variant of the 16S rRNA. In certain other embodiments where the engineered ribosome is a 16S construct, the linking moiety may covalently bond close to the E-site of a permuted variant of the 16S rRNA. In specific embodiments where the engineered ribosome is a 16S-23S construct, the linking moiety may covalently bond helix 44 of a permuted variant 16S rRNA with helix 101 of a permuted variant 23 S rRNA, the linking moiety may covalently bond helix 26 of a permuted variant 16S rRNA with helix 10 of a permuted variant 23S rRNA, the linking moiety may covalently bond helix 33 of a permuted variant 16S rRNA with helix 38 of a permuted variant 23 S rRNA, the linking moiety may covalently bond helix 11 of a permuted variant 16S rRNA with helix 58 of a permuted variant 23 S rRNA, the linking moiety may covalently bond helix 44 of a permuted variant 16S rRNA with helix 58 of a permuted variant 23 S rRNA, the linking moiety may covalently bond helix 26 of a permuted 1 variant 6S rRNA with helix 54 of a permuted variant 23 S rRNA, the linking moiety may covalently bond helix 11 of a permuted variant 16S rRNA with helix 63 of a permuted variant 23 S rRNA, or the linking moiety may covalently bond helix 44 of a permuted variant 16S rRNA with helix 63 of a permuted variant 23 S rRNA.

[0083] As explained above, the linking moiety must be sufficiently short to prevent degradation and to ensure subunit cis-association while long enough for minimal inhibition of subunit movement required for translation initiation, elongation, and peptide release. As a result, the linking moiety must span tens of Angstroms between the new termini on the large subunit and the short subunit. Polynucleotides Encoding the Tethered Ribosome

[0084] Polynucleotides encoding the tethered ribosome are also disclosed. The

polynucleotide encoding for the tethered ribosome may be any polynucleotide capable of being expressed to produce the rRNA of the tethered ribosome. FIG. 2B illustrates a polynucleotide for preparing the rRNA of the tethered ribosome. The polynucleotide 400 comprises a sequence that encodes for the rRNA of a SI domain 401 followed, in order, by a sequence that encodes for the rRNA of a Tl linker 405, a sequence that encodes for the rRNA of a LI domain 402, a sequence that encodes for the rRNA of a C domain 406, a sequence that encodes for the rRNA of a L2 domain 403, a sequence that encodes for the rRNA of a T2 linker 407, and a sequence that encodes for the rRNA of a S2 domain 404, from 5 ' to 3 ' .

[0085] The polynucleotides encoding for the tethered ribosome may further comprise genes encoding for other rRNA subunits of the ribosome or ribosomal proteins. For example, the polynucleotide encoding for an engineered ribosome comprising a permuted 23 S rRNA tethered to a permuted 16S rRNA, the polynucleotide may further comprise a gene encoding for a 5S rRNA.

[0086] In certain embodiments the polynucleotide is a vector that may introduce foreign genetic material into a host cell. The vector may be a plasmid, viral vector, cosmid, or artificial chromosome.

[0087] FIGS. 4A, B provide examples of plasmids that encode for a prokaryotic ribosome having separable subunits (FIG. 4A) and a polynucleotide encoding for a tethered ribosome

(FIGS. 4B). In a FIG. 4A, the plasmid 600 comprises a promoter 612, a gene encoding for a 16S subunit 601, including a representation of the processing stems indicated by the smaller rectangles, a tRNA gene 613, a gene encoding a 23S subunit 602, including a representation of the processing stems indicated by the smaller rectangles, a gene encoding a 5S subunit 611, a gene encoding antibiotic resistance 614, and a origin of replication gene 615.

[0088] In contrast to the plasmid encoding the ribosome having separable subunits, the plasmid encoding a tethered ribosome 700 has a chimeric gene encoding for a large subunit, a small subunit, and a linking moiety connecting the large subunit with the small subunit 701-707.

Plasmid comprises the genes for the expression of the tethered ribosome 720. Optionally, the plasmid may further comprise one or more addition genes 740.

[0089] The gene encoding for the tethered subunits comprises the sequence that encodes for the rRNA of a SI domain 701 followed, in order, by a sequence that encodes for the rRNA of a

Tl linker 705, a sequence that encodes for the rRNA of a LI domain 702, a sequence that encodes for the rRNA of a C domain 706, a sequence that encodes for the rRNA of a L2 domain 703, a sequence that encodes for the rR A of a T2 linker 707, and a sequence that encodes for the rRNA of a S2 domain 704, from 5' to 3'. The processing sequences of a small subunit flanking the chimeric gene, indicated by the small rectangles, may be retained for proper maturation of the small subunit termini, whereas the processing sequences for the large subunit 716 may be moved to another location in the plasmid or eliminated entirely to prevent cleavage of the large subunit out of the hybrid.

[0090] In certain embodiments, the plasmid encoding the tethered subunits further comprises a gene encoding a 5S subunit 711, a gene encoding antibiotic resistance 714, and an origin of replication gene 715.

[0091] Optionally, the gene encoding the tethered subunits may comprise a modified anti- Shine-Dalgarno sequence 708 (circle). Although the modified anti-SD sequence is shown in FIG. 4B to be located within the sequence encoding the S2 domain, the modified anti-Shine Dalgarno sequence may be located in either of the small subunit domains, i.e. SI or S2.

[0092] Optionally, the plasmid encoding the tethered subunits comprises one or more additional genes 740. The additional gene may comprise a modified Shine-Dalgarno sequence that is complimentary with a modified anti-Shine-Dalgarno sequence of the tethered ribosome. In certain embodiments that additional gene may be a reporter gene. In specific embodiments, the reporter gene is a green fluorescent protein.

Preparing the polynucleotide

[0093] Methods of preparing the polynucleotide are also disclosed herein. The method comprises preparing a plasmid encoding a permuted subunit rRNA construct, identifying a viable permuted subunit rRNA constructs, and preparing a polynucleotide encoding the engineered ribosome comprising a large subunit, a small subunit, and a linking moiety that tethers the small subunit with the large subunit.

[0094] Preparation of a plasmid encoding a permuted subunit rRNA construct may be accomplished by the circular permutation approach that connects the native ends of the subunit and prepares new termini FIG. 3. Preparation of the plasmid may comprise the steps of template preparation, plasmid backbone preparation, and assembly. The template preparation step may be accomplished by plasmid digestion and ligation. By way of example, a CP23S template may be prepared from pCP23S-EagI plasmid by Eagl digestion and ligation. Each CP23S variant is generated by PCR using a circularized 23 S rRNA gene as a template and a unique primer pair, with added sequences overlapping the destination plasmid backbone. The plasmid backbone preparation step may be accomplished by digestion of a plasmid with a restriction enzyme that linearized the backbone at the subunit processing stem site. By way of example, Plasmid backbone is prepared by digestion of pAM552-23S-AflII with Aflll restriction enzyme, which linearizes the backbone at the 23 S processing stem site. The assembly step incorporates the template with the plasmid backbone to prepare the plasmid encoding the permuted subunit rR A. The assembly step may be accomplished by Gibson assembly.

[0095] To identify permuted subunit rRNA viable constructs, the plasmid encoding the permuted subunit rRNA may be introduced in to host cell strains and a screening mechanism is used to identify transformants. The host cells comprise the plasmid as well as a plasmid encoding for the wild-type rRNA operon and may be spotted onto an agar plate along with an antibiotic. The selection mechanism includes identifying transformants resistant to the antibiotic. By way of example, the plasmids may be transformed into Δ7 rrn SQ171 strain carrying pCSacB plasmid with wild-type rRNA operon and transformants resistant to ampicillin, erythromycin and sucrose are selected. To confirm complete replacement of the wild-type rRNA operon with the plasmid encoding for the permuted subunit rRNA, a three-primer diagnostic PCR check may be performed on the total plasmid extract.

[0096] Preparing a polynucleotide encoding the engineered ribosome comprising a large subunit, a small subunit, and a linking moiety that tethers the small subunit with the large subunit comprises grafting the permuted subunit rRNA construct and the linking moiety into the other subunit. In certain embodiments the preparation step may also include preparing a plasmid comprising the polynucleotide encoding the engineered ribosome comprising a large subunit, a small subunit, and a linking moiety that tethers the small subunit with the large subunit. In other embodiments, the preparation step may also include preparing a plasmid comprising the polynucleotide encoding the engineered ribosome comprising a large subunit, a small subunit, and a linking moiety that tethers the small subunit with the large subunit and a polynucleotide encoding for an additional gene.

Preparing the Tethered Ribosome

[0097] Also disclosed are methods for preparing the tethered ribosome. The tethered ribosome may be prepared by expressing a polynucleotide encoding the engineered ribosome. In certain embodiments preparation of the tethered ribosome further comprises preparing the polynucleotide encoding the engineered ribosome. In other embodiments the preparation of the tethered ribosome further comprises transforming a cell with the polynucleotide encoding the engineered ribosome. In some specific embodiments, the preparation of the tethered ribosome further comprises preparing the polynucleotide and transforming a cell with the polynucleotide. Tethered Ribosome Evolution

[0098] Also discloses are methods for evolving the tethered ribosome. Methods for tethered ribosome evolution include expressing a polynucleotide encoding for the engineered ribosome and selecting a mutant. The selection step may comprise a negative selection step, a positive selection step, or both a negative and a positive selection step. The mutant selected may comprise a tethered ribosome having a change-of-function mutation. The change-of-function mutation may be a gain-of-function mutation or a loss-of- function mutation.

Utility and applications of Tethered Ribosomes

[0099] Some uses and applications of the tethered ribosomes are described below.

Artificial Cells

[00100] Artificial cells are disclosed. The artificial cell may comprise a polynucleotide encoding an engineered ribosome, the engineered ribosome comprising a small subunit, a large subunit, and a linking moiety, wherein the linking moiety tethers the small subunit with the large subunit. The artificial cell comprising a polynucleotide encoding the engineered ribosome may be capable of expressing the polynucleotide to prepare the engineered ribosome. In other embodiments, the artificial cell comprises the engineered ribosome. In some specific

embodiments the artificial cell comprises a polynucleotide encoding the engineered ribosome and the engineered ribosome.

[00101] Artificial cells may comprise one or more translations mechanism. In a first embodiment, the artificial cell has one translation mechanism comprising an engineered ribosome, the engineered ribosome comprising a small subunit, a large subunit, and a linking moiety, wherein the linking moiety tethers the small subunit with the large subunit.

[00102] In another embodiment, the artificial cell may comprise two translation mechanisms. The first translation mechanism may comprise a ribosome wherein the ribosome lacks a linking moiety between the large subunit and the small subunit. The second translation mechanism comprises an engineered ribosome, the engineered ribosome comprising a small subunit, a large subunit, and a linking moiety, wherein the linking moiety tethers the small subunit with the large subunit. In some embodiments the second translation mechanism is an orthogonal translation mechanism. In some specific embodiments the first translation mechanism and the second translation mechanism are orthogonal translation mechanisms. An orthogonal translation mechanism may be prepared by modifying the anti-Shine Dalgarno sequence of the engineered ribosome to permit translation of templates having a complementary Shine-Dalgarno sequences different from the endogenous cellular mR As. [00103] In another embodiment, a cell comprising a first mechanism and a second mechanism for protein translation is disclosed. The first mechanism is the natural translation mechanism wherein mR A is translated by a ribosome in accordance with the natural genetic code (that is, triplet code endogenous to the cell). The second mechanism includes an artificial mechanism derived from a tethered ribosome that functions to allow for expression of a heterologous gene. Preparation of Sequence-defined Polymers

[00104] Methods for preparing sequence-defined polymers are also provided. In certain embodiments the method for preparing a sequence defined polymer comprises providing an engineered ribosome and providing an mRNA or DNA template encoding the sequence-defined polymer, wherein the engineered ribosome comprises a small subunit, a large subunit, and a linking moiety and wherein the linking moiety tethers the small subunit with the large subunit. In one aspect of the method, one of any of the steps includes adding at least one exogenous DNA template encoding an mRNA for the sequence-defined polymer.

[00105] In one aspect of the method, the sequence-defined polymer is a natural biopolymer. In another aspect of the method, the sequence-defined polymer is a non-natural biopolymer. In certain embodiments, the sequence-defined polymer comprises an amino acid. In certain embodiments the amino acid may be a natural amino acid. As used herein a natural amino acid is a proteinogenic amino acid encoded directly by a codon of the universal genetic code. In certain embodiments the amino acid may be an unnatural amino acid. As used here an unnatural amino acid is a nonproteinogenic amino acid. Examples of unnatural amino acids include, but are not limited to a p-acetyl-L-phenylalanine, a p-iodo-L-phenylalanine, an O-methyl-L-tyrosine, a p- propargyloxyphenylalanine, a p-propargyl-phenylalanine, an L-3-(2-naphthyl)alanine, a 3- methyl-phenylalanine, an O-4-allyl-L-tyrosine, a 4-propyl-L-tyrosine, a tri-O-acetyl-GlcNAcpP- serine, an L-Dopa, a fluorinated phenylalanine, an isopropyl-L-phenylalanine, a p-azido-L- phenylalanine, a p-acyl-L-phenylalanine, a p-benzoyl-L-phenylalanine, an L-phosphoserine, a phosphonoserine, a phosphonotyrosine, a p-bromophenylalanine, a p-amino-L-phenylalanine, an isopropyl-L-phenylalanine, an unnatural analogue of a tyrosine amino acid; an unnatural analogue of a glutamine amino acid; an unnatural analogue of a phenylalanine amino acid; an unnatural analogue of a serine amino acid; an unnatural analogue of a threonine amino acid; an unnatural analogue of a methionine amino acid; an unnatural analogue of a leucine amino acid; an unnatural analogue of a isoleucine amino acid; an alkyl, aryl, acyl, azido, cyano, halo, hydrazine, hydrazide, hydroxyl, alkenyl, alkynl, ether, thiol, sulfonyl, seleno, ester, thioacid, borate, boronate, phospho, phosphono, phosphine, heterocyclic, enone, imine, aldehyde, hydroxylamine, keto, or amino substituted amino acid, or a combination thereof; an amino acid with a photoactivatable cross-linker; a spin-labeled amino acid; a fluorescent amino acid; a metal binding amino acid; a metal-containing amino acid; a radioactive amino acid; a photocaged and/or photoisomerizable amino acid; a biotin or biotin-analogue containing amino acid; a keto containing amino acid; an amino acid comprising polyethylene glycol or polyether; a heavy atom substituted amino acid; a chemically cleavable or photocleavable amino acid; an amino acid with an elongated side chain; an amino acid containing a toxic group; a sugar substituted amino acid; a carbon-linked sugar-containing amino acid; a redox-active amino acid; an a-hydroxy containing acid; an amino thio acid; an α,α disubstituted amino acid; a β-amino acid; a O-amino acid, a cyclic amino acid other than proline or histidine, and an aromatic amino acid other than phenylalanine, tyrosine or tryptophan. In certain embodiments the sequence-defined polymer is a polypeptide or protein.

[00106] In one aspect of the method, the tethered subunit arrangement comprises a linking moiety between the 23S and 16S rR As. In one respect of this aspect, the linking moiety covalently bonds helix 101 of the 23 S rRNA to helix 44 of the 16S rRNA. In another respect of this aspect, the linking moiety comprises a polynucleotide having a length ranging from 5 nucleotides to 200 nucleotides. The engineered ribosome can further include an engineered 16S rRNA having a modified anti-Shine-Dalgarno sequence to permit translation in vitro of translation templates having a complementary SD sequence differing from endogenous cellular mRNAs. In this way, selective translation in vitro of mRNA to produce sequence defined biopolymers with high efficiency is possible.

[00107] In one aspect of the method, the mRNA or DNA template encodes a modified Shine- Dalgarno sequence. In certain embodiments the engineered ribosome comprises an anti-Shine- Dalgarno sequence complementary to the Shine-Dalgarno sequence encoded by the mRNA or DNA template.

[00108] Sequence-defined polymers may be prepared in vitro. The method for preparing a sequence-defined polymer in vitro further comprises providing a ribosome-depleted cellular extract or a purified translation system. In certain embodiments, the wherein the ribosome- depleted cellular extract comprises an SI 50 extract prepared from mid- to late- exponential growth phase cell cultures or cultures having an O.D.600 ~ 3.0 at time of harvest. In one aspect of the method, the ribosome-depleted extract is prepared with one or more polyamines, such as spermine, spermidine and putrescine, or combinations thereof. In one aspect of the method, the ribosome-depleted extract is prepared with a concentration of salts from about 50 mM to about 300 mM. [00109] The preparation of ribosome-depleted cellular extracts and methods of using them for supporting translation in vitro of sequence-defined polymers is disclosed in International Patent Application No. PCT/US 14/35376 to Michael Jewett et al, entitled IMPROVED METHODS FOR MAKING RIBOSOMES, filed April 24, 2014, the contents of which are incorporated by reference herein in its entirety.

[00110] In one aspect of the method, mRNA encodes a modified Shine-Dalgarno sequence differing from endogenous cellular mRNAs present in the ribosome-depleted cellular extract. In one respect of this aspect, the engineered ribosome further includes an engineered 16S rRNA having a modified anti-Shine-Dalgarno sequence complementary to the modified Shine- Dalgarno sequence to permit translation in vitro of the mRNA to prepare the sequence defined biopolymer in vitro.

[00111] In one aspect, the method is configured for fed-batch operation or continuous operation. In another aspect of the method, at least one substrate is replenished during operation.

[00112] In one aspect of the method, at least one step includes a DNA-dependent RNA polymerase. In one aspect of the method, at least one macromolecular crowding agent is included in one of the steps. In one aspect of the method, at least one reducing agent (e.g., dithiothreitol, tris(2-carboxyethyl) phosphine hydrochloride, etc.) is included in one of the steps.

[00113] Sequence-defined polymers may be prepared in vivo. The method for preparing a sequence-defined polymer in vivo may occur in an artificial cell as disclosed above. The artificial cell may have a translation mechanism comprising an engineered ribosome, wherein the engineered ribosome comprises a small subunit, a large subunit, and a linking moiety and wherein the linking moiety tethers the small subunit with the large subunit. In certain

embodiments the artificial cell has one translation mechanism. In other embodiments the cell has two translations mechanisms. In specific embodiments, the cell has two translations mechanisms, the first protein translation mechanism comprising a ribosome, wherein the ribosome lacks a linking moiety between the large subunit and the small subunit and the second protein translation mechanism comprises the engineered ribosome.

Terminology

[00114] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of skill in the art to which the invention pertains. All definitions, as defined and used herein, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and/or ordinary meanings of the defined terms. [00115] The indefinite articles "a" and "an," as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean "at least one." [00116] A range includes each individual member. Thus, for example, a group having 1-3 members refers to groups having 1, 2, or 3 members.

[00117] It should also be understood that, unless clearly indicated to the contrary, in any methods claimed herein that include more than one step or act, the order of the steps or acts of the method is not necessarily limited to the order in which the steps or acts of the method are recited.

[00118] The modal verb "may" refers to the preferred use or selection of one or more options or choices among the several described embodiments or features contained within the same. Where no options or choices are disclosed regarding a particular embodiment or feature contained in the same, the modal verb "may" refers to an affirmative act regarding how to make or use an aspect of a described embodiment or feature contained in the same, or a definitive decision to use a specific skill regarding a described embodiment or feature contained in the same. In this latter context, the modal verb "may" has the same meaning and connotation as the auxiliary verb "can."

[00119] In the claims, as well as in the specification above, all transitional phrases such as "comprising," "including," "carrying," "having," "containing," "involving," "holding,"

"composed of," and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases "consisting of and "consisting essentially of shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.

[00120] The terms "nucleic acid" and "oligonucleotide," as used herein, refer to

polydeoxyribonucleotides (containing 2-deoxy-DRibose), polyribonucleotides (containing DRibose), and to any other type of polynucleotide that is an N glycoside of a purine or pyrimidine base. There is no intended distinction in length between the terms "nucleic acid", "oligonucleotide" and "polynucleotide", and these terms will be used interchangeably. These terms refer only to the primary structure of the molecule. Thus, these terms include double- and single-stranded DNA, as well as double- and single-stranded RNA. For use in the present invention, an oligonucleotide also can comprise nucleotide analogs in which the base, sugar or phosphate backbone is modified as well as non-purine or non-pyrimidine nucleotide analogs.

[00121] Oligonucleotides can be prepared by any suitable method, including direct chemical synthesis by a method such as the phosphotriester method of Narang et al., 1979, Meth.

Enzymol. 68:90-99; the phosphodiester method of Brown et al., 1979, Meth. Enzymol. 68: 109- 151; the diethylphosphoramidite method of Beaucage et al., 1981, Tetrahedron Letters 22: 1859- 1862; and the solid support method of U.S. Pat. No. 4,458,066, each incorporated herein by reference. A review of synthesis methods of conjugates of oligonucleotides and modified nucleotides is provided in Goodchild, 1990, Bioconjugate Chemistry 1(3): 165-187, incorporated herein by reference.

[00122] The term "primer," as used herein, refers to an oligonucleotide capable of acting as a point of initiation of DNA synthesis under suitable conditions. Such conditions include those in which synthesis of a primer extension product complementary to a nucleic acid strand is induced in the presence of four different nucleoside triphosphates and an agent for extension (for example, a DNA polymerase or reverse transcriptase) in an appropriate buffer and at a suitable temperature.

[00123] A primer is preferably a single-stranded DNA. The appropriate length of a primer depends on the intended use of the primer but typically ranges from about 6 to about 225 nucleotides, including intermediate ranges, such as from 15 to 35 nucleotides, from 18 to 75 nucleotides and from 25 to 150 nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with the template. A primer need not reflect the exact sequence of the template nucleic acid, but must be sufficiently complementary to hybridize with the template. The design of suitable primers for the amplification of a given target sequence is well known in the art and described in the literature cited herein.

[00124] Primers can incorporate additional features which allow for the detection or immobilization of the primer but do not alter the basic property of the primer, that of acting as a point of initiation of DNA synthesis. For example, primers may contain an additional nucleic acid sequence at the 5' end which does not hybridize to the target nucleic acid, but which facilitates cloning or detection of the amplified product, or which enables transcription of RNA (for example, by inclusion of a promoter) or translation of protein (for example, by inclusion of a 5'-UTR, such as an Internal Ribosome Entry Site (IRES) or a 3'-UTR element, such as a poly(A)n sequence, where n is in the range from about 20 to about 200). The region of the primer that is sufficiently complementary to the template to hybridize is referred to herein as the hybridizing region.

[00125] The term "promoter" refers to a cis-acting DNA sequence that directs RNA polymerase and other trans-acting transcription factors to initiate RNA transcription from the DNA template that includes the cis-acting DNA sequence. [00126] The terms "target, "target sequence", "target region", and "target nucleic acid," as used herein, are synonymous and refer to a region or sequence of a nucleic acid which is to be amplified, sequenced or detected.

[00127] The term "hybridization," as used herein, refers to the formation of a duplex structure by two single-stranded nucleic acids due to complementary base pairing. Hybridization can occur between fully complementary nucleic acid strands or between "substantially

complementary" nucleic acid strands that contain minor regions of mismatch. Conditions under which hybridization of fully complementary nucleic acid strands is strongly preferred are referred to as "stringent hybridization conditions" or "sequence-specific hybridization

conditions". Stable duplexes of substantially complementary sequences can be achieved under less stringent hybridization conditions; the degree of mismatch tolerated can be controlled by suitable adjustment of the hybridization conditions. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length and base pair composition of the oligonucleotides, ionic strength, and incidence of mismatched base pairs, following the guidance provided by the art

(see, e.g., Sambrook et al, 1989, Molecular Cloning-A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Wetmur, 1991, Critical Review in Biochem. and Mol. Biol. 26(3/4):227-259; and Owczarzy et al, 2008, Biochemistry, 47: 5336-5353, which are incorporated herein by reference).

[00128] The term "amplification reaction" refers to any chemical reaction, including an enzymatic reaction, which results in increased copies of a template nucleic acid sequence or results in transcription of a template nucleic acid. Amplification reactions include reverse transcription, the polymerase chain reaction (PCR), including Real Time PCR (see U.S. Pat. Nos. 4,683,195 and 4,683,202; PCR Protocols: A Guide to Methods and Applications (Innis et al, eds, 1990)), and the ligase chain reaction (LCR) (see Barany et al, U.S. Pat. No. 5,494,810).

Exemplary "amplification reactions conditions" or "amplification conditions" typically comprise either two or three step cycles. Two-step cycles have a high temperature denaturation step followed by a hybridization/elongation (or ligation) step. Three step cycles comprise a denaturation step followed by a hybridization step followed by a separate elongation step.

[00129] As used herein, a "polymerase" refers to an enzyme that catalyzes the polymerization of nucleotides. "DNA polymerase" catalyzes the polymerization of deoxyribonucleotides.

Known DNA polymerases include, for example, Pyrococcus furiosus (Pfu) DNA polymerase, E. coli DNA polymerase I, T7 DNA polymerase and Thermus aquaticus (Taq) DNA polymerase, among others. "RNA polymerase" catalyzes the polymerization of ribonucleotides. The foregoing examples of DNA polymerases are also known as DNA-dependent DNA polymerases. RNA-dependent DNA polymerases also fall within the scope of DNA polymerases. Reverse transcriptase, which includes viral polymerases encoded by retroviruses, is an example of an RNA-dependent DNA polymerase. Known examples of RNA polymerase ("RNAP") include, for example, T3 RNA polymerase, T7 RNA polymerase, SP6 RNA polymerase and E. coli RNA polymerase, among others. The foregoing examples of RNA polymerases are also known as DNA-dependent RNA polymerase. The polymerase activity of any of the above enzymes can be determined by means well known in the art.

[00130] As used herein, the term "sequence defined polymer" refers to a polymer having a specific primary sequence. A sequence defined polymer can be equivalent to a genetically- encoded defined polymer in cases where a gene encodes the polymer having a specific primary sequence.

[00131] As used herein, a primer is "specific," for a target sequence if, when used in an amplification reaction under sufficiently stringent conditions, the primer hybridizes primarily to the target nucleic acid. Typically, a primer is specific for a target sequence if the primer-target duplex stability is greater than the stability of a duplex formed between the primer and any other sequence found in the sample. One of skill in the art will recognize that various factors, such as salt conditions as well as base composition of the primer and the location of the mismatches, will affect the specificity of the primer, and that routine experimental confirmation of the primer specificity will be needed in many cases. Hybridization conditions can be chosen under which the primer can form stable duplexes only with a target sequence. Thus, the use of target-specific primers under suitably stringent amplification conditions enables the selective amplification of those target sequences that contain the target primer binding sites.

[00132] As used herein, "expression template" refers to a nucleic acid that serves as substrate for transcribing at least one RNA that can be translated into a polypeptide or protein. Expression templates include nucleic acids composed of DNA or RNA. Suitable sources of DNA for use a nucleic acid for an expression template include genomic DNA, plasmid DNA, cDNA and RNA that can be converted into cDNA. Genomic DNA, cDNA and RNA can be from any biological source, such as a tissue sample, a biopsy, a swab, sputum, a blood sample, a fecal sample, a urine sample, a scraping, among others. The genomic DNA, cDNA and RNA can be from host cell or virus origins and from any species, including extant and extinct organisms. As used herein, "expression template" and "transcription template" have the same meaning and are used interchangeably. [00133] As used herein, "tethered," "conjoined," "linked," "connected," "coupled" and "covalently-bonded" have the same meaning as modifiers.

[00134] As used herein, "tethered ribosome," "engineered ribosome," and "Ribo-T" will be used interchangeably.

[00135] As used here, "CP" refers to a circularly permuted subunit. As used herein, when CP is followed by "23 S" that refers to a circularly permuted 23 S rRNA. As used herein, when CP followed by a number may refer to the location of the new 5' end in a secondary structure, e.g. CP101 means the new 5' end is in helix 101 of the 23 S rRNA, or to the location of the new 5' nucleotide, e.g. CP2861 means the new 5 ' nucleotide is the nucleotide 2861 of the 23 rRNA, depending on context.

[00136] As used herein, "translation template" refers to an RNA product of transcription from an expression template that can be used by ribosomes to synthesize polypeptide or protein.

Miscellaneous

[00137] All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., "such as") provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.

[00138] Preferred aspects of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred aspects may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect a person having ordinary skill in the art to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context. EXAMPLES

Viable variants of permuted large subunits

[00139] A comprehensive collection of 91 cp23S rDNA mutants with new ends placed at nearly every 23 S rRNA hairpin was prepared (FIG. 1A). The CP23S sequences were introduced in place of the wild-type 23S gene of pAM552 plasmid (FIG.3) and the resulting constructs were transformed in the E. coli SQ171 cells lacking chromosomal rRNA alleles [Asai 1999]. Twenty-two constructs were able to replace the resident plasmid pCSacB carrying wild-type rRNA operon. Most of the viable CP variants had new 23 S rRNA ends at the subunit solvent side, including several locations close to the interface rim. Table 1 characterizes the growth of E. coli SQ171 cells pressing a pure population of ribosomes with circularly permuted 23 S rRNA. Table 1: Characterization of the growth of E. coli SQ171 cells expressing a pure population of ribosomes with circularly permuted 23 S rRNA

Doubling time (min)^a) Cell Density (OD600) at

saturation^

30 °C 30 °C 30 °C 30 °C n^ pAM552^c) 61.0±3.2 53.9 ± 1.0 1.04 ±0.06 0.93 ±0.03 4 pAM552-Afill^d) 67.4 ± 1.0 53.3 ±2.4 1.07 ±0.01 0.97 ±0.00 4

CP67^e) 106.4 ±5.4 69.6 ±2.1 0.83 ±0.05 0.41 ±0.07 3

CP95 144.9 ±35.9 82.4 ±24.4 0.66 ±0.31 0.51 ±0.18 6

CP 104 90.8 ± 10.3 52.7 ±3.2 0.98 ±0.03 0.95 ±0.02 3

CP 168 123.8 ±27.9 57.7 ± 1.9 0.70 ±0.22 0.88 ±0.12 10

CP281 100.1 ± 11.0 54.6 ± 10.1 1.01 ±0.04 0.93 ±0.13 3

CP549 101.7 ± 18.2 46.5 ±3.9 1.00 ±0.02 0.98 ±0.03 3

CP617 231.7 ±20.5 91.5 ± 18.5 0.16 ±0.03 0.85 ±0.05 4

CP634 162.0 ±34.2 212.5 ±58.1 0.46 ±0.19 0.50 ±0.10 3

CP879 106.6 ±4.7 51.4±4.6 1.03 ±0.02 0.99 ±0.04 3

CP891 144.5 ±41.8 60.7 ±4.1 0.56 ±0.43 0.76 ±0.23 6

CPU 12 89.6 ±6.0 57.8 ± 12.2 0.96 ±0.02 0.91 ±0.12 3

CP1178 102.5 ± 11.0 46.2 ± 1.3 0.96 ±0.02 0.99 ±0.01 3

CP1498 167.5 ± 17.5 118.0 ± 17.1 0.56 ±0.32 0.52 ±0.19 3

CP1511 131.5 ±4.2 76.7 ± 1.5 0.88 ±0.01 0.88 ±0.01 3

CP1587 98.1 ± 12.4 55.1 ±6.6 0.93 ±0.05 0.92 ±0.08 3

CP1716 174.4 ±31.9 117.8 ± 16.5 0.44 ±0.16 0.62 ±0.34 3

CP1733 117.3 ±8.2 83.8 ±2.2 0.95 ±0.01 0.80 ±0.01 3

CP1741 230.0 ± 14.7 269.0 ±50.3 0.28 ±0.00 0.66 ±0.09 3

CP 1873 108.4 ±6.5 52.9 ±0.8 0.94 ±0.01 0.91 ±0.01 3

CP2148 83.0 ±2.9 52.4 ±3.9 0.73 ±0.09 0.82 ±0.02 4 CP2800 85.9 ± 15.7 53.5 ± 9.7 1.04 ± 0.03 0.91 ± 0.12 3

CP2861 138.4 ± 10.7 93.7 ± 4.5 0.88 ± 0.00 0.83 ± 0.04 3 ^a) Growth in 100 LB media supplemented with 50 μ§/ι 1 carbenicillin in 96-well plate with shaking.

b After 18 hours of growth.

° pAM552: wild type rrnB operon.

d⁾ pAM552-AflII: rrnB operon with the 23S rRNA mutations G2C and C2901G used to introduce the Aflll restriction sites.

e CPx: rrnB with 23 S circular permutations and G2C/C2901G mutations; x indicates the 5' starting nucleotide of the circularly permuted 23 S gene, n: number of individual colonies used for growth analysis.

^ Biological replicates are indicated in the "n" column, which is number of separate colonies that were used for each number average and standard deviation.

[00140] One of the viable mutants (CP2861 ) had 23 S rRNA ends within the loop of helix 101 (H101), near the apex loop of the 16S rRNA helix 44 (h44) (FIG. 1A). Since h44 length varies among different species and its terminal loop sequence can tolerate significant alterations

[Dorywalska 2005], h44 was a promising site for grafting the CP2861 23S rRNA and generating a hybrid 16S-23S rRNA molecule (FIG. 2A). In the chimeric rRNA, the processing sequences flanking the mature 16S rRNA would remain intact for proper maturation of the 16S rRNA termini, whereas endonuclease processing signals of 23 S rRNA would be eliminated thereby preventing its cleavage from the hybrid molecule.

Ribosomes with tethered subunits can support protein synthesis and cell growth

[00141] The RNA linkers must span the 3θΑ - 40 A distance between h44 and HI 01 loops and allow for -10 A subunit ratcheting during protein synthesis [Yusupov 2001; Voorhees 2009; Dunkle 2011; Frank 2000]. We prepared a library of constructs, pRibo-T, in which the length of two tethers, Tl connecting 16S rRNA G1453 with 23S rRNA C2858 and T2 linking 23S C2857 with 16S G1454, varied from 7 to 12 adenine residues (Table 2). Plasmid exchange in SQ171 cells yielded several very slowly growing colonies, and the pattern of extracted RNA showed a single major RNA species corresponding to the 16S-23S chimera instead of the individual 16S and 23 S bands (FIG. 6A). This result suggested that translation in these cells was carried out exclusively by Ribo-T and revealed for the first time that the bipartite nature of the ribosome is dispensable for successful protein synthesis and cell viability. Table 2: The results of sequencing of the oligo(A) linkers Tl and T2 in pRibo from randomly picked POP2136 clones transformed with the linker library

Tl T2 No. of clones

5A 10A 1

7A 9A 1

7A 10A 1

7A 11A 1

8A 10A 1

9A 9A 1

9A 11A

9A 12A 1

10A 8A 1

10A 10A

10A 11A 1

11A 9A 1

11A 12A 1

12A 8A 1

12A 12A ¹

[00142] The linker combinations 8A/9A or 9A/8A (for T1/T2) were found in the 6 best- growing clones. The first combination showed slightly better behavior in some subsequent experiments and was chosen for further investigation. In the pRibo-T plasmid the native 5' and 3' ends of the 23 S rRNA were linked via a tetranucleotide sequence GAGA (connector C), and circularly permuted 23 rRNA gene, Opened' in the apex loop of H101, and inserted in the apex loop of 16S rRNA helix h44 via an A8 linker Tl and an A9 linker T2. The original

SQ171/pRibo-T clones, although viable, grew slowly (doubling time 107 + 3 min compared to 35 + 1 min for SQ171 cells expressing wild-type ribosomes), exhibited poor recovery from the stationary phase, and low cell density at saturation (FIG. 6). By passaging cells in liquid culture for approximately 100 generations, we isolated faster growing mutants. One such clone, SQ171fg/pRibo-T (for fast growing), exhibited better growth characteristics and shorter doubling time (70 + 2 min) (FIG. 6). PCR and primer extension analysis showed the lack of wild-type rDNA and rRNA respectively, confirming the notion that every ribosome in this strain was assembled with the tethered rRNA. Because pRibo-T plasmid from the SQ171fg clone was unaltered, we sequenced the entire genome and found a nonsense mutation in the Leu codon 22 of the ybeX gene encoding a putative Mg²⁺/Co²⁺ transporter and a missense mutation in the codon 549 of the rpsA gene encoding ribosomal protein SI . Either one of these mutations or their combined effect must account for the faster growth of SQ171fg/pRibo-T cells (henceforth called Ribo-T cells).

[00143] To firmly establish that protein synthesis in Ribo-T cells was carried out by ribosomes with tethered subunits, we carefully examined the integrity of Ribo-T rRNA. Analysis of Ribo-T preparations in a denaturing gel showed only very faint 16S and 23S-like rRNA bands possibly reflecting the linker cleavage either in the cell or during Ribo-T isolation. In most of the multiple Ribo-T preparations, these cleavage products accounted for less than 4% of the total Ribo-T rRNA. In some of the preparations, these bands were completely absent showing that more than 99% of Ribo-T remained intact. Consistently, primer extension across the Tl and T2 linkers did not show any major stops attesting to the general stability of the oligo(A) connectors. Protein synthesis rate in Ribo-T cells reached 50.5 ± 3.5 % of that in cells with wild type ribosomes and thus cannot be accounted for by a small fraction of Ribo-T with cleaved tethers. Unequivocal proof of active Ribo-T translation in vivo came from analysis of polysomes prepared from Ribo-T cells, where intact 16S-23S hybrid rRNA (rather than the products of its cleavage) was associated with the heavy polysomal fractions (FIGS. 5B-D). This result provided clear evidence that intact Ribo-T composed of covalently-linked subunits is responsible for protein synthesis in the Ribo-T cells. 2D-gel analysis showed that the absolute majority of the proteins present in SQ171 cells that express wild-type ribosomes are efficiently synthesized in the Ribo-T cells (FIG. 7).

Compositions and Properties of Ribo-T

[00144] We isolated ribosomes with tethered subunits from Ribo-T cells and characterized their composition and properties. The tethered ribosome contains an apparently equimolar amount of 5S rRNA and the full complement of ribosomal proteins in quantities closely matching the composition of wild-type ribosome (FIGS. 8A, B). Chemical probing showed that the rRNA hairpins h44 and HI 01 remain largely unperturbed, while both linkers were highly accessible to chemical modification, indicating that they are solvent-exposed.

[00145] Sucrose gradient analysis of Ribo-T showed that at 15 mM Mg²⁺ the majority of the ribosomal material sedimented as a 70S peak with a minor faster-sedimenting peak likely representing Ribo-T dimers due to crossRibosome subunit association at a high Mg²⁺

concentration (FIG. 9). At lower Mg²⁺ concentration (1.5 mM), when the native ribosome completely dissociates into subunits, Ribo-T still sediments as a single peak with an apparent sedimentation velocity of 65 S (FIG. 9). The distinctive resistance of Ribo-T to subunit dissociation offers a venue for isolating Ribo-T if it is expressed in cells concomitantly with wild type ribosomes.

Ribo-T functions in cell-free protein synthesis

[00146] We tested the activity of Ribo-T in the PURExpress in vitro translation system

[Shimizu 2001] lacking native ribosomes. Ribo-T efficiently synthesized the 18 kDa

dihydro folate reductase (DHFR) (FIG. 10A). By following the kinetics of accumulation of the functional 27kDa super folder green fluorescence protein (sf-GFP) [Pedelacq 2006], we calculated that the rate of Ribo-T-catalyzed protein synthesis reaches ca. 45% of that of the wild- type ribosomes (FIG. 10B). To assess which translation step is the most problematic for Ribo-T, progression of Ribo-T through a short synthetic gene [Orelle 2013] was analyzed by toe-printing. A more pronounced band of the ribosomes at the ORF start codon indicated that Ribo-T is somewhat impaired in translation initiation at a step subsequent to the start codon recognition. Similary slow initiation was observed during in vitro translation of several other genes. Because increasing the concentration of initiation factors could not rescue the initiation defect, it is unlikely to stem from a lower affinity of the factors for Ribo-T.

Othogonal Ribo-T translates an orthogonal reporter in vivo and in vitro

[00147] To enable a fully orthogonal ribosome system, we next engineered a Ribo-T version (oRibo-T) committed to translation of a particular orthogonal cellular mRNA. The wild-type 16S anti-SD region was altered from ACCUCCUUA to AUUGUGGUA [Rackham 2005] producing a poRibo-Tl construct. When poRibo-Tl was introduced in E. coli carrying the sf-gfp gene with the SD sequence CACCAC cognate to oRibo-T, notable sfGFP expression was observed (FIG. 11 A), demonstrating the activity of oRibo-T.

[00148] Ribosome preparation from poRibo-Tl transformed cells (containing a mixture of wild-type ribosomes and oRibo-T) translated an orthogonal sf-gfp gene in a cell-free system

(FIG. 11B). However, because the orthogonal sf-gfp transcript is the only mRNA available during in vitro translation and no native mRNA engage wild-type 30S subunits, a fraction of orthogonal sf-gfp translation is accounted for by wild-type ribosomes (FIG. 11B). Therefore, to isolate oRibo-Tl activity in vitro, we used the A2058G mutation in the 23S rRNA portion of oRibo-T, which rendered ribosomes resistant to macrolide {e.g., erythromycin) and lincosamide

{e.g., clindamycin) antibiotics. Addition of clindamycin to the reaction with wild-type ribosomes completely inhibited expression of the reporter (FIG. 11B), whereas significant expression of

GFP was observed in the reaction carrying the oRibo-T preparation (FIG. 11B), fully

attributable to the in vitro activity of the engineered orthogonal ribosome. [00149] Selective inhibition of the wild-type ribosomes in the oRibo-T preparation could be a useful tool for in vitro applications. Importantly, the unique nature of Ribo-T allows for utilizing antibiotic resistance mutations in any of the ribosomal subunits. We demonstrated this by introducing a G693A mutation in the small subunit moiety of oRibo-T, rendering oRibo-T resistant to pactamycin [Mankin 1997; Orelle 2 2013]. Pactamycin (100 μΜ) completely inhibited the activity of the wild-type ribosomes in the PURE translation system, whereas oRibo- T (G693A) remained fully active (FIG. 11C). The combination of an orthogonal translation initiation signal with the antibiotic resistance mutations embedded in oRibo-T allows for exploring unique properties of oRibo-T in cell-free system even in preparations carrying a substantial fraction of wild-type ribosomes.

The evolvability of oRibo-T

[00150] We next used the oRibo-T system to search for gain-ofFunction mutations in the PTC, which could facilitate translation of a problematic protein sequence by the ribosome. Such experiments would require highly efficient transformation of the recipient cells with poRibo-T constructs. We noted, however, that in contrast to the selected SQ171fg cells, transformation of several E. coli strains (e.g. JM109, BL21 or C41 26) with poRibo-Tl was rather poor and resulted in slowly growing colonies, which varied significantly in size. Fortuitously, in the course of these experiments we isolated a spontaneous mutant plasmid, poRibo-T2, which showed notably improved transformation efficiency and produced evenly-sized colonies which appeared on the plate after an overnight incubation (as opposed to a 36 hr incubation for the poRibo-Tl transformants). Sequencing showed that poRibo-T2 acquired a single mutation in the PL promoter that controls Ribo-T expression, which altered its '-10' box from GAT ACT to TATACT bringing it closer to the TATAAT consensus. Although we do not fully understand why the promoter mutation improves performance of poRibo-T (as well as of non-orthogonal pRibo-T) in the 'unselected' E. coli cells, all the subsequent in vivo experiments were carried out using the poRibo-T2-derived constructs.

[00151] Translation of the secM gene, which regulates the expression of the essential SecA

ATPase involved in protein secretion, is controlled by nascent peptide-dependent translation arrest. The ribosome stalls when it reaches the Pro 166 codon of secM because specific interactions of the SecM nascent chain with the ribosomal exit tunnel impair the PTC function preventing the transfer of the 165-amino acid long peptide to the incoming Pro-tRNA 27-29.

Thus, the SecM polypeptide represents a classic example of an amino acid sequence whose translation is problematic for the ribosome. Several mutations in the ribosomal exit tunnel (e.g.,

A2058G) have been previously identified as relieving translation arrest possibly by disrupting the nascent chainRibosome interactions [Nakatogawa 2002; Cruz -Vera 2005; Vazquez-Laslop 2010]. However, exploring the role of the PTC in the mechanism of the translation arrest and identifying the catalytic center mutations alleviating ribosome stalling during SecM translation has been impossible so far because of the lethal nature of the mutations in the PTC active site [Thompson 2001; Sato 2006]. To search for the translation arrest bypass mutations in the PTC, we removed the A2058G mutation from poRibo-T2 and engineered an orthogonal SecM-based reporter, poSML. In the pACYC177-based poSML, the reporter gene, equipped with an orthogonal SD sequence, includes 46 codons of secM, encoding the problematic amino acid sequence, fused in frame in front of the lacZa gene [Nakatogawa 2002] (FIG. 12). When the reporter plasmid was introduced in the poRibo-T2 transformed C41(DE3) cells capable of a- complementation, colonies formed on the indicator plates were white, likely because SecM- induced translation arrest prevents oRibo-T from reaching the lacZa segment of the reporter mRNA.

[00152] We then engineered a library of oRibo-T mutants with alterations in rRNA residues in the PTC A site since it has been proposed to play a key role in the mechanism of ribosome stalling [Ramu 2011; Gong 2002; Muto 2006; Arenz 2014]. In addition, the ability to manipulate the ribosomal A-site could be crucial for future efforts to engineer ribosomes capable of programmed polymerization of unnatural amino acids and backbone-modified analogs. Two splayed-out residues, A2451 and C2452, whose mutations are dominantly lethal in E. coli

[Thompson 2001; Sato 2006], form the pocket that accommodates the amino acid side chain of the A site -bound aminoacyl-tRNA. Thus, the poRibo-T2 library we prepared contained each of the 16 possible dinucleotide combinations at positions 2451-2452 in the 23 S rRNA segment of oRibo-T.

[00153] Strikingly, when the C41 (DE3) cells with the poSML plasmid were transformed with the poRibo-T2 2451/2452 library and plated on indicator plates, some of the colonies appeared notably blue-colored (FIG. 13A). This meant that some of the oRibo-T mutants were able to bypass the SecM-induced arrest and continue active translation through the lacZa segment of the reporter. Sequencing 15 blue colonies showed that they all carried a C2451-C2452 sequence (the

A2451C mutation) in the PTC. In contrast, none of the 16 analyzed 'white' colonies had this sequence and instead exhibited a variety of dinucleotide combinations at positions 2451-2452

(FIG. 13A). Because of the relatively small size of the 2451/2452 mutant library, we verified these results by introducing 16 individual poRibo-T2 plasmids with all possible 2451-2452 mutations into poSML-transformed C41(DE3) cells. Importantly, all the individual oRibo-T

2451/2452 mutants were viable confirming that oRibo-T is suitable for expression of dominantly lethal 23 S rRNA mutations and indicating a low degree of cross-association of Ribo-T with free wild-type 30S subunits. Three transformants of each type were then tested on the indicator plate. Consistent with the previous result (FIG. 13 A), the A2451C mutation confers the most pronounced blue color of the transformants, comparable to that seen in cells expressing oRibo-T with the tunnel mutation A2058G (FIG. 13B). The A2451U mutation also increased the blue hue of the cells although to a lesser extent. Our results suggested that the A2451C (and A2451U) mutants were not only functional in cellular protein synthesis but in addition gained the ability to bypass translation arrest caused by the problematic SecM sequence. Interestingly, a mutation of another essential nucleotide in the PTC (U2585G), which has been proposed to be implicated in some translation arrest scenarios [Arnez 2014] showed no effect on SecM arrest. We verified the discovered role of A2451 in the mechanism of SecM translation arrest by testing the expression of the orthogonal secM-lacZ reporter in vitro by isolated wild-type or A2451C mutant oRibo-T. In order to assure that the in vitro effects are attributed exclusively to oRibo-T, a pactamycin resistance mutation G693A 23 was introduced in the 16S segment of oRibo-T constructs and cell-free translation in the PURE system was carried out in the presence of pactamycin. Under our experimental conditions, only a small fraction of original oRibo-T were able to bypass the SecM arrest signal and synthesize the full-size hybrid protein (Fig. 4e, lane oRibo-T(A2451). In contrast the A2451C mutant was able to bypass the SecM arrest site twice as efficiently as the unmodified oRibo-T (FIG. 13C), confirming that the selected (and otherwise lethal) mutation has altered the functional properties of the PTC and improved the ability of oRibo-T to polymerize a polypeptide sequence problematic for wild-type ribosome.

Preparation of circularly permuted variants of the 23 S rRNA

[00154] The A2058G mutation was introduced into the pAM552 plasmid by inverse PCR using primers CCGTCTTGCCGCGGGTAC (SEQ ID NO: 1) and

GTGTACCCGCGGCAAGACGGGAAGACCCCGTGAACC (SEQ ID NO: 2) (the underlined sequence is complementary to the second primer and the mutation is shown by italicized bold character) followed by re-circularization by Gibson assembly reaction [Gibson 2009] (all primers used in this study were synthesized by Integrated DNA Technology). A 23S-A2058G gene with native 5 ' and 3 ' ends linked by a GAGA tetra-loop was generated by inverse PCR using primers GGTTAAGCCTCACGGTTC (SEQ ID NO: 3) and

CCGTGAGGCTTAACCGAGAGGTTAAGCGACTAAGCGTAC (SEQ ID NO: 4) (GAGA tetra loop in bold) and pAM552-A2058G as template. Purified PCR product (50 ng) was circularized by Gibson assembly reaction for 1 hour at 50 °C. The resulting circular 23S rRNA gene was then cloned at its native unique Eagl restriction site (position 1905 in wild-type 23 S rRNA gene) into T7FLAG -4 plasmid (Sigma Aldrich) as follows. The circularized 23 S rRNA gene was amplified by inverse PCR using primers

G AG AC AC AAC GTGGCTTTC CGGC CGT AACT AT AAC G (SEQ ID NO: 5) and

CACTCGTCGAGATCGATCTTCGGCCGCCGTTTACC (SEQ ID NO: 6) (added homology to the T7FLAG™-4 vector underlined) and Gibson-assembled with the T7FLAG™-4 vector amplified with the primers AAGATCGATCTCGACGAGTG (SEQ ID NO: 7) and

GAAAGCCACGTTGTGTCTC (SEQ ID NO: 8). The cloned circularly permuted 23S rRNA gene in the resulting plasmid pCP23S-EagI containing a pBR322 origin of replication and KanR selective marker was fully sequenced.

[00155] The pCP23S-EagI plasmid was then digested with Eagl (New England Biolabs) for 1 hour at 37 °C, and the CP 23S rRNA gene was isolated from a SYBRSafe-stained 0.7% agarose gel using an E.Z.N.A. Gel Extraction kit (Omega). The 23S rRNA was circularized by T4 DNA ligase (New England Biolabs) in a 50 μΐ reaction with 2.5 ng/μΐ DNA for 14 hrs at 16 °C, followed by heat inactivation at 65 °C for 10 minutes. The reaction was diluted 1 : 100 for use as a template in the PCR reactions for generating the circular permutants.

[00156] Ninety-one CP23S mutants were designed by introducing new 23 S rRNA 5 ' and 3 ' ends at most of the apex loops and some internal loops of rRNA helices in order to assure spatial proximity of the new rRNA termini in the fully assembled 50S ribosomal subunit. Each CP23S rRNA gene was PCR-amplified in a 40 μΐ reaction using Phusion High Fidelity DNA

polymerase (New England Biolabs) with primer pairs SEQ. ID NOS: 9-190 (Table 3) and 4 μΐ of the 1 : 100 diluted 23 S circular ligation reaction as template. Each primer pair adds to the 5 ' and 3' ends of the amplified CP23S gene 20 bp of homology to the 23 S rRNA processing stem retained in the target vector pAM552-A23S-AflII (described below). PCR reactions catalyzed by the Phusion High Fidelity DNA polymerase were run under the following conditions: 98 °C, 10 min followed by 25 cycles (98 °C, 30 sec; 60 °C, 30 sec; 72 °C, 180 sec), followed by the final incubation for 15 min at 72 °C. The reaction product was purified using E.Z.N.A. Cycle Pure kit (Omega) and the size of the amplified DNA was confirmed by electrophoresis in a 1% agarose gel. For CPs with off target bands (12 CPs total), the PCR product of the correct size was extracted from the agarose gel.

Table 3: Primer pairs used for construction of circularly permuted 23 S rRNA genes.

Primer³^ Primer sequence^ SEQ

ID NO 67 60F AACATCTTCGGGTTGTGAGcTTAAGCTGCGATAAGCGTCG 9

67 60R ACAGCTTCGGCGTTGTAAGcTTAAGCCACGTCCTTCATCG 10

95 87F AACATCTTCGGGTTGTGAGcTTAAGCACCGTTATAACCGGCGA 11

TTTC

95 87R ACAGCTTCGGCGTTGTAAGcTTAAGCACCTTACCGACGCTTATC 12

104 97F AACATCTTCGGGTTGTGAGcTTAAGCACCGGCGATTTCCG 13

104 97R ACAGCTTCGGCGTTGTAAGcTTAAGCGGTTCATATCACCTTACC 14

128 123F AACATCTTCGGGTTGTGAGcTTAAGCCCCAGTGTGTTTCGAC 15

128 123R ACAGCTTCGGCGTTGTAAGcTTAAGCCCCATTCGGAAATCG 16

142 137F AACATCTTCGGGTTGTGAGcTTAAGCACACACTATCATTAACTG 17

AATC

142 137R ACAGCTTCGGCGTTGTAAGcTTAAGCACACACTGGGTTTCC 18

168 158F AACATCTTCGGGTTGTGAGcTTAAGCGGTTAATGAGGCGAAC 19

168 158R ACAGCTTCGGCGTTGTAAGcTTAAGCAGTTAATGATAGTGTGTC20

200 195F AACATCTTCGGGTTGTGAGcTTAAGCTCTAAGTACCCCGAGG 21

200 195R ACAGCTTCGGCGTTGTAAGcTTAAGCTCAGTTCCCCCGGTTC 22

230 225F AACATCTTCGGGTTGTGAGcTTAAGCGAGATTCCCCCAGTAG 23

230 225R ACAGCTTCGGCGTTGTAAGcTTAAGCGATTTCTTTTCCTCGGGG 24

TAC

252 246F AACATCTTCGGGTTGTGAGcTTAAGCGCGAACGGGGAGCAG 25

252 246R ACAGCTTCGGCGTTGTAAGcTTAAGCGCTACTGGGGGAATCTC 26

281 274F AACATCTTCGGGTTGTGAGcTTAAGCCAGTGTGTGTGTTAGTG 27

281 274R ACAGCTTCGGCGTTGTAAGcTTAAGCGCTCTGGGCTGCTC 28 312 305F AACATCTTCGGGTTGTGAGcTTAAGCGGCGCGCGATACAG 29

312 305R ACAGCTTCGGCGTTGTAAGcTTAAGCGACGCTTCCACTAACAC 30

335 327F AACATCTTCGGGTTGTGAGcTTAAGCCCCGTACACAAAAATGC 31

AC

335 327R ACAGCTTCGGCGTTGTAAGcTTAAGCCCCTGTATCGCGCGCCTT 32

TC

347 343F AACATCTTCGGGTTGTGAGcTTAAGCAATGCACATGCTGTGAG 33

347 343R ACAGCTTCGGCGTTGTAAGcTTAAGCGTGTACGGGGCTGTC 34

391 383F AACATCTTCGGGTTGTGAGcTTAAGCATCCTGTCTGAATATGG 35

391 383R ACAGCTTCGGCGTTGTAAGcTTAAGCGTCCCGCCCTACTC 36

416 411 F AACATCTTCGGGTTGTGAGcTTAAGCTCCTCCAAGGCTAAATAC37

416 411R ACAGCTTCGGCGTTGTAAGcTTAAGCCCCCCCATATTCAGACA 38

G

467 462F AACATCTTCGGGTTGTGAGcTTAAGCGGGAAAGGCGAAAAGAA39

C

467 462R ACAGCTTCGGCGTTGTAAGcTTAAGCGGTACTGGTTCACTATCG40

493 487F AACATCTTCGGGTTGTGAGcTTAAGCGGGGAGTGAAAAAGAAC 41

493 487R ACAGCTTCGGCGTTGTAAGcTTAAGCGGGGTTCTTTTCGCCTTT 42

C

502 497F AACATCTTCGGGTTGTGAGcTTAAGCAAAAGAACCTGAAACCG 43

TG

502 497R ACAGCTTCGGCGTTGTAAGcTTAAGCTCCCCTCGCCGGGGTTC 44 549 544F AACATCTTCGGGTTGTGAGcTTAAGCGCGTGTGACTGCGTACC 45 549 544R ACAGCTTCGGCGTTGTAAGcTTAAGCGCGTGCTCCCACTG 46 617 61 IF AACATCTTCGGGTTGTGAGcTTAAGCGGGGAGCCGAAGG 47

617 611R ACAGCTTCGGCGTTGTAAGcTTAAGCGGTTAACCTTGCTACAG 48

634 629F AACATCTTCGGGTTGTGAGcTTAAGCCCGAGTCTTAACTGG 49

634 629R ACAGCTTCGGCGTTGTAAGcTTAAGCCCTTCGGCTCCCCTATTC 50

647 64 IF AACATCTTCGGGTTGTGAGcTTAAGCGGGCGTTAAGTTGCAGG 51

647 641R ACAGCTTCGGCGTTGTAAGcTTAAGCAGACTCGGTTTCCCTTC 52

719 _712F AACATCTTCGGGTTGTGAGcTTAAGCCTAACTGGAGGACC 53

719 712R ACAGCTTCGGCGTTGTAAGcTTAAGCCCAACCTTCAACCTG 54

753_ 744F AACATCTTCGGGTTGTGAGcTTAAGCATTAGCGGATGACTTGTG55

753_ 744R ACAGCTTCGGCGTTGTAAGcTTAAGCATTAGTCGGTTCGGTCC 56

785_ _779F AACATCTTCGGGTTGTGAGcTTAAGCGCCAATCAAACCGGGAG 57

785_ 779R ACAGCTTCGGCGTTGTAAGcTTAAGCACCCCCAGCCACAAG 58

831 826F AACATCTTCGGGTTGTGAGcTTAAGCGTAGCGCCTCGTGAATTC 59

831 826R ACAGCTTCGGCGTTGTAAGcTTAAGCATAGCTTTCGGGGAGAA 60

CC

879 875F AACATCTTCGGGTTGTGAGcTTAAGCGGGGGTCATCCCGAC 61

879 875R ACAGCTTCGGCGTTGTAAGcTTAAGCCCGAAACAGTGCTCTAC 62

C

891 885F AACATCTTCGGGTTGTGAGcTTAAGCGACTTACCAACCCGATG 63

891 885R ACAGCTTCGGCGTTGTAAGcTTAAGCGACCCCCTTGCCGAAAC 64

962 955F AACATCTTCGGGTTGTGAGcTTAAGCGTCCGTCGTGAAGAGG 65

962 955R ACAGCTTCGGCGTTGTAAGcTTAAGCACCCGCCGTGTGTC 66

985 978F AACATCTTCGGGTTGTGAGcTTAAGCCCCAGACCGCCAGC 67 985 978R ACAGCTTCGGCGTTGTAAGcTTAAGCCCCTCTTCACGACGGAC 68

1011 1004F AACATCTTCGGGTTGTGAGcTTAAGCGTCATGGTTAAGTGGGA 69

AAC

1011 1004R ACAGCTTCGGCGTTGTAAGcTTAAGC ACCTTAGCTGGCGGTC 70

1051 1043F AACATCTTCGGGTTGTGAGcTTAAGCGCCAGGATGTTGGCTTA 71

G

1051 1043R ACAGCTTCGGCGTTGTAAGcTTAAGCGCCTTCCCACATCGTTTC 72

1074 1064F AACATCTTCGGGTTGTGAGcTTAAGCGCCATCATTTAAAGAAA 73

GC

1074 1064R ACAGCTTCGGCGTTGTAAGcTTAAGCGCCAACATCCTGGCTG 74

1086 1082F AACATCTTCGGGTTGTGAGcTTAAGCAGAAAGCGTAATAGCTC 75

AC

1086 1082R ACAGCTTCGGCGTTGTAAGcTTAAGC AATGATGGCTGCTTCTAA76

G

1099 1092F AACATCTTCGGGTTGTGAGcTTAAGCGCTCACTGGTCGAG 77

1099 1092R ACAGCTTCGGCGTTGTAAGcTTAAGCGCTTTCTTTAAATGATGG 78

CTG

1112 1108F AACATCTTCGGGTTGTGAGcTTAAGCGTCGGCCTGCGCGGAAG 79

1112 1108R ACAGCTTCGGCGTTGTAAGcTTAAGCACCAGTGAGCTATTACG 80

CTTTC

1177 1172F AACATCTTCGGGTTGTGAGcTTAAGCGCGTTGTTGGGTAGG 81

1177 1172R ACAGCTTCGGCGTTGTAAGcTTAAGCGCGTCGCTGCC 82

1215 1208F AACATCTTCGGGTTGTGAGcTTAAGCGGTGTGCTGTGAGG 83

1215 1208R ACAGCTTCGGCGTTGTAAGcTTAAGCGGCTTACAGAACGCTC 84 1227_ 1222F AACATCTTCGGGTTGTGAGcTTAAGCGGCATGCTGGAGG 85

1227_ 1222R AC AGCTTCGGCGTTGTAAGcTTAAGC AGC AC ACCTTCGC AG 86

1289_ 1281 F AACATCTTCGGGTTGTGAGcTTAAGCCCCGCTCGCCGGAAG 87

1289_ 1281 R ACAGCTTCGGCGTTGTAAGcTTAAGCCCCGCTTTATCGTTACTT 88

ATG

1330_ 1324F AACATCTTCGGGTTGTGAGcTTAAGCCGGGGCAGGGTG 89

1330_ 1324R ACAGCTTCGGCGTTGTAAGcTTAAGCCGTTGGACAGGAACC 90

1368_ 1363F AACATCTTCGGGTTGTGAGcTTAAGCGGCGTAGTCGATGG 91

1368_ 1363R ACAGCTTCGGCGTTGTAAGcTTAAGCGGCCTCGCCTTAGG 92

1398 1389F AACATCTTCGGGTTGTGAGcTTAAGCCCTGTACTTGGTGTTAC 93

1398 1389R ACAGCTTCGGCGTTGTAAGcTTAAGCCCTGTTTCCCATCGAC 94

1420_ 1417F AAC ATCTTCGGGTTGTGAGcTTAAGC AGGGGGGACGGAG 95

1420_ 1417R ACAGCTTCGGCGTTGTAAGcTTAAGCGCAGTAACACCAAGTAC 96

AG

1461 1450F AACATCTTCGGGTTGTGAGcTTAAGCCCCGGTTTAAGCGTG 97

1461 1450R ACAGCTTCGGCGTTGTAAGcTTAAGCCCCGGCCAACATAG 98

1478_ 1474F AACATCTTCGGGTTGTGAGcTTAAGCGGCTGGTTTTCCAGG 99

1478_ 1474R AC AGCTTCGGCGTTGTAAGcTTAAGC ACGCTTAAACCGGGAC 100

1498_ 1492F AACATCTTCGGGTTGTGAGcTTAAGCCCGGAAAATCAAGGCTG 101

1498_ 1492R ACAGCTTCGGCGTTGTAAGcTTAAGCCCTGGAAAACCAGCCTA 102

C

1511 1508F AACATCTTCGGGTTGTGAGcTTAAGCGCTGAGGCGTGATG 103

1511 1508R ACAGCTTCGGCGTTGTAAGcTTAAGCTGATTTTCCGGATTTGC 104 1523 1520F AACATCTTCGGGTTGTGAGcTTAAGCTGACGAGGCACTACG 105

1523 1520R ACAGCTTCGGCGTTGTAAGcTTAAGCACGCCTCAGCCTTG 106

1538 1533F AACATCTTCGGGTTGTGAGcTTAAGCGTGCTGAAGCAACAAAT 107

G

1538 1533R ACAGCTTCGGCGTTGTAAGcTTAAGCGTGCCTCGTCATCACG 108

1547 1543F AACATCTTCGGGTTGTGAGcTTAAGCCAACAAATGCCCTGC 109

1547 1543R ACAGCTTCGGCGTTGTAAGcTTAAGCCAGCACCGTAGTGC 110

1587 1582F AACATCTTCGGGTTGTGAGcTTAAGCGGTAACATCAAATCGTA 111

C

1587 1582R ACAGCTTCGGCGTTGTAAGcTTAAGCGCTTAGAGGCTTTTCC 112

1619 1612F AACATCTTCGGGTTGTGAGcTTAAGCGGTGGTCAGGTAGAG 113

1619_ 1612R ACAGCTTCGGCGTTGTAAGcTTAAGCGGTTTGGGGTACGATTTG 114

1636 1630F AACATCTTCGGGTTGTGAGcTTAAGCTACCAAGGCGCTTG 115

1636 1630R ACAGCTTCGGCGTTGTAAGcTTAAGCTACCTGACCACCTGTG 116

1696 1691F AACATCTTCGGGTTGTGAGcTTAAGCGGAGAAGGCACGCTG 117

1696 1691 R ACAGCTTCGGCGTTGTAAGcTTAAGCGTTACGGCACCATTTTG 118

1716 1712F AACATCTTCGGGTTGTGAGcTTAAGCTAGGTGAGGTCCCTC 119

1716 1712R ACAGCTTCGGCGTTGTAAGcTTAAGCATCAGCGTGCCTTC 120

1733 1727F AACATCTTCGGGTTGTGAGcTTAAGCGGATGGAGCTGAAATC 121

1733 1727R ACAGCTTCGGCGTTGTAAGcTTAAGCGGACCTCACCTACATATC122

1741 1736F AACATCTTCGGGTTGTGAGcTTAAGCCTGAAATCAGTCGAAGA 123

TAC

1741 1736R AC AGCTTCGGCGTTGTAAGcTTAAGC ATCCGCGAGGGACCTC 124 1756 1752F AACATCTTCGGGTTGTGAGcTTAAGCGATACCAGCTGGCTG 125

1756 1752R ACAGCTTCGGCGTTGTAAGcTTAAGCGACTGATTTCAGCTCC 126

1787 1777F AACATCTTCGGGTTGTGAGcTTAAGCACACAGCACTGTGC 127

1787 1777R ACAGCTTCGGCGTTGTAAGcTTAAGC ACAGTTGCAGCCAG 128

1811 1806F AACATCTTCGGGTTGTGAGcTTAAGCGTGGACGTATACGGTG 129

1811 1806R ACAGCTTCGGCGTTGTAAGcTTAAGCGTGTTTGCACAGTGC 130

1840 1837F AACATCTTCGGGTTGTGAGcTTAAGCGTGCCGGAAGGTTAATT 131

G

1840 1837R ACAGCTTCGGCGTTGTAAGcTTAAGCGGCAGGCGTCACAC 132

1849 1846F AAC ATCTTCGGGTTGTGAGcTTAAGCGGTTAATTGATGGGGTTA 133

G

1849 1846R ACAGCTTCGGCGTTGTAAGcTTAAGCCCGGCACCGGGCAG 134

1873 1868F AACATCTTCGGGTTGTGAGcTTAAGCGCGAAGCTCTTGATC 135

1873 1868R ACAGCTTCGGCGTTGTAAGcTTAAGCGCTAACCCCATCAATTA 136

AC

1919 191 IF AACATCTTCGGGTTGTGAGcTTAAGCACGGTCCTAAGGTAGC 137

1919_ 1911 R ACAGCTTCGGCGTTGTAAGcTTAAGCACGGCCGCCGTTTAC 138

1931 1926F AACATCTTCGGGTTGTGAGcTTAAGCTAGCGAAATTCCTTGTCG 139

1931 1926R ACAGCTTCGGCGTTGTAAGcTTAAGC AGGACCGTTATAGTTAC 140

G

1956 1950F AACATCTTCGGGTTGTGAGcTTAAGCTCCGACCTGCACG 141

1956 1950R ACAGCTTCGGCGTTGTAAGcTTAAGCCCCGACAAGGAATTTC 142

1991 1988F AACATCTTCGGGTTGTGAGcTTAAGCTGTCTCCACCCGAG 143 1991 1988R ACAGCTTCGGCGTTGTAAGcTTAAGCCTGGCCATCATTACG 144

2036 2027F AACATCTTCGGGTTGTGAGcTTAAGCCAGTGTACCCGCGGCAA 145

G

2036 2027R ACAGCTTCGGCGTTGTAAGcTTAAGCCAGCGAGTTCAATTTCAC 146

TG

2147 2144F AACATCTTCGGGTTGTGAGcTTAAGCAGTCTGCATGGAGC 147

2147 2144R ACAGCTTCGGCGTTGTAAGcTTAAGCCGTCCACACTTCAAAG 148

2148 2143F AACATCTTCGGGTTGTGAGcTTAAGCGTCTGCATGGAGCCGAC 149

2148 2143R ACAGCTTCGGCGTTGTAAGcTTAAGCGTCCACACTTCAAAGCCT 150

C

2215 2209F AACATCTTCGGGTTGTGAGcTTAAGCCGGGTTGCGGACAG 151 2215 2209R ACAGCTTCGGCGTTGTAAGcTTAAGCCGGGTCAACGTTAGAAC 152 2254 2250F AACATCTTCGGGTTGTGAGcTTAAGCCGGTCTCCTCCTAAAGAG 153 2254 2250R ACAGCTTCGGCGTTGTAAGcTTAAGCCAGTCAAACTACCCACC 154 2276 2264F AACATCTTCGGGTTGTGAGcTTAAGCGGAGGAGCACGAAGG 155 2276 2264R ACAGCTTCGGCGTTGTAAGcTTAAGCGGAGGAGACCGCCCCAG 156 2312 2304F AACATCTTCGGGTTGTGAGcTTAAGCTCAGGAGGTTAGTGC 157 2312 2304R ACAGCTTCGGCGTTGTAAGcTTAAGCCCAGGATTAGCCAACC 158 2331 2324F AACATCTTCGGGTTGTGAGcTTAAGCGCATAAGCCAGCTTGAC 159 2331 2324R ACAGCTTCGGCGTTGTAAGcTTAAGCACTAACCTCCTGATGTCC 160 2362 2355F AACATCTTCGGGTTGTGAGcTTAAGCCGCGAGCAGGTGC 161 2362 2355R ACAGCTTCGGCGTTGTAAGcTTAAGCCGCTCGCAGTCAAG 162 2379 2374F AACATCTTCGGGTTGTGAGcTTAAGCGCAGGTCATAGTGATCC 163 2379 2374R ACAGCTTCGGCGTTGTAAGcTTAAGCGCACCTGCTCGCGCCGTC 164

2413 2404F AACATCTTCGGGTTGTGAGcTTAAGCGGGCCATCGCTCAAC 165

2413 2404R ACAGCTTCGGCGTTGTAAGcTTAAGCAGAACCACCGGATC 166

2479 247 IF AACATCTTCGGGTTGTGAGcTTAAGCTCGACGGCGGTGTTTG 167

2479 2471 R ACAGCTTCGGCGTTGTAAGcTTAAGCTCTTGGGCGGTATCAG 168

2534 2529F AACATCTTCGGGTTGTGAGcTTAAGCAGGTCCCAAGGGTATG 169

2534 2529R ACAGCTTCGGCGTTGTAAGcTTAAGCCAGCCCCAGGATGTG 170

2557 2551F AACATCTTCGGGTTGTGAGcTTAAGCGCCATTTAAAGTGGTAC 171

G

2557 2551R ACAGCTTCGGCGTTGTAAGcTTAAGCGCCATACCCTTGGGAC 172

2567 256 IF AACATCTTCGGGTTGTGAGcTTAAGCGTGGTACGCGAGCTG 173

2567 2561 R ACAGCTTCGGCGTTGTAAGcTTAAGCATGGCGAACAGCCATAC 174

2599 2594F AACATCTTCGGGTTGTGAGcTTAAGCGACAGTTCGGTCCCTATC 175

2599 2594R ACAGCTTCGGCGTTGTAAGcTTAAGCGACGTTCTAAACCCAGC 176

2663 2658F AACATCTTCGGGTTGTGAGcTTAAGCGGACCGGAGTGGAC 177

2663 2658R ACAGCTTCGGCGTTGTAAGcTTAAGCGTACTAGGAGCAGC 178

2706 270 IF AACATCTTCGGGTTGTGAGcTTAAGCATGGCACTGCCCGGTAG 179

2706 2701 R ACAGCTTCGGCGTTGTAAGcTTAAGCATGACAACCCGAACACC 180

2742 2737F AACATCTTCGGGTTGTGAGcTTAAGCGTGCTGAAAGCATCTAA 181

G

2742 2737R ACAGCTTCGGCGTTGTAAGcTTAAGCCTCTTCCGCATTTAGCTA 182

C

2758 2746F AACATCTTCGGGTTGTGAGcTTAAGCAGCACGAAACTTGC 183 2758_ 2746R ACAGCTTCGGCGTTGTAAGcTTAAGCAGCACTTATCTCTTCC 184

2800 2796F AACATCTTCGGGTTGTGAGcTTAAGCAGGGTCCTGAAGGAAC 185

2800 2796R ACAGCTTCGGCGTTGTAAGcTTAAGCAGGGTCAGGGAGAAC 186

2827_ 2819F AACATCTTCGGGTTGTGAGcTTAAGCCGACGTTGATAGG 187

2827_ 2819R ACAGCTTCGGCGTTGTAAGcTTAAGCCAACGTTCCTTCAGG 188

2861 2856F AACATCTTCGGGTTGTGAGcTTAAGCTGCGTTGAGCTAAC 189

2861 2856R ACAGCTTCGGCGTTGTAAGcTTAAGCTGCGCTTACACAC 190

F: forward primer, R: reverse primer.

' In each primer name, the first number indicates the new 5' nucleotide for the target circular permutant, and the second number indicates the new 3' nucleotide, both in reference to the wild-type 23 S rRNA nucleotide numbering scheme. Non-underlined nucleotides indicate added homology to pAM-A23S-AflII linearized backbone. Underlined nucleotides indicate primer segments that anneal to CP23S template.

[00157] To minimize PCR errors in generating the vector backbone, which carried 16S and 5S rRNA sequences, and prevent carry-through of the wild-type rrnB operon, universal backbone vector pAM552-A23S-AflII lacking the 23S rRNA gene and containing added Aflll restriction site for cloning of CP23S was prepared. The plasmid pAM552-AflII was constructed from pAM552 by adding Aflll restriction sites within the terminal stem of the wild-type 23S rRNA gene by introducing the G2C and C2901G mutations. First the G2C mutation was introduced by inverse PCR using 5'-phosphorylated primers C TT AAGC G ACT AAGC GT AC AC (SEQ ID NO: 191) and CTCACAACCCGAAGATGTTTC (SEQ ID NO: 192), followed by blunt-end ligation, transformation into E. coli POP2136 electrocompetent cells, plating on LB-agar plates supplemented with 50 μg/ml carbenicillin, growth overnight at 30 °C, single colony isolation and sequencing. The C2901G mutation was added by the same method using 5'-phosphorylated primers GCTTACAACGCCGAAGCTG (SEQ ID NO: 193) and

TTAAGCCTCACGGTTCATTAG (SEQ ID NO: 194). The introduced mutations preserved the integrity of the 23 S rRNA terminal stem and did not affect growth of SQ171 cells expressing only ribosomes with the pAM552-AflII-encoded rRNA (growth rates 53.9 ± 1.0 min for SQ 171 cells transformed with pAM552 and 53.3 ± 2.4 min for SQ171 transformed with pAM552-AflII, as determined from 4 separate colonies each on Biotek Synergy HI plate readers in 96 well flat bottom plates (Costar) in 100 μΐ LB supplemented with 50 μg/ml carbenicillin, 37°C, linear shaking with 2 mm amplitude, at 731 cycles per min). In order to remove the 23 S rR A gene, pAM552-AflII was digested with Aflll (New England Biolabs) for 1 hr at 37 °C, the backbone portion of the vector was gel-purified and ligated with T4 DNA ligase (New England Biolabs) overnight at 16 °C. It was then transformed into POP2136 cells, plated on LB/agar plates supplemented with 50 μg/ml carbenicillin, and grown at 30 °C. Plasmids from several colonies were isolated and fully sequenced. The resulting pAM552-A23S-AflII plasmid contains the 16S rRNA, 23 S processing stems with an added Aflll restriction site, 5S rRNA, and β-lactamase resistance gene and ColEl ori. Vector backbone was prepared by digesting pAM552-A23S-AflII with Aflll restriction enzyme at 37 °C for 2 hrs and purification using an E.Z.N.A. Cycle Pure kit.

[00158] All the CP23S constructs were assembled in parallel by Gibson assembly reaction in a 96-well PCR plate. For each CP23S target, 50 ng of 7II-digested purified backbone was added to 3Fold molar excess of the PCR-amp lifted and purified CP23S insert. Gibson assembly mix [Gibson 2009] (15 μΐ) was added, the final volumes brought to 48 μΐ with nucleaseFree water, and incubated at 50 °C for 1 hr in the PCR machine. No CP23S insert was added to the negative control reaction. To check the efficiency of DNA assembly, 2 μΐ of selected assembly reactions were transformed into electrocompetent POP2136 cells. Following 1 hour recovery at 37 °C in SOC media, a quarter of each transformation was plated on LB-agar plates

supplemented with 50 μg/ml carbenicillin and grown for 20 hours at 30 °C. A typical CP23S assembly reaction generated 30-120 POP2136 colonies with the control reaction generating only few colonies.

Testing cp23S rRNA constructs

[00159] Transformation of SQ 171/pCSacB rubidium chloride-competent cells was carried out in a 96-well plate. Two μΐ of the Gibson Assembly reactions were added to 20 μΐ competent cells in the pre-chilled plate. After 45 min incubation in ice/water bath, 45 sec at 42°C and 2 min on ice, 130 μΐ of SOC medium were added to the wells and the plate was incubated 2 hr at 37°C with shaking at 600 rpm on a microplate shaker. Forty μΐ of medium were then transferred from each well to the wells of another 96-well plate containing 120 μΐ SOC supplemented with 100 μg/ml ampicillin and 0.25% sucrose. The plate was incubated overnight at 37°C with shaking at

600 rpm. A 96-pin replicator was used to spot aliquots of the cultures onto a rectangular LB agar plate containing 100 μg/ml ampicillin, 5% sucrose and 1 mg/ml erythromycin. The plate was incubated overnight at 37°C and the appearance of AmpVEry¹ transformants was recorded. The completeness of the replacement of the wild type pCSacB plasmid with the plasmids carrying circularly permuted 23 S rRNA gene was verified by PCR using a mixture of three primers: primer 1 (GCAGATTAGCACGTCCTTCA [SEQ ID NO: 195]) complementary to the 23S rRNA segment 50-69), primer 2 (CGTTGAGCTAACCGGTACTA [SEQ ID NO: 196]) containing the sequence of the 23S rRNA segment 2863-2882, and primer 3

(GGGTGATGTTTGAGATATTTGCT [SEQ ID NO: 197]) corresponding to the sequence of the 16S/23S intergenic spacer 139 - 116 bp upstream from the 23S rRNA gene in rrnB. The combination of the primers 1 and 3 produces a 207 bp PCR band if wild type rrn operon is present; the combination of the primers 1 and 2 produces a 112 bp PCR band on the templates with circularly permuted 23 S rRNA gene.

[00160] In order to reduce the number of false-negative cp23S rRNA variants, the experiment was repeated one more time using de novo assembled Gibson reactions with the cp23S rRNA constructs that failed to replace pCSacB in the first experiment. Two additional functional cp23S rRNA constructs were recovered from the second attempt. Altogether, 22 cp23S rRNA variants were able to replace pCSacB in the SQ171 cells. CP23S identity was confirmed by plasmid sequencing. Growth rates were analyzed on Biotek Synergy HI plate readers in 96 well flat bottom plates (Costar) in 100 LB with 50 μg/ml carbenicillin. Doubling times and final OD600 after 18 hours are shown in Table 1.

Construction of pRibo-T

[00161] In order to avoid generation of mutations in the 23 S rRNA gene during PCR amplification for Gibson assembly, the 23 S rRNA gene variant circularly permuted at HI 01 (corresponding to CP2861) was first cloned in the pUC18 vector. For that, the 23 S rRNA gene circularly permuted at was PCR-amp lifted from circularized 23 S rRNA gene prepared in the circular permutation study (above) by using the highFidelity AccuPrime Taq polymerase (Life Technologies) and primers containing BamHl restriction sites (shown in bold)

TATTGGATCCGATGCGTTGAGCTAACCGGTA (SEQ ID NO: 198) and

TTATGGATCCTGCGCTTACACACCCGGCCTAT (SEQ ID NO: 199). The amplified fragment was cut with BamHl and cloned in dephosphorylated BamHl-cut pUC18 plasmid. A plasmid containing CPlOl 23 S rRNA (pUC23S) was fully sequenced to verify the lack of mutations in the 23S rRNA gene.

[00162] For preparation of pRibo-T (FIG. 4B), pAM552-A23S-AfiII plasmid (see above) served as a recipient for the CPlOl 23 S rRNA gene. The CPlOl 23 S RNA gene was excised from the pUC23S plasmid by BamHl digestion and gel purified. In order to graft the CPlOl 23 S rRNA gene into the 16S rRNA gene, the plasmid backbone was prepared by PCR-amplifying the plasmid pAM552-A23S-AflII (5 ng in 50 μΐ reaction) using primers introducing poly-A linkers and sequences corresponding to HI 01 of 23 S rR A (underlined) and h44 in 16S rR A

(italicized) TTAGTACCGGTTAGCTCAACGCATCGfTV

nCGAA GGTTAA GCTACCTA CTTCTTTTGC (SEQ ID NO: 200) (reverse primer with tether Tl) and TTGATAGGCCGGGTGTGTAAGCGC AGfAVi ?. GGA GGGCGCTTA CCACTTTGT (SEQ ID NO: 201) (forward primer with tether T2). The PCR reaction, which was catalyzed by Phusion High Fidelity DNA polymerase, was carried out under the following conditions: 98°C for 2 min followed by 30 cycles of (98°C, 30 sec; 62°C , 30 sec; 72°C, 2 min) followed by 72°C for 5 min. The resulting 4.6 kb PCR fragment was treated with Dpnl for 4 hr at 37°C and purified using Wizard SV Gel and PCR Clean-Up kit (Promega). The PCR-amplified plasmid backbone and the gel-purified CP101 23 S rRNA gene fragment were combined in a Gibson Assembly reaction. Five μΐ of the reaction mixture was transformed into 50 μΐ electrocompetent POP2136 E. coli cells. Cells were plated onto LB/agar plate supplemented with 100 μg/ml ampicillin. After 24 hr incubation at 30°C, the colonies appeared. Seventeen colonies were picked, grown in LB/ampicillin at 30°C, plasmids were isolated and linkers were sequenced using the primers GAACCTTACCTGGTCTTGACATC (SEQ ID NO: 202) (corresponding to the 16S rRNA sequence 976-998) and ATATCGACGGCGGTGTTTG (SEQ ID NO: 203) (corresponding to the 23 S rRNA sequence 2476-2495) to verify the complexity of the linker library (Table 2). All the colonies were then washed off the plate and total plasmid was extracted and used to transform SQ171 competent cells.

Functional replacement of the wild-type ribosome by Ribo-T

[00163] SQ171 cells carrying pCSacB plasmid, which contains wild-type rrnB operon, were transformed with the total pRibo-T preparation isolated from the POP2136 cells. Briefly, 250 ng of plasmid preparation were added to 250 μΐ of rubidium chloride-competent cells. Cells were incubated 45 min on ice, 45 sec at 42°C and 2 more min on ice followed by addition of 1 ml SOC medium and incubation at 37°C for 2 hours with shaking. A 150 μΐ aliquot of the culture was transferred to 1.85 ml SOC supplemented with 100 μg/ml ampicillin and 0.25% sucrose (final concentrations) and grown overnight at 37°C with shaking. Cells were spun down and plated on an LB agar plate containing 100 μg/ml ampicillin, 5% sucrose and 1 mg/ml erythromycin. Eighty of the colonies that appeared after 48 hrs incubation of the plate at 37°C were inoculated in 2 ml LB supplemented with 100 μg/ml ampicillin and grown for 48 hrs. The growth rate of -30 clones that managed to grow during that period was then assessed in

LB/ampicillin medium in the 96-well plate. Plasmids were isolated from 6 faster growing clones and linkers were sequenced. The linker Tl in five sequenced clones was composed of 9 adenines and linker T2 was composed of 8 adenines, while one clone had the reverse combination. Total RNA was extracted from these clones using RNeasy Mini Kit (Qiagen) and analyzed by agarose electrophoresis. The successful replacement of the wild type pCSacB plasmid with the pRibo-T plasmids carrying Ribo-T was verified by PCR using primers GACAGTTCGGTCCCTATCTG (SEQ ID NO: 204)(corresponding to the 23S rRNA sequence 2599-2618) and

TTAAGCCTCACGGTTCATTAG (SEQ ID NO: 205) (complementary to the 23 S rRNA sequence 2880-2900) and additionally verified by primer extension on the total cellular rRNA. The growth of the cells was monitored at 37 °C in 150 μΐ of LB supplemented with 100 μg/ml of ampicillin in the wells of a 96-well plate in the TEC AN microplate reader (15 min orbital shaking with a 3 mm amplitude followed by 5 min rest prior to reading). The doubling time (τ) values estimated from the logarithmic parts of the growth curves are indicated in FIG. 6.

Polysome analysis

[00164] The cultures of cells (250 ml) of the SQ171fg strain transformed with either pAM552 (WILD-TYPE) or pRibo-T8/9 were grown at 37°C with vigorous shaking. When the optical density reached A₆oo 0.4-0.7, chloramphenicol solution was added to obtain final concentration of 125 μg/ml and, after 5 min, cells were pelleted by centrifugation at 4°C. Polysomes were prepared following the published protocol [Fredick 2000] by freezing-thawing in the lysis buffer (20 mM Tris-HCl, pH 7.5, 15 mM MgCb) supplemented with 1 mg/ml lysozyme 0.25 % sodium deoxycholate and 2 U of RQl DNase (Promega). The lysates were centrifuged at 20,000g for 30 min at 4°C and polysomes-containing supernatants (20 A₂6o) were loaded onto the 12 ml 10%- 50% sucrose gradient (buffer: 20 mM Tris-HCl, pH 7.5, 10 mM MgCb, 100 mM NH4CI2, 2 mM β-mercaptoethanol). Polysomes were resolved by centrifugation in a SW-41 rotor (39,000 rpm, 3 hr, 4°C). Gradients were fractionated using BioComp Instrument gradient fractionator and fractions were collected in the wells of a 96-well plate. Appropriate fractions were pooled, ribosomes were ethanol-precipitated and resuspended in 200 μΐ of buffer containing 300 mM sodium acetate, pH 5.5, 5 mM EDTA, 0.5%> SDS. rRNA was isolated by successive extractions with phenol (pH 6.6), phenol/chloroform and chloroform. After ethanol precipitation, RNA was analyzed by non-denaturing agarose gel electrophoresis.

Analysis of protein synthesis rate and proteins synthesized in Ribo-T cells

[00165] Protein synthesis rate in SQ171fg cells expressing either wild-type ribosomes (plasmid pAM552) or Ribo-T (pRiobo-T plasmid) was measured by following incorporation of [³⁵S]-methionine into proteins as described ³⁰. Specifically, 0.25 μα of [³⁵S]-methionine (specific activity 1,175 Ci/mmol) (ARC) was added to 1 ml of exponentially growing cells at 37°C and after 45 sec incubation proteins were precipitated by addition of 1 ml of ice-cold 25% trichloroacetic acid (TCA) containing 2% casamino acids. After incubating for 30 min on ice and then 30 min at 100°C, samples were passed through G4 glass fiber filters. The filters were washed three times with 3 ml of ice cold 5% TCA, and once with 3 ml of acetone and air dried, and the amount of retained radioactivity was determined by scintillation counting. Preliminary measurements of the time course of [³⁵S]-methionine incorporation in the faster-growing

SQ171fg/pAM552 cells showed that radioactivity curve plateaus after 120 sec of incubation of cells with [³⁵S]-methionine.

[00166] Exponential cultures (250 ml) of the SQ171fg strain transformed with either pAM552 (A2058G) or pRibo-T8/9 growing in LB medium supplemented with 100 μg/ml of ampicillin and 50 μg/ml of spectinomycin were harvested by centrifugation and cells were flashFrozen in liquid nitrogen. Protein isolation and two-dimensional gel electrophoresis was performed by Kendrick Labs, Inc. (Madison, WI).

Preparation of Ribo-T and wild type ribosomes and analysis of their RNA and protein content

[00167] Ribosomes were prepared from the exponentially growing cells of the SQ171fg strain transformed with either pAM552 (WILD-TYPE) or pRibo-T8/9 as described ³¹. RNA was phenol extracted, precipitated as previously described and resolved by electrophoresis in a denaturing 6% (acrylamide : bis-acrylamide ratio 1 : 19 w/w) polyacrylamide gel (for the 5S rRNA analysis) or 4% (acrylamide : bis-acrylamide ratio 1 : 29 w/w) polyacrylamide gel (for the analysis of large rRNAs).

[00168] Ribo-T associated ribosomal proteins were analyzed by mass spectrometry at the Proteomics Center of Excellence, Northwestern University. Ribosomes were precipitated by incubation in 20% trichloracetic acid at 4 °C overnight and centrifugation at 14,000 g for 10 min. Precipitated ribosomes were washed once with cold 10% trichloracetic acid and twice with acetone. The pellet was air dried for 10-20 min prior to resuspension in 20 μΐ 8 M urea. Proteins were reduced with 10 mM dithiothreitol and cysteine residues alkylated with 50 mM

iodoacetamide in the final volume of 160 μΐ. Sequencing grade trypsin (Promega) was added at a 1 :50 enzyme :protein ratio and after overnight digestion at room temperature, the reaction was stopped by addition of formic acid to 1%. Following digestion, peptides were desalted using C18 Spin columns (Pierce, cat # 89870) and lyophilized. Amino reactive TMT reagents (126/127, Thermo Scientific, cat# 90065) was used for peptide labeling. The reagents were dissolved in 41 μΐ acetonitrile and added to the lyophilized peptides dissolved in 100 μΐ of 100 mM triethylammonium bicarbonate. After 1 hr at room temperature, the reaction was quenched by adding 8 μΐ of 5% hydroxylamine. Following labeling, the two samples under analysis were mixed in 1 : 1 ratio. Peptides were desalted using C18 ZipTip Pipette Tips (EMD Millipore) and resuspended in 30 μΐ, of solvent A (95% water, 5% acetonitrile, 0.2%> formic acid).

[00169] Peptides were analyzed using nanoelectrospray ionization on an Orbitrap Elite mass spectrometer (Thermo Scientific). Proteome Discoverer (Thermo Scientific) and the Sequest algorithm was used for data analysis. Data was searched against a custom database containing UniProt entries using Escherichia coli taxonomy, allowing 3 missed cleavages, 10 ppm precursor tolerance, and carbamidomethylation of cysteine as a static modification. Variable modifications included oxidation of methionine, TMT of lysine and N-terminal TMT. For quantification via the reporter ions the intensity of the signal closest to the theoretical m/z, within a ±10 ppm window, was recorded. Reporter ion intensities were adjusted based on the overlap of isotopic envelopes of all reporter ions as recommended by the manufacturer. Only peptides with high confidence were used for quantification. Ratios of 126/127 were normalized based on median.

Sucrose gradient analysis of ribosomes and ribosomal subunits

[00170] Wild type 70S ribosomes or Ribo-T isolated from SQ171fg cells as described above were diluted ca. 70 fold in high Mg²⁺ buffer (20 mM Tris-HCl, pH 7.5, 100 mM NH₄C1, 2 mM 2-mercaptoethanol, 15 mM MgCb) or low Mg²⁺ buffer (20 mM Tris-HCl, pH 7.5, 100 mM NH₄C1, 2 mM 2-mercaptoethanol, 1.5 mM MgCl₂). After incubation for 30 min at 4°C, ribosomes and subunits were resolved in 10-40%) 12 ml sucrose gradients prepared with the same buffers. Gradients were centrifuged in the SW41 rotor at 38,000 rpm for 3 hr at 4°C. Ribosome profiles were then analyzed using gradient fractionator (BioComp Instrument).

Probing the structure of the Ribo-T tethers

[00171] The structure of the tethers was probed by dimethylsulfate (DMS) modification following a published protocol [Merryman 1998]. Briefly, 10 pmol of Ribo-T or WILD-TYPE ribosomes were activated by incubation for 5 min at 42°C in 50 μΐ of buffer 80 mM HEPES- KOH, pH 7.6, 15 mM MgCl₂, 100 mM NH₄C1 containing 20 U of RiboLock RI RNase inhibitor (Thermo Fisher Scientific). Two μΐ of DMS (SIGMA) diluted 1 : 10 in ethanol were added (2 μΐ of ethanol were added to the unmodified controls) and samples were incubated for 10 min at 37°C. The modification reaction was stopped and rRNA extracted as described [Merryman 1998]. Primer extensions were carried out using the primers GACTGCCAGGGCATCCACCG (SEQ ID NO: 206) and AAGGTTAAGCCTCACGG (SEQ ID NO: 207) (for tether Tl) or C CCT AC GGTT AC CTTGTT AC G (SEQ ID NO: 208) for tether T2. [00172] Additionally, the integrity of the tethers in the Ribo-T preparation was tested by extension of the primers annealing immediately 3 ' to the tether. Primer

GTACCGGTTAGCTCAACGCATC (SEQ ID NO: 209) was extended by reverse transcriptase across tether Tl in the presence of dATP, dTTP, dGTP and ddCTP and primer

CACAAAGTGGTAAGCGCCCTCCT (SEQ ID NO: 210) was extended across tether T2 in the presence of dATP, dTTP, dCTP and ddGTP.

Testing Ribo-T activity in cell-free translation system

[00173] DNA template containing the T7 promoter and the gene of the superfolder green fluorescence protein [Pedelacl 2006] was PCR amplified from a pY71-sfGFP plasmid [Bundy 2010] using primers T AAT ACGACTC ACT ATAGGG (SEQ ID NO : 21 1 ) and

CTTCCTTTCGGGCTTTGTT. (SEQ ID NO: 212)GFP niRNA was prepared by in vitro transcription and purified by size-exclusion chromatography on a Sephadex G50 mini-column, phenol extraction and ethanol precipitation. The transcript was translated in the A(ribosome, amino acid, tRNA) PURExpress system kit (New England Biolabs). A typical translation reaction was assembled in a total volume of 10 μΐ and contained 2 μΐ of the kit solution A, 1.2 μΐ of factor mixture, 1 μΐ amino acid mixture (3 mM each), 1 μΐ tRNA (20 μg/ml), 0.4 μΐ Ribolock RNase inhibitor (40υ/μ1), 5 μg (-20 pmol) GFP transcript and 22 pmol of wild type ribosomes or Ribo-T. Samples were placed in wells of a 384-well black wall/clear flat bottom tissue-culture plate (BD Biosciences) and covered with the lid. Reactions were incubated at 37°C in a microplate reader (Tecan), and fluorescence values were recorded every 20 min at

nm and nm over 7 hrs. Protein synthesis rates were calculated by linear regression over the time points 0, 40 and 60 min with a R²>0.9 using the trendline function of Excel (Microsoft). Time point 20 min was not taken into consideration because the plate was switched from ice to 37°C at time 0.

[00174] Transcription/translation of the DHFR template supplied with the A(ribosome, amino acid, tRNA) PURExpress kit (New England Biolabs) was carried in the presence of [³⁵S] L- methionine (1 175 Ci/mmol) using manufacturers protocol. A typical 5 μΐ reaction, assembled as described above but using 50 ng of the DNA template, was supplemented with 5 μ£\ [³⁵S] L- methionine and 10 pmol of wild type or Ribo-T ribosomes. When needed, the reactions were supplemented with 50 μΜ erythromycin. Reactions were incubated 2 hours at 37°C and protein products were analyzed by SDS gel electrophoresis in 16.5% Bis-Tris gels (Biorad) using NuPAGE MES/SDS running buffer (Invitrogen). Gels were stained, dried and exposed to a phosphorimager screen overnight. Radioactive bands were visualized by Typhoon phosphorimager (GE Healthcare).

Toe-printing analysis

[00175] Toe-printing was performed as previously described [Vazquez-Lasop 2008; Orelle 2013]. When needed, the threonyl-tRNA synthetase inhibitor borrelidin or the initiation inhibitor thiostrepton were added to the reactions to the final concentrations of 50 μΜ.

Construction of the plasmids for testing oRibo-T activity in vivo

[00176] The backbone plasmid pT7wtK was first prepared from the commercial plasmid T7FLAG™-4 (Sigma Aldrich) by introducing the following changes. First, the bla gene was deleted using inverse PCR with phosphorylated primers TAACTGTCAGACC AAGTTTACTC (SEQ ID NO: 213) and ACTCTTCCTTTTTCAATATTATTGAAG (SEQ ID NO: 214) and Phusion High Fidelity DNA polymerase. Following purification with E.Z.N.A. Cycle Pure kit, DNA was blunt-end ligated for 14 hours at 16 °C using T4 DNA ligase, and transformed into electrocompetent DH5a E. coli cells and plated on LB-agar supplemented with 30 μg/ml kanamycin. Next, a Bglll-Notl cloning site was introduced using phosphorylated primers

AGATCTGTTGCTACGCAGCGTTGCGGCCGCTGAAGATCGATCTCGACG (SEQ ID NO: 215) and

GCCTCCTATGAAAAAATAACAGATATAGTCTCCCTATAGTGAGTCGTATTAGG (SEQ ID NO: 216), with Bglll and Notl sites in bold. A sequence 3 ' of the T7 promoter, termed N15 (underlined), optimized for T7 expression of an orthogonal gene [An 2009] was introduced on one of the primers. Purified PCR product was blunt-end ligated with T4 DNA ligase for 14 hours at 16 °C, transformed into DH5a electrocompetent cells and plated on LB-agar supplemented with 30 μg/ml kanamycin. The resulting plasmid pT7wtK contains a T7 promoter, wild-type SD sequence, a Bglll-Notl cloning site, T1/T2 terminator, pMBl origin of replication, a lacl gene and a kanamycin resistance gene.

[00177] To create plasmid pT7wtGFP, primers

GGTGGTAGATCTATGAGCAAAGGTGAAGAAC (SEQ ID NO: 217) and

GGTGGTGCGGCCGCGGGCTTTGTTAGCAG (SEQ ID NO: 218) were used to PCR amplify the sf-gfp gene from pY71-sfGFP [Bundy 2010], adding Bglll and Notl restriction sites (bold) at the ends of the sf-gfp PCR product. Purified PCR product and plasmid pT7wtK were digested with Bglll and Notl (New England Biolabs) for 1 hour at 37 °C. The pT7wtK digested vector was treated with alkaline phosphatase CIP (New England Biolabs) for 1 hour at 37 °C. Both reactions were purified with E.Z.N.A. Cycle Pure kit. The sf-gfp insert was added in 3Fold molar excess to 50 ng pT7wtK backbone, and ligated with T4 DNA ligase (NEB) for 14 hrs at 16 °C, transformed into DH5 electrocompetent cells and plated on LB-agar supplemented with 30 μg/ml kanamycin.

[00178] To create pT7oGFP containing sf-gfp whose translation is controlled by an orthogonal SD sequence, the wild-type SD sequence of pT7wtGFP (AGGAGG) was mutated to an orthogonal sequence CACCAC [Rackham 2005] by inverse PCR using phosphorylated primers ATGAGCAAAGGTGAAGAAC (SEQ ID NO: 219) and

AGATCTGTGGTGTGAAAAAATAACAGATATAGTCTC (SEQ ID NO: 220). PCR product purified with E.Z.N. A. Cycle Pure kit was blunt-end ligated with T4 DNA ligase for 14 hours at 16 °C, transformed into electrocompetent DH5a cells and plated on LB-agar supplemented with 30 μg/ml kanamycin.

[00179] Finally, the T7 promoter was replaced with the lpp5 promoter [An 2009]. To achieve that, inverse PCR was performed using pT7oGFP as template and phosphorylated primers

TATACTTGTGGAATTGTGAGCGGATAACAATTCTATATCTGTTATTTTTTCA (SEQ ID NO: 221) and

ACACAAAGTTTTTTATGTTGTCAATATTTTTTTGATAGTGAGTCGTATTAGGATC

(SEQ ID NO: 222), (the lpp promoter is underlined). The lacO site (bold) was included in order to provide for inducible expression in POP2136 strain controlled with isopropyl β-D-l- thiogalactopyranoside (IPTG). DNA was purified, blunt-end ligated, transformed into DH5a cells and plated on LB-agar supplemented with 30 μg/ml kanamycin. The resulting plasmid pLpp5oGFP contains a lpp5 promoter, lacO site, orthogonal SD sequence, sf-gfp gene, T1/T2 terminator, pMBl origin of replication, a lacl gene and a kanamycin resistance gene.

[00180] The anti-Shine-Dalgarno sequence of pRibo-T 16S rRNA was mutated from wild- type (5'-ACCUCCUUA-3' [SEQ ID NO: 223]) to an orthogonal sequence (5 -AUUGUGGUA- 3' [SEQ ID NO: 224]) [Rackham 2005] by inverse PCR using phosphorylated primers

CCTTAAAGAAGCGTACTTTGTAG (SEQ ID NO: 225) and

TACCACAATGATCCAACCGCAGG (SEQ ID NO: 226), pRibo-T as template and Phusion High Fidelity DNA polymerase. PCR was run at the following conditions: 98 °C, 3 min followed by 25 cycles (98 °C, 30 sec; 55 °C, 30 sec; 72 °C, 120 sec), followed by final extension 72 °C, 10 min. Correct size band was purified by agarose gel electrophoresis and extracted using the E.Z.N.A. Gel Extraction kit. It was circularized by blunt-end ligation and transformed into POP2136 electrocompetent cells. Cells were plated on LB/agar plates supplemented with 50 μg/ml carbenicillin and grown at 30 °C overnight. Colonies were isolated and poRibo-T was fully sequenced. Testing activity of oRibo-T in vivo

[00181] Electrocompetent POP2136 cells were transformed with the following plasmid combinations: i) pAM552 and pT7wtK (no gfp control), ii) pAM552 and pLpp5oGFP, iii) pAM552o and pLpp5oGFP and iv) poRibo-Tl and pLpp5oGFP. Transformants were plated on LB plates supplemented with 50 μg/ml carbenicillin and 30 μg/ml kanamycin and incubated for 24 hours at 30 °C. Wells of a 96-well plate with low evaporation lid (Costar) was filled with 100 μΐ of LB media supplemented with 50 μg/ml carbenicillin and 30 μg/ml kanamycin. The wells were inoculated with colonies from each plasmid combination above (six colonies each), and incubated at 30 °C for 14 hours with shaking. Clear bottom chimney wells of another 96-well plate (Costar) were filled with 100 μΐ, of LB media supplemented with 50 μg/ml carbenicillin, 30 μg/ml kanamycin, and 1 mM IPTG. The plate was inoculated with 2 μΐ of saturated initial inoculation plate, and incubated with linear shaking (731 cycles per min) for 16 hrs at 42 °C on a Biotek Synergy HI plate reader, with continuous monitoring of cell density (A₆oo) and sf-gfp fluorescence (excitation 485 and emission 528 with sensitivity setting at 80).

Testing oRibo-T activity in a Cell- free translation system

[00182] Ribosomes (wild-type) or oRibo-T (mixed with wild-type ribosomes) were prepared from SQ171fg cells transformed with pAM552 or poRibo-Tl , respectively. An orthogonal sf-gfp gene was PCR amplified from the plasmid pT7oGFP using primers

TAATACGACTCACTATAGGG (SEQ ID NO: 227) and ACTCGTCGAGATCGATCT (SEQ ID NO: 228). The transcription-translation reaction was carried out in A(ribosome, amino acid, tRNA) PURExpress system as described above. The 7.5 μΐ reactions were supplemented with 18.75 ng DNA template and 7.5 pmol ribosomes and when needed, clindamycin or pactamycin were added to the reactions to the final concentrations of 50 μΜ or 100 μΜ respectively.

[00183] For in vitro translation of an orthogonal secM-lacZa template it was PCR amplified from the poSML plasmid using a direct primer TAATACGACTCACTATAGGG (SEQ ID NO : 229) corresponding to the T7 promoter and a reverse primer TTCCCAGTCACGACGTT (SEQ ID NO: 230), which allowed preserving 18 codons after the SecM arrest site. mRNA was prepared by in vitro transcription and purified. It was then translated in the A(ribosome, amino acid, tRNA) PURExpress system assembled in a total volume of 5 μΐ and containing 1 μΐ of the kit solution A, 0.6 μΐ of factor mixture, 0.5 μΐ amino acid mixture (3 mM each) lacking methionine, 0.2 μΐ of [³⁵S] L-methionine 8.5 μΜ (1 175 Ci/mmol), 0.5 μΐ tRNA (20 μ^πιΐ), 0.2 μΐ Ribolock RNase inhibitor (401Ι/μ1), 100 μΜ pactamycin, 10 pmol transcript and 10 pmol of total ribosomes. Translation was carried out for 5 min at 37°C, followed by addition of 1 μg of RNAse A and incubation for 5 min at 37°C. Translation products were analyzed in 16.5% Tricine SDS polyacrylamide gel [Schagger 1987]. The gel was stained, dried, and exposed to a phosphorimager screen overnight.

Construction of C41(DE3)/AlacZ58(M15)

[00184] The AlacZ58(M\5) allele required for alpha complementation was transduced from the E. coli strain K1342 (E. coli Genetic Stock Center, Yale) into E. coli C41(DE3) strain by PI phage transduction protocol ³⁸. Transductants were selected on LB agar supplemented with 10 μg/ml tetracycline. Then colonies were re-streaked on LB-agar plates containing 10 μg/ml tetracycline, 200 μΜ IPTG and 80 μg/ml X-Gal. The replacement of wild-type lacZ with the AlacZ58(M\5) allele was verified by PCR using primers ACCATGATTACGGATTCACTGG (SEQ ID NO: 231) and C CGTTGC AC C AC AG ATG AA (SEQ ID NO: 232) (the sizes of the expected PCR products are 467 bp for wild-type and 374 bp for the mutant).

Construction of the orthogonal secM-lacZa reporter poSML

[00185] The backbone of the pACYC 177 vector was PCR-amplified using primers

ATCTCATGACCAAAATCCCTTAACGTGAGT (SEQ ID NO: 233) and

GCGGTTAGCTTTTACCCCTGCATCTTTGAG (SEQ ID NO: 234). A 568 bp DNA fragment whose ends overlapped with the amplified pACYC177 backbone and which contained T7 promoter, the orthogonal SD sequence CACCAC [Rackham 2005], the secM(\2\-\66)-lacZa fusion from the plasmid pNH122 [Nakatogawa 2002], was synthesized by Integrated DNA Technologies. The pACYC177 backbone and the secMllacZa construct were combined using Gibson Assembly and introduced in the C41(DE3)/AlacZ58(M15) cells.

Construction of the 2451/2452 mutant poRibo-T library and selecting mutants capable of alleviating SecM-mediated translation arrest

[00186] A library of A2451N/C2452N mutants was generated by inverse PCR using plasmid poRibo-T2 as a template, Phusion High Fidelity DNA polymerase, and primers

AGGCTGATACCGCCCAAG (SEQ ID NO: 235) and

CTCTTGGGCGGTATCAGCCTNNTATCCCCGGAGTACCTTTTATC (SEQ ID NO: 236), with added sequence (underlined) used for re-circularization with Gibson assembly. PCR reaction was carried out under the following conditions: 98 °C, 3 min followed by 25 cycles (98 °C, 30 sec; 55 °C, 30 sec; 72 °C, 120 sec), followed by final extension 72 °C, 10 min. The PCR- amplified DNA band was purified by extraction from the agarose gel with an E.Z.N.A. Gel Extraction kit, and re-circularized by Gibson assembly for 1 hour at 50 °C. Two μΐ of the reaction were transformed into electrocompotent POP2136 cells plated on LB plates supplemented with 50 μ§/ι 1 carbenicillin and grown for 24 hrs at 30 °C. Individual colonies were picked and sequenced to identify all possible 16 variants of the library.

[00187] The C41(DE3)/AlacZ58(M15) cells were transformed with the poSML reporter plasmid and plated on LB-agar containing 50 μg/ml kanamycin. One of the colonies, which appeared after overnight incubation at 37°C, was inoculated into liquid culture, grown in the presence of 50 μg/ml kanamycin and cells were rendered chemically competent. Cells were transformed with the pooled library of sixteen 2451/2452 mutants. Transformed cells were plated on LB agar containing 50 μg/ml kanamycin, 100 μg/ml ampicillin, IPTG 0.5 mM, X-Gal 40 μg/ml and 2 mM lacZ inhibitor phenylethyl- -d-thiogalactopyranoside (PETG). Plates were incubated at 37°C for 24 hours and photographed. 16 white colonies or 15 blue colonies were inoculated in 5 ml of LB medium supplemented with 100 μg/ml ampicillin and grown overnight. The plasmids were isolated and the identities of nucleotide residues at the position 2451 and 2452 of the 23S rR A were analyzed by sequencing. Alternatively, the poSML-trans formed C41(DE3)/AlacZ58(M15) cells were transformed with individual plasmids representing all possible 16 variants of the nucleotide combinations at positions 2451 and 2452. The poRibo-T2 plasmid carrying A2058G mutation was used as a control. In addition, the poRibo-T2 plasmid carrying the U2585G mutation was included in the transformation experiment. The transformed cells were plated on LB/agar containing 50 μg/ml kanamycin and 100 μg/ml ampicillin and incubated overnight at 37°C. Three colonies from each transformation were then streaked on LB/agar plates containing 50 μg/ml kanamycin and 100 μg/ml ampicillin and supplemented with 0.5 mM IPTG, 40 μ^πιΐ X-Gal and 2 mM PETG. Plates were incubated at 37°C for 22 hours and photographed.

Dual orthogonal Ribo-T expression vector and orthoganol reportor

[00188] A single-plasmid coding for orthogonal Ribo-T and an orthogonal reporter gene to replace the previous two-plasmid system was prepared. The plasmid contains the Ribo-T operon with orthogonal anti-SD sequence, under the pL promoter, and an sfGFP gene with 0, 1 or 5 TAG codons under an lpp5 promoter with lacO site for IPTG inducibility, and t500 terminator, with AmpR gene for antibiotic selection.

[00189] Plasmid oRibo-T-sfGFP with wt-sfGFP gene under orthogonal SD site and variations to the oRibo-T portion of the plasmid was transformed into E. coli POP2136 strain, and plated on LB agar plates supplemented with 50 μg/ml carbenicillin. 6 colonies each variant were randomly picked and used to inoculate a 96 well plate with 100 μΐ, LB supplemented with 50 μg/ml carbenicillin per well, and incubated overnight at 30 °C (pL promoter repressed). A fresh 96 well plate with 100 LB supplemented with 50 μ§/ι 1 carbenicillin and 1 mM IPTG per well was inoculated with 2 μΐ_^ of saturated overnight, and grown at 42 °C (pL promoter on), monitoring OD600 and sfGFP expression. We identified a variant that showed 3.1 Fold increase in orthogonal sfGFP (FIG. 14, variant C).

Incorporating p-azido-L-phenylalanine into sfGFP-5TAG with Ribo-T

[00190] Plasmid oRibo-T-sfGFP with sfGFP gene modified with 5-TAG as prepared in the example above under orthogonal SD site and variations to the oRibo-T portion of the plasmid was transformed into rEcolOprfA mutS+ upp- Ored strain containing pEVOL-pAzF plasmid [Young 2010], and plated on LB agar plates supplemented with 50 μg/ml carbenicillin and 25 μg/ml chloramphenicol (for pEVOL-pAzF). Variants were randomly selected from a plate, and used to inoculate a 96-well plate containing in each well 100 μΐ, LB supplemented with 50 μg/ml carbenicillin and 25 μg/ml chloramphenicol, and incubated overnight at 37 °C with shaking. A fresh 96-well plate (100 μΐ_^ LB with 50 μg/ml carbenicillin and 25 μg/ml chloramphenicol) was inoculated with 2 μΐ_^ of saturated overnight, and incubated at 37 °C with shaking until OD600 0.2-0.3. IPTG (1 mM final), L-arabinose (0.02% final), and p-azido-L-phenylalanine (1 mM final) was added to each well, and incubated for 18 hrs at 37 °C with shaking, monitoring OD600 and sfGFP fluorescence. FIG. 15 shows final endpoint sfGFP fluorescence normalized with OD600. Variants A, B, C, D and H showed significant increased pAzF incorporation, ranging from 86% increase to 264% increase over oRibo-T control. REFERENCES

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Claims

claimed:

An engineered ribosome, the engineered ribosome comprising a small subunit, a large subunit, and a linking moiety,

wherein the linking moiety tethers the small subunit with the large subunit and wherein the engineered ribosome is capable of supporting translation of a sequence

defined polymer.

The engineered ribosome of claim 1 , wherein the small subunit comprises rRNA, wherein the large subunit comprises rRNA, and wherein the linking moiety tethers the rRNA of the small subunit with the rRNA of the large subunit.

The engineered ribosome of claim 1 or 2, wherein the large subunit comprises a permuted variant of a 23 S rRNA.

The engineered ribosome of any of claims 1-3, wherein the small subunit comprises a permuted variant of a 16S rRNA.

The engineered ribosome of any of claims 1-4, wherein the small subunit comprises a modified anti-Shine-Dalgarno sequence to permit translation of templates having a complementary Shine-Dalgarno sequence difference from an endogeneous cellular mRNAs.

The engineered ribosome of any of claims 1-5, wherein the linking moiety covalently bonds a helix of the large subunit to a helix of the small subunit.

The engineered ribosome of any of claims 3-6, wherein the linking moiety covalently bonds helix 10, helix 38, helix 42, helix 54, helix 58, helix 63, helix 78, or helix 101 of the permuted variant of the 23 S rRNA.

The engineered ribosome of any of claims 4-7, wherein the linking moiety covalently bonds helix 11, helix 26, helix 33, or helix 44 of the permuted variant of the 16S rRNA. The engineered ribosome of any of claims 1-8, wherein the large subunit comprises a LI polynucleotide domain, a L2 polynucleotide domain, and a C polynucleotide domain, wherein the LI domain is followed, in order, by the C domain and the L2 domain, from 5' to 3'.

The engineered ribosome of claim 9, wherein the polynucleotide consisting essentially of the L2 domain followed by the LI domain, from 5' to 3', is substantially identical to 23 S rRNA.

11. The engineered ribosome of claim 9 or 10, wherein the polynucleotide consisting essentially of the L2 domain followed by the LI domain, from 5' to 3', is at least 95% identical to a 23 S rR A.

12. The engineered ribosome of any of claims 9-11, wherein the C domain comprises a

polynucleotide having a length ranging from 1-200 nucleotides.

13. The engineered ribosome of any of claims 9-12, wherein the C domain comprises a

GAGA polynucleotide.

14. The engineered ribosome of any of claims 1-13, wherein the small subunit comprises a S 1 polynucleotide domain and a S2 polynucleotide domain, wherein the S 1 domain is followed, in order, by the S2 domain, from 5' to 3'.

15. The engineered ribosome of claim 14, wherein the polynucleotide consisting essentially of the SI domain followed by the S2 domain, from 5' to 3', is substantially identical to a 16S rRNA.

16. The engineered ribosome of claim 14 or 15, wherein the polynucleotide consisting

essentially of the SI domain followed by the S2 domain, from 5' to 3', is at least 95% identical to a 16S rRNA.

17. The engineered ribosome of any of claims 1-16, wherein the linking moiety comprises a Tl polynucleotide domain and a T2 polynucleotide domain.

18. The engineered ribosome of claim 17, wherein the Tl domain links the SI domain and the LI domain and wherein the SI domain is followed, in order, by the Tl domain and the LI domain, from 5' to 3'.

19. The engineered ribosome of claim 17 or 18, wherein the Tl domain comprises a

polynucleotide having a length ranging from 5 to 200 nucleotides.

20. The engineered ribosome of claim 19, wherein the Tl domain comprises a polynucleotide having a length ranging from 7 to 20 nucleotides.

21. The engineered ribosome of any of claims 17-20, wherein the Tl domain comprises a polyadenine polynucleotide.

22. The engineered ribosome of any of claims 17-20, wherein the Tl domain comprises a polyadenine polynucleotide having a length of 7 to 12 adenine nucleotides.

23. The engineered ribosome of any of claims 17-22, wherein the T2 domain links the S2 domain and the L2 domain and wherein the L2 domain is followed, in order, by the T2 domain and the S2 domain, from 5' to 3'.

24. The engineered ribosome of any of claims 17-24, wherein the T2 domain comprises a polynucleotide having a length ranging from 5 to 200 nucleotides.

25. The engineered ribosome of claim 17, 23, or 24, wherein the T2 domain comprises a polynucleotide having a length ranging from 7 to 20 nucleotides.

26. The engineered ribosome of any of claims 17-25, wherein the T2 domain comprises a polyadenine polynucleotide.

27. The engineered ribosome of any of claims 17-26, wherein the T2 domain comprises a polyadenine polynucleotide having a length of 7 to 12 adenine nucleotides.

28. The engineered ribosome of any of claims 17-27, wherein the ribosome comprises the SI domain followed, in order, by the Tl domain, the LI domain, the C domain, the L2 domain, the T2 domain, and the S2 domain, from 5 ' to 3 ' .

29. The engineered ribosome of any of claims 17-28, wherein the ribosome comprises a polynucleotide consisting essentially of the SI domain is followed, in order, by the Tl domain, the LI domain, the C domain, the L2 domain, the T2 domain, and the S2 domain, from 5' to 3'.

30. The engineered ribosome of any of claims 1-29, wherein the engineered ribosome

comprises a mutation.

31. The engineered ribosome of claim 30, wherein the mutation is a change-of-function mutation.

32. The engineered ribosome of claim 31 , wherein the change-of-function mutation is in a peptidyl transferase center.

33. The engineered ribosome of claim 31 , wherein the change-of-function mutation is in an A-site of the peptidyl transferase center.

34. The engineered ribosome of claim 31 , wherein the change-of-function mutation is in the exit tunnel of the engineered ribosome.

35. The engineered ribosome of any of claims 1-35, wherein the engineered ribosome has an antibiotic resistance mutation.

36. A polynucleotide, the polynucleotide encoding the rRNA of the engineered ribosome of any of claims 1-35.

37. The polynucleotide of claim 36, wherein the polynucleotide is a vector.

38. The polynucleotide of claim 36 or 37, wherein the polynucleotide further comprises a gene to be expressed by the engineered ribosome.

39. The polynucleotide of claim 38, wherein the gene is a reporter gene.

40. The polynucleotide of claim 39, wherein the reporter gene is a green fluorescent protein gene.

41. The polynucleotide of any of claims 36-40, wherein the engineered ribosome comprises a modified anti-Shine-Dalgarno sequence and the gene comprises a complementary Shine- Dalgarno sequence to the engineered ribosome.

42. The polynucleotide of any of claims 36-41, wherein the gene comprises a codon and the codon encodes for an unnatural amino acid.

43. A method for preparing an engineered ribosome, the method comprising expressing the polynucleotide of any of claims 36-42.

44. The method of claim 43, the method further comprising selecting a mutant.

45. The method of claim 44, wherein the selection step comprises a negative selection step, a positive selection step, or both a negative and a positive selection step.

46. A cell, the cell comprising (i) the polynucleotide of any of claims 36-42, (ii) the

engineered ribosome of any of claims 1-35, or both (i) and (ii).

47. A cell, the cell comprising a first protein translation mechanism and a second protein translation mechanism,

wherein the first protein translation mechanism comprises a ribosome, wherein the

ribosome lacks a linking moiety between the large subunit and the small subunit and

wherein the second protein translation mechanism comprises the engineered ribosome of any of claims 1-35.

48. A method for preparing a sequence-defined polymer, the method comprising

(a) providing the engineered ribosome of any of claims 1-35 and

(b) providing an mR A or DNA template encoding the sequence-defined polymer.

49. The method of claim 48, wherein the sequence-defined polymer is prepared in vitro.

50. The method of claim 49, the method further comprising providing a ribosome-depleted cellular extract or purified translation system.

51. The method of claim 50, wherein the ribosome-depleted cellular extract comprises an SI 50 extract prepared from mid- to late- exponential growth phase cell cultures or cultures having an O.D.600 ~ 3.0 at time of harvest.

52. The method of claim 48, wherein the sequence defined polymer is prepared in vivo.

53. The method of claim 48 or 52, wherein the sequence defined polymer is prepared in the cell of any of claims 46 or 47.

54. The method of any of claims 48-53, wherein the mRNA or DNA encodes a modified

Shine-Dalgarno sequence and the engineered ribosome comprises an anti-Shine-Dalgarno sequence complementary to the modified Shine-Dalgarno sequence.

55. The method of any of claims 48-54, wherein the sequence-defined polymer comprises an amino acid.

56. The method of claim 55, wherein the amino acid is a natural amino acid.

57. The method of claim 55, wherein the amino acid is an unnatural amino acid.