CA2465724A1 - Engineering of leader peptides for the secretion of recombinant proteins in bacteria - Google Patents

Abstract

The present invention provides methods of isolating of leader peptides capab le of directing export of heterologous proteins from the bacterial cytoplasm. T he methods rely on the screening of libraries of putative leader peptides or of leader peptide mutants for sequences that allow rapid export and thus can rescue a short-lived reporter protein from degradation in the cytoplasm. The mutant leader peptides identified herein are shown to confer significantly higher steady state levels of export not only for short-lived reporter prote in but also for other stable, long-lived proteins. These leader peptides can be used to direct or enhance protein secretion. The present invention further discloses methods for the export of cytoplasmically folded protein via the T at pathway. Proteins having disulfide bonds are first folded within the cytopla sm in suitable oxidizing mutant strains. Such cytoplasmically pre-folded protei ns containing disulfide bonds are then exported via the Tat pathway.

Description

ENGINEERING OF LEADER PEPTIDES FOR THE SECRETION OF RECOMBINANT
PROTEINS IN BACTERIA
BACKGROUND OF THE INVENTION
This application claims the priority of U.S. Provisional Patent Application Ser. No.
60/337,452, filed November 5, 2001, and U.S. Provisional Patent Application Ser. No. 60/---,---, filed August 21, 2002, in the name of George Georgiou and Matthew DeLisa and entitled "Engineering of Leader Peptides for the Secretion of Recombinant Proteins in Bacteria." Both of the foregoing disclosures are specifically incorporated herein by reference in the entirety.
1. Field of the Invention The present invention relates generally to the fields of genetic engineering and protein secretion. More specifically, the present invention relates to engineering of leader peptides for the secretion of recombinant proteins in bacteria.

2. Description of the Related Art Proteins destined for secretion from the cytoplasm are synthesized with an N-terminal peptide extension of generally between 15-30 amino acids known as the leader peptide. The leader peptide is proteolytically removed from the mature protein either concomitant to or immediately following export into an exocytoplasmic location.
Recent findings have established that there are actually four protein export pathways in Gram-negative bacteria (Stuart and Neupert, 2000): the general secretory (Sec) pathway (Danese and Silhavy, 1998; Pugsley, 1993), the signal recognition particle (SRP)-dependent pathway (Meyer et al., 1982), the recently discovered YidC-dependent pathway (Samuelson et al., 2000) and the twin-arginine translocation (Tat) system (Berks, 1996).

With the first three of these pathways, polypeptides cross the membrane via a 'threading' mechanism, i.e., the unfolded polypeptides insert into a pore-like structure formed by the proteins Sect, SecE and Sect and are pulled across the membrane via a process that requires the hydrolysis of ATP (Schatz and Dobberstein, 1996).
In contrast, proteins exported through the Tat-pathway transverse the membrane in a partially or perhaps even fully folded conformation. The bacterial Tat system is closely related to the '~pH-dependent' protein import pathway of the plant chloroplast thylakoid membrane (Settles et al., 1997). Export through the Tat pathway does not require ATP
hydrolysis and does not involve passage through the SecY/E/G pore. In most instances, the natural substrates for this pathway are proteins that have to fold in the cytoplasm in order to acquire a range of cofactors such as FeS centers or molybdopterin. However, proteins that do not contain cofactors but fold too rapidly or too tightly to be exported via any other pathway can be secreted from the cytoplasm by fusing them to a Tat-specific leader peptide (Berks, 1996; Berks et al., 2000).
The membrane proteins TatA, TatB and TatC are essential components of the Tat translocase in E. coli Sargent et al., 1998; Weiner et al., 1998). In addition, the TatA
homologue TatE, although not essential, may also has a role in translocation and the involvement of other factors cannot be ruled 'out. TatA, TatB and TatE are all integral membrane proteins predicted to span the inner membrane once with their C-terminal domain facing the cytoplasm. The TatA and B proteins are predicted to be single-span proteins, whereas the TatC protein has six transmembrane segments and has been proposed to function as the translocation channel and receptor for preproteins (Berks et al., 2000;
Bogsch et al., 1998; Chanal et al., 1998). Mutagenesis of either TatB or C
completely abolishes export (Bogsch et al., 1998; Sargent et al., 1998; Weiner et al., 1998). The Tat complex purified from solubilized E. coli membranes contained only TatABC
(Bolhuis et al., 2001). hZ vitro reconstitution of the translocation complex demonstrated a minimal requirement for TatABC and an intact membrane potential (Yahr and Wickner, 2001).
The choice of the leader peptides, and thus the pathway employed in the export of a particular protein, can determine whether correctly folded functional protein will be produced (Bowden and Georgiou, 1990; Thomas et al., 2001). Feilmeier et al.
(2000) have shown that fusion of the green fluorescent protein (GFP) to a Sec-specific leader peptide or to the C-terminal of the maltose binding protein (MBP which is also exported via the Sec pathway) resulted in export of green fluorescent protein and MBP-GFP into the periplasm.
However, green fluorescent protein in the periplasm was non-fluorescent indicating that the secreted protein was misfolded and thus the chromophore of the green fluorescent protein could not be formed. Since proteins exported via the Sec pathway transverse the membrane in an unfolded form, it was concluded that the environment in the bacterial secretory compartment (the periplasmic space) does not favor the folding of green fluorescent protein Feilmeier et al., 2000). In contrast, fusion of a Tat-specific leader peptide to green fluorescent protein resulted in accumulation of fluorescent green fluorescent protein in the periplasmic space. In this case, the Tat-GFP
propeptide was first able to fold in the cytoplasm and then be exported into the periplasmic space as a completely folded protein (Santini et al., 2001; Thomas et al., 2001).
However, there has been no evidence that leader peptides other than TorA can be employed to export heterologous proteins into the periplasmic space of E. coli.

The cellular compartment where protein folding fakes place can have a dramatic effect on the yield of biological active protein. The bacterial cytoplasm contains a large number of protein folding accessory factors, such as chaperones whose function and ability to facilitate folding of newly synthesized polypeptides is controlled by ATP
hydrolysis. In contrast, the bacterial periplasm contains relatively few chaperones and there is no evidence that ATP is present in that comparhnent. Thus many proteins are unable to fold in the periplasm and can reach their native state only within the cytoplasmic milieu. The only known way to enable the secretion of folded proteins from the cytoplasm is via fusion to a Tat-specific leader peptide. However, the protein flux through the Tat export system is significantly lower than that of the more widely used Sec pathway.
Consequently, the accumulation and steady state yield of proteins exported via the Tat pathway is low.
The prior art is thus deficient in methods of directing efficient export of folded proteins from the cytoplasm. The present invention fulfills this long-standing need and desire in the art.
SUMMARY OF THE INVENTION
The present invention provides methods for the isolation of sequences that can serve as leader peptides to direct the export of heterologous proteins. One aspect of the invention allows the isolation of leader peptides capable of directing proteins to the Tat secretion pathway. Further, the present invention discloses methods for identifying leader peptide mutants that can confer improved protein export.
In one aspect, the invention thus provides methods of identifying leader peptides that direct enhanced protein secretion in bacteria. In one embodiment, the methods disclosed herein comprise screening libraries of mutated leader peptides for sequences that allow rapid export and thus can rescue a short-lived reporter protein from degradation in the cytoplasm. Leader peptides that mediate secretion through the Esclaerichia coli Twin Arginine Translocation (Tat) pathway, as well as those that direct other secretion pathways such as the sec pathway in bacteria can be isolated by the methods disclosed herein.
Mutant leader peptide sequences conferring improved export are also disclosed.
The mutant leader peptides are shown to confer significantly higher steady state levels of export not only for the short lived reporter protein but also for other stable, long lived proteins.
In one aspect of the present invention, there is provided a method of identifying leader peptides that direct increased protein export through pathways that include, but are not limited to, the Twin Arginine Translocation (TAT) pathway and the sec pathway. Such a method may involve constructing expression cassettes that place mutated leader peptides upstream of a gene encoding a short-lived reporter protein. The short-lived reporter protein can be created by attaching a cytoplasmic degradation sequence to the gene encoding the reporter protein. The resulting expression cassettes may then be expressed in bacteria, and reporter protein expressions in these bacteria measured. Mutated leader peptides expressed in cells that exhibit increased reporter protein expression comprise leader peptides that would direct increased protein export in bacteria. Representative leader peptides identified from the above methods include SEQ m NOs:120-136.
In another aspect of the present invention, there is provided a method of increasing polypeptide export through pathways that include, but are not limited to, the Tat pathway and the sec pathway. This method involves expressing expression cassettes that place mutated leader peptides identified in the methods disclosed herein upstream of the gene encoding a heterologous polypeptide of interest.
In yet another aspect of the present invention, there is provided a method of screening for a compound that inhibits or enhances protein export through pathways that include, but are not limited to, the Tat pathway and the sec pathway. This method may comprise first constructing expression cassettes that place mutated leader peptides identified in the methods disclosed herein upstream of a gene encoding a short-lived reporter protein. The short-lived reporter protein can be created by attaching a cytoplasmic degradation sequence to the gene encoding the reporter protein. The resulting expression cassettes may then be expressed in bacteria, and reporter protein expression in these bacteria are measured in the presence or absence of the candidate compound.
Increased reporter protein expression measured in the presence of the candidate compound indicates that the candidate compound enhances protein export, whereas decreased reporter protein expression measured in the presence of the candidate compound indicates that the candidate compound inhibits protein export.
In another aspect of the present invention, there is provided a method for producing soluble and biologically-active heterologous polypeptide containing multiple disulfide bonds in a bacterial cell. The method may involve constructing an expression cassette that places a leader peptide that directs protein export through the Twin Arginine Translocation pathway upstream of a gene encoding the heterologous polypeptide. The heterologous polypeptide is then expressed in bacteria that have an oxidizing cytoplasm.

Other and further aspects, features, and advantages of the present invention will be apparent from the following description of the presently preferred embodiments of the invention. These embodiments are given for the purpose of disclosure.
S BRIEF DESCRIPTION OF THE DRAWINGS
So that the matter in which the above-recited features, advantages and objects of the invention as well as others which will become clear are attained and can be understood in detail, more particular descriptions and certain embodiments of the invention briefly summarized above are illustrated in the appended drawings. These drawings form a part of the specification. The drawings illustrate certain embodiments of the invention and are not to be considered limiting in their scope.
FIG. 1 shows the expression of green fluorescent protein in different plasmid constructs. FIG. lA shows minimal green fluorescent protein fluorescence in cells expressing pGFPSsrA, indicating that cytoplasmic SsrA-tagged green fluorescent protein is degraded almost completely. FIG. 1B shows enhanced green fluorescent protein fluorescence in cells expressing pTorAGFPSsrA, indicating improved green fluorescent protein export directed by the TorA leader peptide. FIG. IC shows green fluorescent protein fluorescence in cells expressing pTorAGFP. The green fluorescent protein was expressed in both the cytoplasm and the periplasm.
FIG. 2 shows green fluorescent protein fluorescence in 6 different clones that exhibit increased Tat-dependent export due to mutated TorA leader peptides.
FIG. 3 shows periplasmic green fluorescent protein accumulation in the B6 and clones. FIG. 3A shows western blot of green fluorescent protein in the periplasm (lanes 1-3) and cytoplasm (lanes 4-6) of cells expressing the wild type construct (lanes 1 and 4), the B6 clone (lanes 2 and 5) and the E2 clone (lanes 3 and 6). GroEL is a cytoplasmic marker whereas DsbA is a periplasmic marker. FIG. 3B shows periplasmic and cytoplasrnic distribution of green fluorescent protein in cells expressing the wild type construct, the B6 clone and the E2 clone.
FIG. 4 shows increased green fluorescent protein fluorescence in cells expressing the wild type construct, the B6, B7 or E2 construct fused to untagged, proteolytically stable green fluorescent protein.
FIG. 5 shows western blot of green fluorescent protein in the periplasm (lanes 1-2), cytoplasm (lanes 3-4) and whole cell lysate (lanes 5-6) of cells expressing the wild type construct (lanes 1,3 and 5) or the B7 clone (lanes 2, 4 and 6). GroEL is a cytoplasmic marker whereas DsbA is a periplasmic marker.
FIG. 6 Shows schematic of export of disulfide linked heterodimer in which only one polypeptide chain was fused to leader peptide.
FIG. 7 Shows western blot analysis and AP activity measurements for both periplasmic and cytoplasmic fractions in six genetic backgrounds.
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides methods of identifying and using leader peptides that direct enhanced protein secretion in bacteria. Numerous proteins of commercial interest are produced in secreted form in bacteria. However, many proteins, including many antibody fragments and several enzymes of eucaryotic origin, cannot be exported efficiently through the main secretory pathway, the sec pathway, of bacteria.

An alternative pathway for the translocation of proteins from the cytoplasm of bacteria is called the t'TAT" (twin-arginine-translocation) pathway. Whether a protein is directed to the sec machinery or the TAT pathway depends solely on the nature of the leader peptide, an amino acid extension of generally 15-30 residues located at the beginning of the polypeptide chain. The leader peptide consists of three distinct regions:
(1) the amino terminal n-region, (2) the hydrophobic core or h-region, and (3) the c-terminal region.
A hallmark of both plant and prokaryotic TAT-specific leader peptides is the presence of the distinctive and conserved (S/T)-R-R-x-F-L-K (SEQ m NO:1) sequence motif. This sequence motif is located at the n-region/h-boundary within leader peptides of known and predicted TAT substrates (Berks, 1996). Mutation of either arginine residue within the signal peptide significantly reduces the efficiency of protein translocation (Cristobal et al., 1999).
Relative to leader peptides specific for the Sec pathway, which is by far the most commonly used export pathway in bacteria, TAT-specific leader peptides are on average 14 amino acids longer due to an extended n-region and more basic residues in the c-region (Cristobal et al., 1999). However, the hydrophobic h-region in the TAT-specific leader peptides is significantly shorter due to a higher occurrence of glycine and threonine residues.
The twin-arginine (RR) motifs of wheat pre-23K and pre-Hcf136 are essential for targeting by the thylakoid TAT pathway; this motif is probably a central feature of TAT
signals. The twin-arginine motif is not the only important determinant in TAT-specific targeting signals, and a further hydrophobic residue two or three residues after this motif seems also to be highly important.
Bacterial twin-arginine-signal peptides are similar to thylakoid TAT signals and can direct TAT-dependent targeting into plant thylakoids with high efficiency.
However, the vast majority of bacterial signal peptides contain conserved sequence elements in addition to the twin-arginine motif that imply special functions. There is a heavy bias towards phenylalanine at the second position after the twin-arginine motif, and many of the signals contain lysine at the fourth position. None of the known thylakoid twin-arginine signals contains phenylalanine at this position and only one (Arabidopsis P29) contains lysine as the fourth residue after the twin-arginine motif. The precise roles of these highly conserved features are unclear; the phenylalanine residue can be replaced by Leu but not by Ala without undue effects, which indicates that hydrophobicity, rather than the phenylalanine side-chain, might be the important determinant. Similarly, replacement of the Lys residue does not impede export (Robinson and Bolhuis, 2001).
Proteins exported through the TAT system first fold into their native conformation within the cytoplasm and are then exported across the cytoplasmic membrane.
The ability to export proteins that have already folded in the cytoplasm is highly desirable with regard to commercial protein production for several reasons. First of all, proteins that fold very rapidly after synthesis is completed cannot be secreted by the more common sec export pathway. Secondly, the bacterial cytoplasm contains a full complement of folding accessory factors, which can assist a nascent polypeptide in reaching its native conformation. In contrast, the secretory compartment of bacteria contains very few folding accessory factors such as chaperones and foldases. Therefore, for the production of many to proteins, it is preferable for folding to occur first within the cytoplasm followed by export into the periplasmic space through the TAT system. Thirdly, the acquisition of cofactors has to occur within the cytoplasm concomitant with folding. Consequently, cofactor-containing proteins must be secreted through the TAT pathway.
A limitation in the use of the protein secretion, and specif cally of the TAT
export pathway, for commercial protein production has been that the amount of protein that can be exported in this manner is low. Tn other words, the overall protein flux through the TAT
system is substantially lower than that of the sec pathway.
Currently, there is no reliable technology that can be used to screen for increased IO periplasmic secretion of recombinant proteins, nor is there an optimized TAT-specific leader peptide. However, results obtained from the methods disclosed herein would lead to characterization of optimized leader peptides that can circumvent the slow transit rates typically observed for wild type or native twin-arginine leader sequences. The present invention also enables a thorough and systematic determination on minimal leader sequence requirements for proper and efficient export through the TAT pathway.
Moreover, the methods disclosed herein can also identify leader peptides that mediate enhanced protein secretion through other pathways such as the sec pathway.
The present invention thus provides, in one aspect, a method of identifying a leader peptide that directs increased protein export through the Twin Arginine Translocation or TAT pathway by constructing expression cassettes that put mutated candidate TAT-specific leader peptides upstream of a gene encoding a short-lived reporter protein. Such a short lived reporter protein exhibits a decreased half life in the cytoplasm relative to reporter protein molecules that have been exported from the cytoplasm. The short-lived reporter protein can be created, for example, by attaching a cytoplasmic degradation sequence to the gene encoding the reporter protein. In general, mutated leader peptides may be generated by random mutagenesis, error-prone PCR and/or site-directed mutagenesis. The resulting expression cassettes can then be expressed in bacteria, and expression of the reporter protein be measured. Mutated TAT-specific leader peptides expressed in cells that exhibit increased expression of reporter protein are leader peptides that would direct increased protein export through the TAT pathway.
Methods that are well known to those skilled in the art can be used to construct expression cassettes or vectors containing appropriate transcriptional and translational control signals. See for example, the techniques described in Sambrook et al., 200, Molecular Cloning: A Laboratory Manual (2nd Ed.), Cold Spring Harbor Press, N.Y.
Vectors of the invention include, but are not limited to, plasmid vectors and viral vectors.
In one embodiment of the screening methods described herein, green fluorescent protein (GFP) may be used as a reporter protein. The method takes advantage of the fact that functional, fluorescent green fluorescent protein can only be secreted using a TAT-specific leader peptide. However, the export of green fluorescent protein via a TAT
specific leader peptide is inefficient and results in the accumulation of an appreciable amount of precursor protein (green fluorescent protein with the TAT-specific leader) in the cytoplasm. The cytoplasmic green fluorescent protein precursor protein is folded correctly and is fluorescent. As a result, the cells exhibit high fluorescence, which in part is contributed by the cytoplasm'ic precursor and in part by the secreted, mature green fluorescent protein in the periplasm. The overall high fluorescence of these cells contributes to a high background signal which complicates the isolation of leader peptide mutations that give rise to a higher flux of exported green fluorescent protein.
To circumvent this problem, a short-lived version of green fluorescent reporter protein may be used. This short-lived version is rapidly degraded within the bacterial cytoplasm. Fusion of the SsrA sequence A.ANDENYALAA (SEQ ID N0:119), for example, to the C-terminal of green fluorescent protein targets the protein for degradation by the CIpXAP protease system (Karzai et al., 2000). As a result, the half life of green fluorescent protein in the cytoplasm is reduced from several hours to less than 10 min, resulting in a significant decrease in whole cell fluorescence.
It was shown that, when the short lived green fluorescent protein was fused to a wild-type TAT-specific leader peptide, a low level of cell fluorescence was observed because most of the protein was degraded prior to export from the cytoplasm.
It was contemplated that mutations in the TAT-specific leader peptide may cause faster and more efficient export that rescues the short lived green fluorescent protein from degradation in the cytoplasm. As a result, folded green fluorescent protein would be accumulated in the periplasm, leading to higher cell fluorescence. Therefore, libraries of mutant TAT-specific leader peptides were constructed by either random mutagenesis (error-prone PCR) or nucleotide directed mutagenesis. These mutant leader peptides were then screened fox their ability to mediate enhanced protein secretion and rescue the short-lived green fluorescent protein from degradation in the cytoplasm, thereby leading to increased fluorescence of the bacteria. Clones exhibiting higher fluorescence were then isolated by flow cytometry.
One particular feature of the present invention is that the genetic screen described herein results in periplasmic-only accumulation of active reporter protein.
The mutated leader peptides direct folded green fluorescent reporter protein to the periplasm where the fluorescent protein remains active. However, due to the presence of the SsrA C-terminal degradation peptide, virtually all cytoplasmic green fluorescent protein is degraded. The resulting cells glow green in a halo-type fashion due to the presence of periplasmic-only green fluorescent protein. In contrast, TAT-dependent export of green fluorescent protein that lacks the SsrA sequence would lead to green fluorescent protein accumulation in both the cytoplasm and the periplasm, resulting in substantial background signal that makes cell-based screening of GFP fluorescence impossible.
In addition to green fluorescent protein, various other reporter proteins can be used in the methods of the present invention. A person having ordinary skill in this art could readily isolate mutant leader peptides that result in higher levels of reporter protein expression in the periplasm in a number of ways. In one example, if the reporter is an antibiotic resistance enzyme (e.g., (3-lactamase), then mutant leader peptides can be isolated by selecting on increasing concentrations of antibiotic. In another example, if the reporter is an immunity protein to a toxin (e.g., colicins), mutant leader peptides can be isolated by selecting for resistance to toxin. In another example, if the reporter protein is a transport protein such as maltose binding protein, export of the transport protein is used to complement chromosomal mutants. In another example, the chromogenic or fluoregenic substrate of a reporter enzyme (e.g. alkaline phosphatase) can be used to score for colonies that produce higher levels of the enzyme in the bacterial periplasm.
There are a number of research and industrial uses for the screening system described herein. Examples of these research and industrial uses include, but are not necessarily limited to, the following:

(1) Bio-Production of Proteins: The secretion of several proteins via the TAT
pathway has been reported to be a relatively slow and inefficient process.
Therefore, the need for improved export must be realized in order to make the TAT pathway a feasible platform for high-level production of high-value recombinant protein products.
Using the genetic screens outlined herein, optimized TAT leader peptides have been isolated and tested fox their ability to rapidly export recombinant proteins of interest.
The recombinant proteins are thus secreted into the periplasmic space or the growth medium in a functional and soluble form, alleviating problems associated with inclusion bodies and simplifying recovery. Furthermore, since proteins are folded and accumulate in the cytoplasm prior to TAT-dependent export, this export system will likely result in higher levels of active product accumulation within the host cell, thus maximizing the efficiency of the recombinant expression system.
(2) In High-Throughput Screening Platforms: The present invention can be applied in the development of technologies that capitalize on TAT-dependent export for IS combinatorial library screening and protein engineering applications. For example, improved cytoplasmic folding of disulfide bond containing proteins (e.g., antibodies, eucaryotic enzymes) can be assayed by fusion to optimized leader peptides that export the folded proteins of interest to the periplasm where it can be easily accessed by FACS-based or phage-based screening protocols. The amount of active protein detected in the periplasm would be a quantitative indicator of the efficiency of folding in the cytoplasm.
(3) In Drug Discovery Programs: Homologues of some TAT proteins have been identified in pathogenic bacteria such as Mycobacteriufn tuberculosis and Helicobacter pylof-i as well as Pseudomonas sp. This indicates that some proteins belonging to this translocation system may be potential new targets fox antibacterial agents.
Using the processes outlined herein, a large number of compounds can easily be screened for inhibition of TAT-dependent secretion. Furthermore, the presence of certain proteins in multicopy derived from genomic libraries or random deletion of genes from the genome can be tested using this process to identify novel enhancers/suppressors of the TAT
secretion process in bacteria, thereby providing a more general approach to developing antimicrobials.
The present invention of identifying and using leader peptides that direct enhanced protein secretion in bacteria is not limited to the TAT pathway. The methods disclosed herein are equally applicable for identifying leader peptides that direct enhanced protein secretion through other secretion pathways as described above. Signal sequences which promote protein translocation to the periplasmic space of Gram-negative bacterial are well-known to one of skill in the art. For example, the E. coli OmpA, Lpp, Lama, MaIE, PeIB, and StII leader peptide sequences have been successfully used in many applications as signal sequences to promote protein secretion in bacterial cells such as those used herein, and are all contemplated to be useful in the practice of the methods of the present invention. A person having ordinary skill in this art can readily employ procedures well-known in the art to construct libraries of mutated leader sequences and expression cassettes that incorporate these mutated leader peptides, and screen these leader peptides according the methods described herein.
The present invention also relates to secretion of partially or fully folded cytoplasmic proteins with disulfide bonds. The formation of disulfide bonds is essential for the correct folding and stability of numerous eukaryotic proteins of importance to the pharmaceutical and bioprocessing industries. Correct folding depends on the formation of cysteine-cysteine linkages and subsequent stabilization of the protein into an enzymatically active structure. However, numerous studies have demonstrated that multiple disulf de bond-containing proteins cannot be expressed in active form in bacteria.
Disulfide bond formation is blocked in the reducing environment of the cytoplasm of a cell due to the presence of thioredoxin reductase or reduced glutathione.
Thus, the production of technologically important proteins with four or more disulfide bonds is costly and complicated and must rely either on expression in higher eukaryotes that provide a favorable environment for the formation of disulfide bonds or refolding from inclusion bodies (~-Ia~l~rieyz. , ~ 994, Georgian. anl', ;~al~.~, ' 19~~). For example, tissue plasminogen activator (tPA) is currently produced in bacteria inclusion bodies. In typical procedures, the proteins are released from inclusion bodies using a variety of chaotropic agents, then isolated and refolded by employing reducing agents.
Generally, refolding results in low yields of biologically active material.
The process of secretion disclosed herein provides an efficient method of producing complex eukaryotic proteins with multiple disulfide bonds. These disulfide bonds form from specific orientations to promote correct folding of the native protein.
Multiple disulfide bonds resulting from improper orientation of nascently formed proteins in the cell lead to misfolding and loss or absence of biological activity. . In contrast, biologically-active polypeptide-containing multiple disulfide bonds produced according to the instant invention will be correctly folded; disulfide bonds will form to provide a tertiary and where applicable, quarternary structure leading to a molecule with native functional activity with respect to substrates and/or catalytic properties. The proteins produced by the method 1~

disclosed herein are correctly folded and biologically active without the need for reactivation or subsequent processing once isolated from a host cell.
The most immediate problem solved by the methods disclosed herein is that proteins with multiple disulfide bonds can now be exported to the periplasm in a fully folded and therefore active conformation. Complex proteins containing multiple disulfide bonds can be folded in the cytoplasm with the assistance of a full complement of folding accessory factors that facilitate nascent polypeptides in reaching their native conformation.
The folded proteins are then secreted into the periplasmic space or the growth medium in a functional and soluble form, thus alleviating problems associated with inclusion bodies and simplifying recovery. In addition, active recombinant proteins accumulate simultaneously in two bacterial compartments (cytoplasm and periplasm), leading to greater overall yields of numerous complex proteins which previously could not actively accumulate in both compartments concurrently.
Thus, the present invention provides a method of producing at least one biologically-active heterologous polypeptide in a cell. A leader peptide that directs protein export through the Twin Arginine Translocation pathway may be placed upstream of a gene encoding the heterologous polypeptide in an expression cassette. The expression cassette can be expressed in a cell, wherein the heterologous polypeptide is produced in a biologically-active form. Generally, the heterologous polypeptide is secreted from the bacterial cell, is isolatable from the periplasm or the culture supernatant of the bacterial cell, or is an integral membrane protein. The heterologous polypeptide produced by this method can be a mammalian polypeptide such as tissue plasminogen activator, pancreatic trypsin inhibitor, an antibody, an antibody fragment or a toxin immunity protein. The heterologous polypeptide may be a polypeptide in native conformation, a mutated polypeptide or a truncated polypeptide.
Using a cell that has an oxidizing cytoplasm, the above method can produce a heterologous polypeptide containing from about 2 to about I7 disulfide bonds.
This method may also produce two heterologous polypeptides that are linked by at least one disulfide bond. Preferably, the leader peptide comprises a sequence of SEQ ID
NOs:25-46, 120-128 or a peptide homologous to SEQ ID NOs:25-46, 120-128. Representative cells which are useful in this method include E. colt trxB mutants, E. coli gor mutants, or E. coli trxB gor double mutants such as E. coli strain FA 113 or E. coli strain DR473.
The present invention also provides a series of putative TAT-specific leader peptides, which can be identified by a bioinformatics search from E. coli, cloned and examined for functional activities. Thus, the present invention encompasses isolated leader peptides that direct protein secretion and export through the Twin Arginine Translocation pathway. Representative leader peptides comprise sequences of SEQ >D NOs:25-46, 120-128. Moreover, the present invention includes isolated TAT leader peptides that are homologous to SEQ ID NOs:25-46, 120-128.
The present invention also provides a method of identifying a leader peptide that directs increased protein export by constructing expression cassettes that put mutated leader peptides upstream of a gene encoding a short-lived reporter protein.
The short-lived reporter protein can be created by attaching a cytoplasmic degradation sequence to the gene encoding the reporter protein. Representative cytoplasmic degradation sequences include SEQ ID NO:I 19, PEST, or sequences recognized by LON, cIPAP, cIPXP, Stsh and HsIUV.
The cytoplasmic degradation sequences are attached to either the N- or C-terminal of the reporter protein. In general, reporter proteins that can be used include fluorescent proteins, an enzyme, a transport protein, an antibiotic resistance enzyme, a toxin immunity protein, a bacteriophage receptor protein and an antibody.
Mutated leader peptides can be generated, for example, by random mutagenesis, error-prone PCR or site-directed mutagenesis, as well as other methods known to those of skill in the art. The resulting expression cassettes can then be expressed in bacteria, and expression of the reporter protein measured. Mutated leader peptides expressed in cells that exhibit increased expression of reporter protein comprise leader peptides that would direct increased protein export in bacteria. This screening method is capable of identifying leader peptides that direct protein secretion through the general secretory (Sec) pathway, the signal recognition particle (SRP)-dependent pathway, the YidC-dependent pathway or the twin-arginine translocation (Tat) pathway.
In another aspect of the present invention, there is provided a method of increasing export of heterologous polypeptide in bacteria. Expression cassettes are constructed that put mutated leader peptides identified according to the methods of the invention upstream of a coding sequence encoding a heterologous polypeptide of interest. These expression cassettes can then be expressed in bacteria.
The present invention also provides a method of screening for a compound that inhibits or enhances protein export in bacteria. A leader peptide that directs protein export in bacteria may be placed upstream of a gene encoding a short-lived reporter protein in an expression cassette. The expression cassette may then be expressed in bacteria in the presence or absence of a test compound. Increased expression of the reporter protein measured in the presence of the test compound indicates the compound enhances protein export, whereas decreased expression of the reporter protein measured in the presence of the compound indicates the compound inhibits protein export. Construction and examples of short-lived reporter protein are described above.
The present invention also provides a method of identifying a leader peptide that directs increased protein export through the Twin Arginine Translocation pathway by constructing expression cassettes that put mutated leader peptides specific for the Twin Arginine Translocation pathway upstream of a coding sequence encoding a short-lived reporter protein. Construction and examples of short-lived reporter protein are described above. The mutated leader peptides can be generated by random mutagenesis, error-prone PCR or site-directed mutagenesis. The resulting expression cassettes can then be expressed in bacteria, and expression of the reporter protein measured.
Mutated leader peptides expressed in cells that exhibit increased expression of reporter protein comprise leader peptides that would direct increased protein export through the Twin Arginine Translocation pathway. Examples of mutated leader peptides comprise sequences of SEQ
m Nos:120-128.
In another aspect of the present invention, there is provided a method of increasing export of heterologous polypeptide through the Twin Arginine Translocation pathway.
Expression cassettes may be constructed that put mutated leader peptides identified according to the methods disclosed herein upstream of a gene encoding a heterologous polypeptide of interest. These expression cassettes may then be expressed in bacteria.
Examples of mutated leader peptides comprise sequences of SEQ ll~ N~s:120-128.
The present invention also provides a method of screening for a compound that inhibits or enhances protein export through the Twin Arginine Translocation pathway. A

leader peptide specific for the Twin Arginine Translocation pathway may be placed upstream of a gene encoding a short-lived reporter protein in an expression cassette. The expression cassette may then be expressed in bacteria in the presence or absence of a test compound. Increased expression of the reporter protein measured in the presence of the test compound indicates the compound enhances protein export, whereas decreased expression of the reporter protein measured in the presence of the compound indicates the compound inhibits protein export through the Twin Arginine Translocation pathway.
Construction and examples of short-lived reporter protein are described above.
As used herein, "polypeptide" or "polypeptide of interest" refers generally to peptides and proteins having more than about ten amino acids. The polypeptides are "heterologous," meaning that they are foreign to the host cell being utilized, such as a human protein produced by a CHO cell, or a yeast polypeptide produced by a mammalian cell, or a human polypeptide produced from a human cell line that is not the native source of the polypeptide. Examples of a polypeptide of interest include, but are not limited to, molecules such as renin, a growth hormone (including human growth hormone), bovine growth hormone, growth hormone releasing factor, parathyroid hormone, thyroid stimulating hormone, lipoproteins, ocl-antitrypsin, insulin A-chain, insulin (3-chain, proinsulin, thrombopoietin, follicle stimulating hormone, calcitonin, luteinizing hormone, glucagon, clotting factors (such as factor V)ZIC, factor IX, tissue factor, and von Willebrands factor), anti-clotting factors (such as Protein C, atrial naturietic factor, lung surfactant), a plasminogen activator, (such as human tPA or urokinase), mammalian trypsin inhibitor, brain-derived neurotrophic growth factor, kallikreins, CTNF, gp120, anti-HER-2, human chorionic gonadotropin, mammalian pancreatic trypsin inhibitor, antibodies, antibody fragments, protease inhibitors, therapeutic enzymes, lymphokines, cytokines, growth factors, neurotrophic factors, insulin chains or pro-insulin, immunotoxins, bombesin, thrombin, tumor necrosis factor-a or (3,.enkephalinase, a serum albumin (such as human serum albumin), mullerian-inhibiting substance, relaxin A-chain, relaxin B-chain, prorelaxin, mouse gonadotropin-associated peptide, a microbial protein (such as (3-lactamase), Dnase, inhibin, activin, vascular endothelial growth factor (VEGF), receptors for hormones or growth factors, integrin, protein A or D, rheumatoid factors, neurotrophic factors (such as neurotrophin-3, -4, -5, or -6), or a nerve growth factor (such as NGF-(3), cardiotrophins (cardiac hypertrophy factor) (such as cardiotrophin-1), platelet-derived growth factor (PDGF), fibroblast growth factor (such as a FGF and [3 FGF), epidermal growth factor (EGF), transforming growth factor (TGF) (such as TGF-a, TGF-(31, TGF-(32, TGF-[33, TGF-[34, or TGF-(35), insulin-like growth factor-I and -II, des(1-3)-IGF-I
(brain IGF-n, insulin-like growth factor binding proteins, CD proteins (such as CD-3, CD-4, CD-8, and CD-19), erythropoietin, osteoinductive factors, bone morphogenetic proteins (BMPs), interferons (such as interferon-a, -(3, and -y), colony stimulating factors (CSFs) (e.g., M-CSF, GM-CSF, and G-CSF), interleukins (Ils) (such as IL-1 to IL-10), superoxide dismutase, T-cell receptors, surface membrane proteins, decay accelerating factor, viral antigens such as a portion of the AIDS envelope, transport proteins, homing receptors, addressins, regulatory proteins, antigens such as gp120(IIIb), or derivatives or active fragments of any of the peptides listed above. The polypeptides may be native or mutated polypeptides, and preferred sources for such mammalian polypeptides include human, bovine, equine, porcine, lupine, and rodent sources, with human proteins being particularly preferred.
The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion.

Bioinformatics Search for TAT-Specific Leader Peptides Putative TAT leader peptides were found using the Protein-Protein "BLAST"
search engine available through the National Center for Biotechnology Information website. The following search strings were entered: SRRRFLK (SEQ ID N0:2), SRRXFLX (SEQ ID N0:3), TRRXFLX (SEQ ID NO:4), SRRXXLK (SEQ 1D NO:S), SRRXXLA (SEQ ID NO:6), TRRX~~L,K (SEQ ID N0:7), TRRX~~I,A (SEQ ID N0:8), SRRXXLT (SEQ ID N0:9), SRl~~XIK (SEQ ll~ NO:10), SRRXXIA (SEQ DJ NO:11), SRR~FIX (SEQ ID NO:12), SRRXFMK (SEQ II? NO:13), SRRXFVK (SEQ ID N0:14), SRRXFVA (SEQ ID NO:l S), SRRQFLK (SEQ ID N0:16), RRXFLA (SEQ 117 N0:17), and RRXFLK (SEQ ZD N0:18). Searches were done for short, nearly exact matches and then screened for only those matches occurring within the first 50 residues of the protein while still maintaining the twin-arginines. The first 100 residues of each leader peptide were then examined by "SignaIP", a program for detecting Sec pathway leader peptides and cleavage sites (N~~lsen~ ~t eel ,. ~i997). The final list of putative TAT
leader peptides is shown in Table 1. These peptides were cloned and examined for their abilities to direct secretion of a reporter protein, GFP-SsrA, through the TAT pathway.

Bacterial Strains and Growth Conditions:
Cells were always grown at 37°C, either on solid LB agar or in liquid LB media and with appropriate antibiotics. Chloramphenicol (Cm) was used at the concentration of 50 p,g/mL. The strain XL1-Blue (recAl endAl gyrA96 thi-1 hsdRl7 supE44 relAl lac [F'proAB lacfqZtlM1 S TnlO (Tet~]) (Stratagene) was used for cloning purposes.
For expression, the high-copy pBAD 18-Cm constructs were transformed into the strains MC4100-P (MC4100 pcnBl) and B1LK0-P (MC4100 ~tatCpcnBl).
Plasmids and Oligonucleotides:
Each putative leader peptide DNA sequence was first subcloned into pKKGS
(~eLisa bet ah, 'Z~?02), which is based on the low-copy pBAD33 plasmid (Guzman et al., 1995). Standard methods were used to amplify DNA and Qiagen kits were used for all DNA purification steps. Each leader peptide gene was first PCR amplified from XL1-Blue genomic DNA using a forward primer that contained a SacI cleavage site and a reverse primer that contained an XbaI cleavage site. Forward primers were designed to incorporate at least the first 18 nucleotides of the leader peptide. All forward primers contained the sequence (5'-GCGATGGAGCTCTTAAAGAGGAGAAAGGTC-3', SEQ ID N0:19) followed by the start codon and leader peptide sequence from the desired gene.
Similarly, all reverse primers contained the sequence (5'-GCGATGTCTAGA-3', SEQ ID N0:20).
Reverse primers were designed such that exactly six amino acid residues beyond the predicted leader peptide cleavage site would be incorporated into the plasmid.
The resulting 58 primers are shown in Tables 2 and 3. All PCR products were gel purified and digested using SacI and XbaI and finally cloned into the SacI and XbaI sites of pKKGS.
All plasmid constructs were confirmed by sequencing.
Similar constructs were made using the high-copy plasmid pBADlB-Cm (Guzman et al., 1995). Briefly, signal sequence-GFP-SsrA fusion constructs were digested from pBAD33 using SacI and HindIll and cloned into the identical sites of pBADlB-Cm. In the case of the HybO leader peptide, the HybO-GFP-SsrA fusion was cut with SacI
and SphI
and cloned into pBAD 18-Cm. As before, all plasmid constructs were confirmed by sequencing.
Subcellular Localization of Proteins:
Cells were pelleted by centrifugation at 5000 x g, resuspended in 1 ml of cell fractionation buffer (30 mM Tris-HCl, pH 8.0, 20% (w/v) sucrose, 1 mM
Na2EDTA), and incubated at 25°C for 10 min. The cells were again centrifuged at 5000 x g, the supernatant discarded, and the pellet resuspended in 133 ~.1 of ice-cold 5 mM MgS04. After 10 min on ice, the cells were centrifuged at full speed, and the supernatant was retained as the periplasmic fraction. The pellet was resuspended in 250 ~.1 of PBS and sonicated for 30 seconds. The cells were centrifuged at full speed and the supernatant was retained as the cytoplasmic fraction.
Western Blotting Analysis:
Western blotting was according to Cl~en, et a~. The following primary antibodies were used: monoclonal mouse anti-GFP (Clontech) diluted 1:5000, monoclonal rabbit anti-DsbC (gift from John Joly, Genentech) diluted 1:10,000 and monoclonal rabbit anti-GroEL

(Sigma). diluted 1:10,000. The secondary antibody was 1:10,00'0 goat anti-mouse-HRP
conjugate and goat anti-rabbit-HRP conjugate. Membranes were first probed with anti-GFP and anti-DsbC antibodies and, following development, were stripped in TBS/2%
SDS/0.7 M (3-mercaptoethanol. Stripped membranes were re-blocked and probed with anti-GroEL antibody.
FRCS Screening of Putative Leader Peptide:
To express the leader peptide-GFP-SsrA constructs, overnight (o/n) cultures of MC4100-P and B1LK0-P containing each of the 30 plasmids were grown in LB media as described above. Single colonies were grown overnight in 2 mL of media. Five hundred p.l of each o/n culture were used to inoculate 10 mL of media. After 1 h shaking at 37°C, cells were induced with arabinose to a final concentration of 0.02%. Following four more hours of incubation at 37°C, 1 mL samples were harvested and centrifuged at 2500xg for 5 min. Cell pellets were resuspended in 1 mL of PBS. Of that, 5 ~,L were added to 1 mL
fresh PBS and analyzed by the Becton-Dickenson FACSort.
Thirty putative TAT leader peptides were screened in a genetic screen as described previously (DeL~sa° et, al 2000. With this genetic screen, a leader peptide that directs GFP
through the TAT pathway would be fluorescent in tatC + cells (MC4100-P) but non-fluorescent in tatC - cells (B 1 LKO-P) since tatC is absolutely necessary for TAT export.
By contrast, a leader peptide that directed GFP to the periplasm via the Sec pathway would be non-fluorescent in both types of cells. Of note is the use of E. coli strains containing a mutation in pcnBl, which lowers the copy number of those plasmids (such as pBADl8-Cm) that contain the pBR322 replicon. Thus pBADl8-Cm, which is normally a high copy vector, is only present at approximately 5-10 copies per cell in pcnBl mutants. This system proved optimal for use with the TAT pathway genetic screen.
The FACS analysis for the pBAD 1 ~-Cm constructs are shown in Table 4 (a list of arithmetic mean fluorescence values). Importantly, the FAGS data for the pBADl~-Crn constructs shows that six leader peptides (BisZ, , NapA, Nape, YaeI, YgfA, and YggJ) gave inconclusive GFP export through the TAT pathway (low signal in both wt and tatC
mutant celsl) while at least 17 (AmiC, DmsA, FdnG, FdoG, FhuD, HyaA, HybA, NrfC, Sufl, TorA, WcaM, YacK, YahJ, YdcG, YdhX, YfhG, and, YnfE) are capable of exporting GFP via the TAT pathway. Five constructs (YagT, YcbK, YcdB, YedY, and YnfF') displayed very high fluorescence means in both MC4100-P and B1LK0-P. It should also be noted that the higher mean fluorescence signals seen for some of the constructs in the tatC mutant (B1LK0-P) reflected emission from only a small population of highly fluorescent cells while the bulk of the cell population was non-fluorescent.
In contrast, the high mean fluorescence of the tatC+ cells (MC4100-P) was indicative of a shift in the fluorescence emission throughout the population.
TABLE 1: E. coli. TAT-Specific Leader Peptides # Gene Sequence SEQ ID
NO.
1 WcaM MPFKKLSRRTFLTASSALAFLHTPFARAL 25 2 NrfC MTWSRRQFLTGVGVLAAVSGTAGRVVAK 26 3 YahJ MKESNSRREFLSQSGKMVTAAALFGTSVPLAHAA 27 4 HyaA MNNEETFYQAMRRQGVTRRSFLKYCSLAATSLGLGA 28 GMAPKIAWAL

YacK MQRRDFLKYSVALGVASALPLWSR.AVFAA 29 6 YcbK MDKFDANRRKLLALGGVALGAAIL,PTPAFAT 30 7 YfhG MRHIFQRLLPRRLWLAGLPCLALLGCVQNHNK 31 8 YcdB MQYKDENGVNEPSRRRLLKVIGALALAGSCPVAHAQ 32 9 AmiA MSTFKPLKTLTSRRQVLKAGLAALTLSGMSQAIAK 33 10YedY MKKNQFLKESDVTAESVFFMKRRQVLKfIL,GISATAL 34 SLPHAAHAD

11FhuD MSGLPLISRRRLLTAMALSPLLWQMNTAHA.A 35 12HybA l~~IVRRNFIKAASCGALLTGALPSVSHAAA 36 13YdcG MDRRRFIKGSMAMAAVCGTSGIASLFSQAAFAA 37 14Sufi MSLSRRQFIQASGIALCAGAVPLKASAA 38 15YagT MSNQGEYPEDNRVGKHEPHDLSLTRRDLIKVSAATA 39 ATAVVYPHSTLAA

16 YdhX MSWIGWTVAATALGDNQMSFTRRKFVLGMGTVIFFT 40 GSASSLLAN
17 HybO MTGDNTLIHSHG11~1RRDFMKLCAALAATMGLSSKAA 41 AE
18 YnfF MMI~ITTEALNIK_AEISRRSLMKTSALGSLALASSAFT 42 LPFS QMVR.A.A
19 DmsA MKTKIPDAVLAAEVSRRGLVKTTAIGGLAMASSALTL 43 PFSRIAHAV
20 YnfE MSKNERMVGISRRTLVKSTAIGSLALAAGGFSLPFTL 44 RNAA.A AV
21FdoG MQVSRRQFFKICAGGMAGTTAAALGFAPSVALAE 45 22AmiC MTDYASFAKVSGQISRLLVTQLRFLLLGRGMSGSNTA 46 ISRRRL,LQGAGAMWLLSVSQVSLAA

23YggJ ilvin-arginine consensus motif: RRRGFLT 47 24YgfA twin-arginine consensus motif QRRRALT 48 25BisZ twin-arginine consensus motif TRREFIK 49 26NapA twin-arginine consensus motif SRRSFMK 50 27Nape twin-arginine consensus motif GRR1ZFLR 51 28FdnG twin-arginine consensus motif-. SRRQFFK 52 29YaeI twin-arginine consensus motif SRRRFLQ 53 *Amino acids highlighted in gray constitute the twin-arginine consensus motif.
TABLE 2: Forward Primers And Their Melting Temperature For Each of The 29 TAT-Specific Leader Peptides Name Tn., Sequence SEQ ID
(°C) NO.
WcaM fort 57.0 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 54 CCATTTAAAAAACTCTCCCGA

NrfC 57.5 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 55 for ACCTGGTCTCGTCGC

YahJ 57.5 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 56 fort AAAGAAAGCAATAGC

HyaA 55.8 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 57 fort AATAACGAGGAAACATTTTACCAG

YggJ 62.5 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCGTG 58 for GGGAGACGACGCGGA

YacK 51.8 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 59 for CAACGTCGTGATTTC

Nape 57.5 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 60 for TCCCGGTCAGCGAAA

YcbK 52.9 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 61 for GACAAATTCGACGCT

YfhG 48.9 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 62 for CGACACATTTTTCAA

YcdB 52.9 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 63 fort CAGTATAAAGATGAAAACGG

AmiA 47.5 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 64 for AGCACTTTTAAACCA

B1971 51.0 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 65 fort AAAAAGAATCAATTTTTAAAAGAATC

FhuD 54.2 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 66 for AGCGGCTTACCTCTT

YgfA 55.6 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 67 for ATTCGGCAACGTCGT

BisZ 50.7 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 68 fort ATCAGGGAGGAAGTT

HybA 60.3 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCGTG 69 fort AACAGACGTAATTTTATTAAAGCAGCCTC

YdcG 48.6 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 70 for GATCGTAGACGATTT

Sufi 57.1 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 71 for TCACTCAGTCGGCGT

YagT 55.8 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 72 for AGCAACCAAGGCGAA

B1671 51.5 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 73 for TCATGGATAGGGTGG

B2997 48.8 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 74 for ACTGGAGATAACACC

NapA for 51.8 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 75 AAACTCAGTCGTCGT

B1588 58.9 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 76 fort ATGAAAATCCATACCACAGAGGCG

DmsA for 53.1 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 77 AAAACGAAAATCCCTGATG

YnfE for 56.3 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 78 TCCAAAAATGAACGAATGGTG

FdnG for 56.8 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 79 GACGTCAGTCGCAGA

FdoG for 55.5 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 80 CAGGTCAGCAGAAGG

AmiC for 60.8 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 81 ACAGATTATGCGTCTTTCGCTAAAGTT

YaeI for 58.5 GCGATGGAGCTCTTAAAGAGGAGAAAGGTCATG 82 ATTTCACGCCGCCGA

TABLE 3: Reverse Primers And Their Melting Temperature For Each of The 29 TAT-Specific Leader Peptides Name Tm (C) Sequence SEQ ID
NO.

WcaTvI 59.7 GCGATGTCTAGAGCTTTGTCGGGCGGG 83 rev2 AAG

NrfC rev3 56.2 GCGATGTCTAGAATTGATATTCAACGTT 84 TTCGCCAC

YahJ rev3 60.1 GCGATGTCTAGATAGGGTGCCAGCTAC 85 CGC

HyaA rev2 57.4 GCGATGTCTAGAGCGCGGTTTGTTCTCC 86 AG

YggJ rev3 57.3 GCGATGTCTAGATACGCGCCCGATATG 87 GTT

YacK rev456.5 GCGATGTCTAGATAACGTTGGGCGTTCT 88 GC

Nape rev265.1 GCGATGTCTAGAGCGCAACCGCACGCC 89 AGA

YcbK rev256.9 GCGATGTCTAGAGCGTGGGGTAGAGAG 90 TGT

YfhG rev253.4 GCGATGTCTAGACGTATCAATGGCTGG 91 CTT

YcdB rev252.1 GCGATGTCTAGACGCACTTTGCGTTTTT 92 TG

AmiA rev447.8 GCGATGTCTAGATTTTAAAAGTTCGTCT 93 TTGG

B 1971 50.2 GCGATGTCTAGAAAACCAGCTAAGCAG 94 rev2 ATC

FhuD rev453.3 GCGATGTCTAGAATTGGGATCAATAGC 95 CGC

YgfA rev250.6 GCGATGTCTAGAGAATACAGCGACCGT 96 ATG

BisZ rev252.3 GCGATGTCTAGATTTACCGCCCTTCTCT 97 TC

HybA rev262.5 GCGATGTCTAGATGGCGGGCGGTTTTC 98 AGC

YdcG rev248.6 GCGATGTCTAGAGGCAATATCAGAATC 99 TGC

Sufl rev263.2 GCGATGTCTAGACGGTTGCTGTTGCCCG 100 GC

YagT rev262.3 GCGATGTCTAGAAGCTGCGGGAACGCT 101 TGC

B1671 51.3 GCGATGTCTAGACTTTTCTTGCCTCGTG 102 rev2 TT

B2997 55.5 GCGATGTCTAGAAACCGATTCGGCCAT 103 rev2 CTC

NapA rev260.3 GCGATGTCTAGACTGACCAACAACGGC 104 GCG

B1588 56.9 GCGATGTCTAGATTCTACCGGAGCCTCT 105 rev4 GC

DmsA rev 55.5 GCGATGTCTAGATGGAATGGCGCTATC 106 GAC

YnfE rev 57.5 GCGATGTCTAGATTTTTCGCGGGCCTGT 107 TG

FdnG rev 54.9 GCGATGTCTAGATAATTTGTAGTTTCGC 108 GCCTG

FdoG rev 54.7 GCGATGTCTAGACAGTTTATACTGCCGG 109 GTTTC

AmiC rev 61.6 GCGATGTCTAGACGCCACGACCTGGCT 110 GAC

YaeI rev 58.9 GCGATGTCTAGAGCTCGTGGCTATCGTC 111 GC

TABLE 4: FRCS Screening of Putative Leader Peptides Leader PeptideMC4100-P B1LK0-P (% Cells) Protein Export AmiC 9 2 (95) +

BisZ 2 3 (100) DmsA 287 11 (95) +++

FdnG 1 2 (100) ND

FdoG 44 2 (97.1) +

FhuD 10 2 (99.5) +

HyaA 90 3 (96.6) ++

HybA 411 2 (95.6) +++

HybO N/A N/A

NapA 1 2 ( 100) Nape 6 7 (95) NrfC 43 9 (95) +

Sufi 337 3(96.6) +;-r-TorA 203 34 (100) +++

WcaM 96 6 (99) ++

YacI~ 72 13 ( 100) ++

YaeI 2 2 (100) -YagT 436 235 (95) -YahJ 684 3 (100) +++

YcbK 367 97 (95) +

YcdB 514 356 (95) -YdcG 59 27 (100) ++

YdhX 18 4 (95) +

YedY 73 35 (95) -YfhG 36 7 (95) +

YgfA 8 3 (100) YggJ 1 2 (100) YnfE 24 8 (100) +

YnfF 203 101 (95) -Arithmetic fluorescent means from FACS data of pBADl8-Cm::leader peptide-GFP-SsrA
constructs in MC4100-P and B1LK0-P cells. Data for the B1LK0-P cells were calculated from all the cells (% cells shown) except the small population of highly fluorescent cells.

Bacterial Strains and Plasmids Construction All strains and plasmids used in the following examples are listed in Table 5.
E.
coli strain XLl-Blue (YecAl endAl gyfA96 thi-I lasdRl7 supE44 relAl lac [F' proAB
lacI9ZdMI5Tn10 (Tet~]) was used for all experiments unless otherwise noted. E.
coli XL1-Blue tatB and XLl-Blue tatC were made using pFAT24 (Sargent et al. 1999) and pFATl66 (Bogsch et al., 1998) respectively according to established procedure (Bogsch et al., 1998). Strains were routinely grown aerobically at 37°C on Luria-Bertani (LB) media and antibiotic supplements were at the following concentrations:
ampicillin, 100 p.g ml-1, chloramphenicol, 25 ~g ml-1.
The plasmids constructed in the following examples were based on pBAD33 (Gunman et al., 1995) and were made using standard protocols Sarnbrook et al., 2000).
Plasmid pGFP was constructed by cloning the GFPmut2 variant (Crameri et al., 1996) using the primers GFPXbaI (5'-GCGATGTCTAGAAGTAAAGG
AGAAGAACTTTTCACT-3', SEQ ID NO:112) and GFPHindlTl (5'-GCGATGAAGCTTCTATTTGTATAGTTCATCCAT-3', SEQ ID N0:113) which introduced unique restriction sites of XbaI and Hindla at the 5' and 3' ends respectively of the 716-by gfpmut2 gene and enabled cloning of this sequence into XbaI-HineIIII digested plasmid DNA. Plasmid pGFPSsrA was made similarly using the primers GFPXbaI and GFPSsrA (5'-GCGATGAAGCTTGCATGCTTAAGCTGCTAAAGCGTAGTTTTCG
TCGTTTGCTGCGTCGACTTTGTATAGTTCATCCATGCC-3', SEQ ID N0:114) to introduce the unique SsrA recognition sequence. Plasmid pTorAGFP and pTorAGFPSsrA
were made by PCR~ amplification of E. coli genomic DNA using primers TorASacI
(5'-GCGATGGAATTCGAGCTCTTAAAGAGGAGAAAGGTCATGAACAATAACGATCT
CTTTCAG-3', SEQ ID NO:115) and TorAXbaI (5'-GCGATGTCTAGAAGCGTCAGTCGCCGCTTGCGCCGC-3', SEQ ID N0:116) to generate a138-by torA cDNA with unique SacI and ~'baI restriction sites at the 5' and 3' ends respectively. This sequence was then inserted into SacI-XbaI digested pGFP or pGFPSsrA plasmid DNA. All plasmids constructed in this study were confirmed by sequencing.
TABLE 5: Bacterial Strains And Plasmids Strain or plasmid Relevent genotype/phenotype Source E. co.li strains XLl-Blue Stratagene XLtatB XLl-Blue with tatB deletion This study XLtatC XL1-Blue with tatC deletion This study Plasmids pFAT24 pMAK.705 carrying tatB deletion allele(Sargent et al., 1999) pFATl66 pMAK705 carrying tatC deletion allele(Bogsch et al., 1998) pGFP Signal sequenceless GFP in pBAD33 This study pGFPssrA Signal sequenceless GFP tagged with This study C-terminal ssrA tag in pBAD33 pTorAGFP TorA leader peptide fused to GFP in This study pBAD33 pTorAGFPssrA TorA leader peptide fused to ssrA-taggedThis study GFP in pBAD33 pB6::GFP Clone B6 leader cloned into pGFP This study pB7::GFP Clone B7 leader cloned into pGFP This study pE2::GFP Clone E2 leader cloned into pGFP This study pTorAR30Q pTorAGFP with R12Q mutation in leader This study pTorAR30QGFPssrA pTorAGFPSsrA with R12Q mutation in leader This study Flow Cytometric Analysis Overnight cultures of XLl-Blue cells harboring GFP-based plasmids were subcultured into fresh LB medium with chloramphenicol and induced with 0.2%
arabinose in mid-exponential phase growth. After 6 h, cells were washed once with PBS
and 5 ul washed cells were diluted into 1 ml PBS prior to analysis using a Becton-Dickinson FACSort.

Generation of torA Combinatorial Libraries A library of random mutants was constructed by error prone PCR of the torA
gene sequence using 3.32 or 4.82 rnM Mg2+ (Fromant et al., 1995), XL1-Blue genomic DNA
and the following primers: torASacI (5'-GCGATGGAATTCGAGCTCTTAAAGAGGAGAAAGGTCATGAACAATAACGATCT
CTTTCAG-3') (SEQ ID N0:117) and torAXbaI (5'-GCGATGTCTAGAAGCGTCAGTCGCCGCTTGCGCCGC-3') (SEQ ID N0:118). To construct libraries with 0.5% error rate, 0.22 mM dATP, 0.20 mM dCTP, 0.34 mM
dGTP
and 2.36 mM dTTP were used, whereas 0.12 mM dATP, 0.1 mM dCTP, 0.55 mM dGTP
and 3.85 mM dTTP were used to construct libraries with 1.5% error rate.
Libraries were digested with SacI XbaI and lzgated into pGFPssrA between SacI ~baI, placing the library upstream of the gfpssrA sequence. Reaction mixtures were electroporated into electrocompetent XLl-Blue cells (Stratagene), and serial dilutions were plated on selective plates to determine the number of independent transformants.

Library Screening Transformants were grown at 37°C in LB medium with chloramphenicol, induced with 0.2% arabinose for 6 h and diluted 200-fold in 1 ml PBS. FAGS gates were set based upon FSC/SSC and FLl/FL2. Prior to sorting, the library cell population was labeled with propidium iodide for preferential labeling of non-viable cells. A total of ca.
3x106 cells were analyzed by flow cytometry and 350 viable cells were collected. The collected solution was filtered, and the filters were placed on LB plates with chloramphenicol. After a 12 hour incubation at 37°C, individual colonies were inoculated into LB with chloramphenicol in triplicate 96-well plates. Following 12 hours of growth at 37°C, cells were similarly subcultured into triplicate 96-well plates containing LB with chloramphenicol and 0.2% arabinose and grown for 6 hours at 37°C.
Individual clones were screened via FACS and fluorescent plate reader (Bio-Tek FL600, Bio-Tek Instrument, Winooski, VT) for verification of fluorescent phenotype.

Cell Fractionations The fraction of periplasmic proteins was obtained by spheroplasting bacteria by lysozyme-EDTA treatment under isotonic conditions according to the procedure of Kaback (1971). Briefly, cells were collected by centrifugation and resuspended to an OD6on of in a buffer containing 100 mM Tris-Cl (pH 8.0), 0.5 M sucrose, and 1 mM Na-EDTA.
Lysozyme (Sigma) was added to 50 ~g/ml, and cells were incubated for 1 h at room temperature to generate spheroplasts. The spheroplasts were pelleted by 15 min of centrifugation at 3,000 x g, and the supernatant containing periplasmic proteins was 10 collected for electrophoretic analysis. The pellet containing spheroplasts was resuspended in 10 ml of TE (10 mM Tris-Cl [pH 7.5~, 2.5 mMNa-EDTA) and homogenized in a French press cell (Carver) at 2,OOOlb/ina. To analyze total proteins of untreated cells, direct resuspension in 10 ml of TE followed by subjection to the French press homogenization was performed.

Screening of Signal Peptide Libraries for Improved Export Phenotypes The plasmid pTorAGFP contains a gene encoding the TAT-specific leader peptide and the first eight amino acids of the E. coli trimethylamine N oxide reductase (TorA) fused to the FACS optimized GFPmut2 gene (Crameri et al., 1996). The TorA-GFP
gene was placed downstream of the arabinose-inducible promoter pBAD. Cells induced with arabinose for 6 hours and analyzed by FAGS gave a mean fluorescence intensity (MFLl) above S00 arbitrary units (FIG. 1C). In agreement with previous reports (Santini et al., 2001), cell fractionation by osmotic shock revealed that ca. 40-50% of total fluorescence was located in the periplasm of wild type cells while cytoplasmic GFP
accounted for the remaining 50-60% of total fluorescence. In tatB and tatC mutants where the TAT
pathway were abolished, greater than 95% of total fluorescence was retained in the cytoplasm, thereby demonstrating that TorA-GFP is exported via the TAT pathway.
A nucleotide sequence encoding a C-terminal SsrA degradation peptide was fused to the TorA-GFP gene. The resulting gene, pTorA-GFP-SsrA, was also placed downstream from a pBAD promoter in the vector pTorAGFPSsrA. As a negative control, GFP without the leader peptide was fused in frame to the SsrA tag and expressed from the plasmid pGFPSsrA. GFP-SsrA-expressing cells showed virtually no appreciable fluorescence intensity, indicating that cytoplasmic SsrA-tagged GFP is degraded almost completely (FIG. lA). Cells expressing TorA-GFP-SsrA were ca. 8 times more fluorescent compared to GFP-SsrA expressing cells (FIG. 1B). Expression of TorA-Gfp-SsrA
in tatB
and tatC mutant cells only led to background fluorescence.
Error prone PCR (Fromant et al., 1995) was used to generate libraries of random mutants of the TorA leader peptide. Three libraries with expected mutation frequencies of 0.5, 1.5 or 3.5% nucleotide substitutions were constructed. The mutated TorA
leader peptides were ligated upstream of the GFP-SsrA sequence in pGFPSrA.
Transformation of E. coli resulted in libraries consisting of between 106 and 107 independent transformants.
Sequence analysis of 20 randomly selected clones confirmed the presence of randomly distributed mutations within the TorA leader peptide.
FACS-based screening of the three libraries resulted in isolation of a total of six clones, 2 from the higher error rate library and four from the lower error rate libraries. All six clones exhibited higher cell fluorescence relative to the parental TorA-Gfp-SsrA
construct (FIG. 2). The increase in the fluorescence level was between 3 and 6-fold relative to what is obtained with the wild type leader peptide. Back transformation of these clones into strains XLl-Blue or DHB4 resulted in maintained fluorescence levels, thus indicating that the increased fluorescence was conferred by the respective plasmids and was not due to an unrelated mutation in the host cell. When the plasmids were transformed into tatB or tatC cells the cell fluorescence was abolished, as would be expected for a process that is dependent on the TAT export system.
Representative Western blots indicate that periplasmic GFP accumulation by cells expressing the B6 and E2 clones was significantly increased relative to those expressing wild type construct (lanes 1-3, FIG. 3). Furthermore, there was virtually no detectable GFP
protein in the cytoplasmic fractions. This was because the presence of the SsrA tag resulted in degradation of the protein. Also shown in FIG. 3 were Western bands of two fractionation marker proteins, the cytoplasmic marker GroEL and the periplasmic marker DsbA. The absence of GroEL in the periplasmic fraction and the high level of DsbA in periplasmic fractions confirm that cell fractionation was successful.
Data on the distribution of fluorescence in the cytoplasmic and periplasmic fractions for two mutant TorA leader peptides are shown in FIG. 3B. Nearly identical results were observed for the remaining four clones (B7, Fl, Fl 1 and H2). The sequences of the six clones were determined and indicated that in all cases either one or two single residue mutations were sufficient to alter the observed export dynamics. In general, these mutations occur within or in close proximity to the conserved S/T-R-R-x-F-L-I~
(SEQ ID
NO:l) consensus motif (Table 6).

It was confirmed that the six mutant TorA leader peptides confer increased GFP
export not only when the protein is tagged with the SsrA tag but also for the untagged, proteolytically stable GFP (FIG. 4). This increase in fluorescence was due to the increased periplasmic flux of folded GFP protein. Similar results were observed for the remaining clones fused to GFP.
A representative Western blot comparing wild type TorA-GfP and TorAB7-Gfp indicated that cells expressing both constructs accumulated nearly identical levels of cytoplasmic GFP (FIG. 5, lanes 3 and 4). However, the amount of exported GFP
was significantly higher in cells expressing the ToAB7-GFP clone (FIG. 5, lanes 1 and 2).
Further support of this can be seen in the whole cell lysates. The intense band denoted as mature (M) GFP represents TorA-Gfp chimeric protein that has been processed most likely by signal peptidase I (Berks et al., 2000). Therefore, the intense band corresponding to mature GFP accumulated by the TorAB7-GfP construct signifies substantially more periplasmic processing of GFP relative to wild type TorAGFP cells (FIG. 5, lanes 5 and 6).
Similar results were observed for all five remaining clones. As described above, the GroEL and DsbA marker proteins confirm successful cell fractionations.

TABLE 6: Sequences Of Six Clones Exhibiting Increasing TAT-Dependent Secretion Clone Amino Acid Sequence m Wild typeMNNNDLFQASRRRFLAQLGGLTVAGMLGPSLLTPRRATAAQA.ATD

(SEQ m NO:120) B6 MNNNDLFQTSRRItLLAQLGGLTVAGMLGPSLLTPRR.ATAAQAATDA

(SEQ m No.121) (SEQ m NO:122) E2 MfNNNDIFQASRRRFLAQPGGLTVAGMLGPSLLTPRRATAAQAATDA

(SEQ m N0:123) F 1 l~fI~NNELFQASRRRFLAQLGGLTVAGMLGPSLLTPRRATAA QAA TDA

(SEQ m N0:124) F 11 I~~INNNDLFQTTRRRFLAQLGGLT VAGMLGPSLLTPRRATAA QAA TDA

(SEQ m N0:125) (SEQ m N0:126) Twin arginine consensus motif is indicated by underlined amino acids; first 8 residues of mature TorA protein are indicated by italics; mutations in TorA leader peptide are indicated by emboldened letters.

EXAMPLE ~
Secretion of Folded Recombinant Proteins Containing Multiple Disulfide Bonds Through The Twin Arginine Translocation Export Pathway One embodiment of the methods disclosed herein comprises use of a fusion between a TAT-specific leader peptide and a heterologous polypeptide of interest. For example, TAT-specific leader peptide TorA may be fused to alkaline phosphatase (TorA-PhoA fusion). Alkaline phosphatase (PhoA) contains two disulfide linkages that. are consecutive in the primary sequence so that they are normally incapable of forming in the cytoplasm of E. coli strains having reducing environment (e.g. strain DHB4).
Since the TAT pathway requires folded or at least partially folded substrates, TAT-dependent secretion of PhoA in DHB4 cells would be blocked due to the accumulation of unfolded PhoA in the cytoplasm.
Hence, there is a need to change the cytoplasm into an oxidizing state for secretion through the TAT pathway. Normally, the bacterial cytoplasm is maintained in a reduced state due to the presence of reducing components such as glutathione and thioredoxins that strongly disfavors the formation of disulfide bonds within proteins. Earlier work by Bessette et al. resulted in the engineering of bacterial strains having a highly oxidizing cytoplasm that allows efficient formation of disulfide bonds (Bessette et al., 1999). As shown in Bessette et al., E. eoli depends on aerobic growth in the presence of either of the two major thiol reduction systems: the thioredoxin and the glutathione-glutaredoxin pathways. Both the thioredoxins and the glutaredoxins are maintained in a reduced state by the action of thioredoxin reductase (TrxB) and glutathione, respectively.
Glutathione is synthesized by the gshA and gshB gene products. The enzyme glutathione oxidoreductase, the product of the gor gene, is required to reduce oxidized glutathione and complete the catalytic cycle of the glutathione-glutaredoxin system.
In a trxB null mutant, stable disulfide bonds can form in normally secreted proteins, such as alkaline phosphatase, when they were expressed in the cytoplasm without a signal sequence. The two thioredoxins were oxidized in the trxB mutant and served as catalysts for the formation of disulfide bonds. Disulfide bond formation was found to be even more efficient in double mutants defective in both the thioredoxin (trxB) and glutathione (gor or gshA) pathways. Double mutants, trxB gor or trxB gshA, grow very poorly (doubling time 300 min) in the absence of exogenous reluctant such as DTT and accumulate suppressor mutations in the alkyl hydroperoxidase (ahpC) gene. The resulting ahpC* allele allows efficient growth in normal (non-reducing media) without compromising the formation of disulfide bonds in the cytoplasm. Thus trxB, gor ahpC* mutant strains (such as E. coli DR473 or FA113) exhibit the ability to support disulfide bond formation in the cytoplasm and also can grow equally well as the corresponding wild-type strain DHB4 in both rich and minimal media.
In the present example, DHB4 cells expressing TorA-PhoA were found to exhibit almost undetectable alkaline phosphatase activity levels while DR473 cells expressing TorA-PhoA showed extremely high PhoA activity levels. Fractionation experiments confirmed that as much as 50% of the measured PhoA activity in cell lysates were attributed to periplasmic accumulation.
Since the major catalyst of disulfide bond formation is a periplasmic protein, DsbA, which oxidizes thiols in newly synthesized and translocated proteins, it was next determined whether the disulfide bonds were formed in the cytoplasm and secreted intact to the periplasm. The TorA-PhoA construct was expressed in an E. coli dsbA
mutant, strain DR473 dsbA::kan. A comparison of PhoA activity in the dsbA mutant versus the isogenic DR473 parental strain revealed nearly identical activity levels in whole cell lysates. This result demonstrates that oxidation of the PhoA protein is completed in the cytoplasm, and stable disulfide bonds are able to transverse the inner membrane as the protein is directed from the cytoplasm into the periplasmic space (Table 9).
In order to measure the extent of folding necessary for substrate compatibility with the TAT secretion pathway, eukaryotic model proteins with increasingly complex patterns of disulfide bond formation were tested. The TorA leader peptide was fused to a truncated version of tissue plasminogen activator (vtPA) consisting of the kringle 2 and protease domains with a total of nine disulfides (TorA-vtPA), or to a heterodimeric 2610 anti-digoxin antibody fragment with 5 disulfide bonds including an interchain disulfide linkage (TorA-Fab). DR473 cells expressing TorA-vtPA and TorA-Fab showed remarkably high levels of activities in cell lysates for each of the expressed proteins relative to DHB4 cells expressing identical constructs. Activities in DHB4 lysates were virtually undetectable in all cases except for vtPA. Fractionation experiments further confirmed that significant portion (30-50%) of the overall activities for each of the proteins was found in the periplasmic fraction.
In conclusion, these results show efficient secretion of disulfide linked proteins can occur via the Tat pathway but only in host cells that are able to fold these proteins into their native conformation. Low background levels of active tPA in the periplasm of DHB4 cells suggests that this protein is able to at least partially fold in a reducing cytoplasm. The resulting folded proteins with multiple disulfide bonds are then secreted into the periplasm as an active homo- (alkaline phosphatase) or heterodimer (2610 antibody fragment).

Demonstration of Export of Multidisuliide Proteins by the Bacterial Twin-Arginine Translocator An examination was carried out to determine whether the formation of disulfide bonds in the cytoplasm of trxB gor aphC mutants was sufficient to render proteins competent for export via the Tat pathway. This was shown to be the case for two model proteins, namely PhoA and Fab fragment raised against digoxin (Fab). PhoA
consists of two polypeptide chains with a total of two disulfide bonds that are required for folding and enzymatic activity while Fab is comprised of two non-identical chains (each with two intermolecular disulfide bonds) linked together by an intermolecular disulfide bond.
Normally, the formation of disulfide bonds in these proteins occurs following export into 1 S the oxidizing environment of the periplasmic space. However, in the analysis, it was demonstrated that proteins with multiple disulfides can be exported via the Tat system after they have first folded in an oxidizing cytoplasm and further, that the transporter mechanistically requires that the substrate be folded properly for periplasmic localization.
A. Procedures Bacterial strains, growth and induction conditions:
The bacterial strains and plasmids used are described in Table 7. Strains DHBA
and DRA were obtained by Pl transduction of the dsbA::kanl allele from JCB571 (MC1000 phoR zihl2::Tn10 dsbA::kan) into E. coli strains DHB4 and DR473, respectively. Strain DASD was obtained by P1 transduction of tatB::kan allele from MCMTA (MC4I00 tatB::kan) into E. coli strain DR473. Strains FUDDY was obtained by P I transduction of the tatC: apec allele from BUDDY (MC4100 tatC: apec) into E. coli strain FA113. E. coli strain XL1-Blue (recAl endAl gyrA96 thi-I hsdRl7 supE44 relAl lac [F' pf~oAB lacl~ZDMlS TialO (Tetr)]) was used for cloning and plasmid propagation.
For phosphatase assays, cells were subcultured from overnight cultures into minimal M9 medium [M9 salts with 0.2% glucose, 1 p.g/ml vitamin Bl, 1 mM MgS04, SO p.g/ml 18 amino acids (excluding methionine and cysteine)] at a 100-fold dilution, and then incubated at 37°C. For Fab studies, cells were subcultured from overnight cultures into fresh LB medium (5% vlv) and then incubated at 30°C. Growth was to mid-log phase (OD6op~0.5) and induction of both alkaline phosphatase and Fab was accomplished by addition of IPTG to a final concentration of 0.1 mM. Co-expression of DsbC was induced using 0.2% arabinose. Antibiotic selection was maintained for all markers on plasmids at the following concentrations: ampicillin, 100 p.g/ml; spectinomycin, 100 p.g/ml; and chloramphenicol, 25 p,g/ml.
Plasmid construction:
Plasmid p33RR was constructed by PCR amplification of the E. coli torA signal sequence (ssTorA) from E. coli genomic DNA using primers TorASacI and TorAXbaI
described above. Amplified DNA was digested using Sacl and XbaI arid inserted into the same sites of pBAD33. Plasrnid p33KK was generated identically as p33RR except that mutagenic primer TorAkk (5'-gcgatggagctcttaaagaggagaaaggtcatgaacaataacgatctctttcaggcatcaaagaaacgttttctggcac aactc-3') (SEQ 1D N0:129) was used to PCR amplify the to3A signal sequence. DNA encoding so signal sequence-Iess phoA (PhoA d2-22) was generated by PCR amplification from E. coli genomic DNA using primers Phofor (5'-gcgatgtctagacggacaccagaaatgcctgt-3') (SEQ
ID
N0:130) and Phorev (5'-gcgatgaagcttttatttcagccccagagcggctt-3') (SEQ ID
N0:131). The amplified phoA DNA was digested with XbaI and HindIQ and inserted into the same sites of p33RR and p33KK resulting in plasmids p33RRP and p33KKP, respectively. A
DNA
fragment encoding torA signal sequence (or torA (R11K;R12K) signal sequence) fused in-frame to phoA was amplified from plasmid p33RRP (or p33KKP) using primers TorASacI
(or TorAKK) and Phorev. The PCR amplified DNA was digested with BSpHI and HindIlI
and inserted into the NcoI-HindIll sites of pTrc99 resulting in plasmid pRRP
(or pKKP).
Construction of alkaline phosphatase fusions to alternate signal sequences (e.g. ssFdnG, ssFdoG) was performed identically as described for pTorA-AP. Plasmid pTorA-Fab was constructed by PCR amplification of the anti-digoxin dicistronic Fab gene encoded in pTrc99-Fab (Levy et al., 2001) using primers Fabfor (5'-gctgctagcgaagttcaactgcaacag-3') (SEQ ID N0:132) and Fabrev (5'-gcgatgcccgggggctttgttagcagccggatctca-3') (SEQ
ID
N0:133) and amplification of torA signal sequence was with primers TorASacI
and TorAover (5'-gcgctgttgcagttgaacttcgctagcagcgtcagtcgccgcttg-3') (SEQ 117 N0:134). The two PCR products were fused via overlap extension PCR using primers TorASacI
and Fabrev. The overlapped product was digested with BspHI and XmaI and inserted into the NcoT and XmaI sites of pTrc99A. All plasmids were confirmed by sequencing.
Cell fractionations:
The fraction of periplasmic proteins was obtained by ice-cold osmotic shock (Sargent et al., 1998). Specifically, cells were collected by centrifugation and resuspended in buffer containing 30 mM Tris-HCl (pH 8.0), 0.5 M sucrose, 1 mM Na-EDTA and mM iodoacetamide was used to prevent spontaneous activation of alkaline phosphatase.
Cells were incubated for 10 min at 25°C followed by centrifugation for 10 min at SOOOxg and 4°C. Pellets were then resuspended in ice-cold 5 mM MgS04 and kept on ice for 10 min. Cells were centrifuged as before and the supernatant containing periplasmic proteins was collected for electrophoretic analysis. The pellet was resuspended in 10 ml of TE
(10 mM Tris-Cl [pH 7.5~, 2.5 mM Na-EDTA) and 20 mM iodoacetamide and homogenized in a French press cell at 2,0001b/in2. To analyze total proteins of untreated cells, direct resuspension in 10 ml of TE and 20 mM iodoacetamide followed by subjection to French press homogenization was performed.
Enzyme activity assays:
Cells expressing alkaline phosphatase were induced for 6 h. Samples were harvested, treated with 20 mM iodoacetamide and pelleted by centrifugation.
Collected cells were fractionated as described above. Soluble protein was quantified by the Bio-Rad protein assay, using BSA as standard. Activity of alkaline phosphatase was assayed as described previously. Briefly, equal amounts of protein were incubated with 200 p.l p-nitrophenyl phosphaste (pNPP; Sigma) solution (1 fast tablet in 100 mM
Tris~HCl, pH 7.4) and DA4os was measured to determine rate of hydrolysis by alkaline phosphatase in each sample. Fractionation efficiency was monitored using (3-galactosidase as a cytoplasmic marker enzyme and was assayed as described previously. Only data from fractionations in which the marker enzyme activities were ~5% correctly localized were analyzed.
ELISA:
Assays were performed as follows. Ninety-six-well high binding assay plates (Corning-Costar) were coated (100 ul/well) with 4 ug ml-1 BSA-digoxin conjugate or with 4 ug ml-1 BSA (100 ul/well). Coated plates were blocked overnight at 4°C with 5% nonfat dry milk in PBS. The presence of anti-digoxin scFv and Fab antibodies was detected using rabbit-anti-mouse IgG (specific to (Fab')2 light chains) diluted 1:2000 followed by goat anti-rabbit IgG (H + L) conjugated with horse radish peroxidase diluted 1:1000.
Development was with addition of OPD substrate (Sigma) and the reaction was quenched by addition of 4.5 N HZS04. Plates were read at 490 nm on a Bio-Tek Instruments microplate reader.
Western blotting analysis:
Western blotting was according to Chen et al. (2001). The following primary antibodies were used: rabbit anti-alkaline phosphatase (Rockland) diluted 1:5,000, rabbit anti-tPA diluted 1:5,000, rabbit anti-mouse IgG (specific for (Fab')2 light chains, Pierce) diluted 1:5,000, monoclonal rabbit anti-DsbA and anti-DsbC (gift from John Joly, Genentech) diluted 1:10,000 and monoclonal rabbit anti-GroEL (Sigma) diluted 1:10,000.
The secondary antibody was 1:10,000 goat anti-mouse-HRP and goat anti-rabbit-HRP.
Membranes were first probed with primary antibodies and, following development, stripped in TBS/2% SDS/0.7 M (3-mercaptoethanol. Stripped membranes were re-blocked and probed with anti-DsbA, anti-DsbC and anti-GroEL antibody.
B. A strategy for Tat-dependent export of multidisulfide proteins in E. coli In bacteria the oxidative folding of secreted proteins is catalyzed by the periplasmic enzyme DsbA which is recycled by the integral membrane protein DsbB. In contrast, the thioredoxin and glutaredoxin. pathways maintain the cytoplasm as a highly reducing environment, which disfavors cysteine oxidation in proteins. For this reason, host proteins requiring disulfide bonds are exported to the periplasmic compartment, a process facilitated almost exclusively by the Sec pathway in E. coli. The export of such proteins by the Tat pathway has been problematic because the Tat pathway normally accepts as substrates proteins that are already folded. Since proteins that contain disulfide bonds in their native state cannot fold in the cytoplasm, these proteins presumably cannot be accepted as substrates for Tat export. Indeed, several earlier studies have demonstrated that proteins requiring disulfide bonds for folding are not exported via the Tat pathway.
It had been established previously and confirmed that PhoA fused to the trimethylamine N oxide reductase A (TorA) leader peptide, or for that matter other Tat specific leader peptides, results in negligible alkaline phosphatase activity, indicating lack of export. Therefore, it was reasoned that proper folding, including the formation of disulfide bonds, in the cytoplasm prior to export would permit export via the Tat pathway. To analyze this, the TorA signal sequence was fused to the N-terminus of E.
coli alkaline phosphatase (AP) devoid of its natural signal sequence. Wild-type E. coli cells (DHB4) harboring plasmid pTorA-AP and induced with IPTG (0.1 mM) produced large quantities of cytoplasmic AP as detected by Western blotting. However, there was no detectable AP in the periplasmic fraction of the DHB4 cells. Activity measurements of the same periplasmic fraction confirmed the lack of extracytoplasrnic AP.
As expected, AP activity in the cytoplasmic fraction of DHB4 cells was almost entirely inactive due to its failure to acquire disulfides bonds in the cytoplasm of this strain. To determine whether the oxidation state of AP was critical for Tat-dependent export, a trxB
gor ahpC triple mutant of E. coli (strain DR473) was used to express the ssTorA-AP
fusion protein. When ssTorA-AP was expressed from plasmid pTorA-AP (0.1 mM

IPTG) in strain DR473, about 25% of the total enzymatic activity was found in the periplasmic space. Western blotting confirmed that partitioning of AP had occurred. It should be noted that the quantity of AP in the cytoplasm of DR473 cells was significantly greater than in DHB4 cells, suggesting that misfolded AP is more highly susceptible to cytoplasmic proteolysis.
In support of this notion, it has been reported that the intracellular stability of alkaline phosphatase was decreased in the absence of either one or both of the disulfide bonds. Importantly, (3-galactosidase (LacZ) activity in subcellular fractions was measured (see above) and only samples with <5% LacZ activity in the periplasm were analyzed herein. As a secondary control, cross-reaction of the cytoplasmic chaperone GroEL with specific antisera was used as a control for subcellular fractionation.
Overall, it was clear that the folding status of AP was the maj or determinant in the ability to export this protein by the Tat pathway.
C. Export of PhoA is Tat-specific ~ It was recently observed that, in the context of certain Tat signals, AP can be exported in a Tat-independent fashion. Therefore, to confirm that export of AP
in DR473 was specific to the Tat pathway, a defective TorA signal peptide mutant in which the Rl l and R12 arginine residues were replaced with lysines (R11K;R12K) was fused in frame to signal-sequenceless AP to generate plasmid pKK-AP. It is well documented that replacement of the two conserved arginines with a pair of lysines within the Tat consensus motif (S/T-R-R-x-F-L-K) effectively abolishes translocation (Cristobal, et al., 1999). As expected, DHB4 and DR473 cells expressing ssTorA(R11K;R12K)-AP
fusion protein were incapable of accumulating periplasmic AP. Importantly, the amount of cytoplasmic AP in DR473 cells was similar irrespective of whether RR or KK was present within the leader peptide. It is noteworthy that ssTorA(R11K;R12K)-AP
accumulated in the cytoplasm of DHB4 cells to a much lesser extent than ssTorA-AP in the same cells. One possible explanation is that a proper Tat signal (Arg-Arg) targets even misfolded AP to the cytoplasmic side of the inner membrane. In turn, membrance localization sequesters some of the misfolded enzyme from proteolysis. In contrast, the defective Lys-Lys leader peptide does not properly interact with the Tat machinery and as a result non-targeted AP is more susceptible to cytoplasmic proteolysis. A
similar phenomena has been observed in plant thylakoids where the N-terminal presequence on a large, bulky avidin-bound precursor is available for membrane binding and initial recognition by the transport machinery, but the attached avidin signals the machinery that the precursor is an incorrectly configured substrate and thus import is aborted.
Consequently, Muser and Theg proposed that the ~pH/Tat machinery's proofreading mechanism must operate after precursor recognition but before the committed step in transport.
As an independent confirmation that export was Tat-dependent, P1 transduction of DR473 with the tatB::kan allele from strain MCMTA was performed to generate strain DQ~D (DR473 tatB::kan). As expected, DQ~D cells expressing ssTorA-AP fusion protein from plasmid pTorA-AP were unable to accumulate AP in the periplasm as evidenced by Western blotting and activity measurements of subcellular fractions. In addition, AP was exported in a Tat-dependent fashion when fused to two different signal sequences from formate dehydrogenase-N (FDH-N) subunit G (ssFdnG) and FDH-O subunit G
(ssFdoG).
rr,llPCtivelv, these results confirm that the appearance of AP in the periplasm was completely dependent on export via the Tat pathuray and that translocation could be accomplished by several different Tat leader peptides.
D, Folding and oxidation occurs in the cytoplasm prior to export To determine whether PhoA oxidation occurred in the cytoplasm prior to translocation, the ssTorA-AP fusion protein was produced in an E. coli dsbA null mutant (strains DHBA and DRA). DsbA is the major periplasmic enzyme involved in catalyzing disulfide bond formation in newly synthesized proteins normally secreted by the Sec pathway. As a result, both the DHBA
and DRA mutant strains were completely unable to oxidize periplasmic proteins due to a null mutation of dsbA. Unexpectedly, expression of ssTorA-AP from plasmid pTorA-AP
(0.1 mM
IPTG) in strain DRA resulted in nearly identical periplasmic AP accumulation and activity compared to that obtained using the DR473 dsbA+ strain. Therefore, the accumulation of active AP in the periplasmic compartment was due almost entirely to the export of AP
that had already been folded and oxidized in the cytoplasm.
To determine whether this phenomenom was specific to the TorA presequence or a general feature of the Tat export system, 10 known and putative Tat leader peptides were analyzed (Table 8). The 10 signal sequences were fused in frame to signal sequenceless AP, expressed in six different but genetically related backgrounds and assayed for periplasmic AP
activity. To establish a baseline for residual periplasmic AP activity, the constructs were all expressed in strain DHA (DHB4 dsbA:: kan). Since AP oxidation is prohibited in both the cytoplasm and periplasm of this strain, the total AP activity measured in DHA
was found to be negligible for all leader peptide-AP fusions (Table 9). The periplasmic AP
activity measured in the remaining S strains was normalized to this baseline level. For comparison, the amount of signal-sequenceless AP (02-22) exported in the same strains was measured and found to be negligible in all six backgrounds.
Next, expression of the constructs in wildtype cells (DHB4) resulted in two distinct outcomes: 1) the Tat leaders AmiA, FdnG, FdoG, HyaA, HybA and TorA were unable to export AP when the cytoplasm was reducing; however 2) certain other Tat leader peptides (DmsA, Sufl, YacK and YcbK) could direct AP to the periplasm even though disulfide bond formation in the cytoplasm was not possible. This was likely due to Sec-dependent export of AP.
As expected, nearly all of the leader peptides were able to direct AP to the periplasm of strain DR473 due in part to the more oxidizing cytoplasm. The notable exceptions were ssAmiA and ssHybA, which were unable to accumulate AP in the periplasm of all the strains tested.
Comparison of AP
activity found in the periplasm of DR473 versus DRA (DR473 dsbA: : kan) confirmed that in the cases of ssFdnG, ssFdoG, ssHyaA and ssTorA, export of AP occurred only after folding and oxidation were accomplished in the cytoplasm. Expression of the constructs in strains having an oxidizing cytoplasm but a defective Tat apparatus (DQjD and DUDDY) demonstrated that ssFdnG, ssFdoG and ssTorA directed AP to the periplasm in a Tat-specific fashion. In contrast, the export of AP directed by ssSufl, ssYacK and ssYcbK was still able to occur in tatB and tatC
mutants confirming the earlier DHB4 results and thus the probable use of the Sec pathway.
Interestingly, export of AP by ssHyaA was blocked in a tatC mutant but not in a tatB strain, suggesting that in the context of this leader peptide-AP fusion, Tat export could occur without the TatB protein. It should be noted that export of CoIV was similarly observed to occur in a tatGdependent, tatB-independent fashion when fused to ssTorA. The quality of subcellular fractionations performed for all samples reported in Table 9 was confirmed by lacZ activity measurements as well as by protein dot blotting.

Finally, Western blot analysis and AP activity measurements for both periplasmic and cytoplasmic fractions were. performed for the case of ssFdnG-AP expressed in all six genetic backgrounds (FIG. 7). It was noted that the total AP activity (periplasmic and cytoplasmic) found in DR473/pFdnG-AP was nearly identical to the amount of AP measured in the cytoplasm of DR473 expressing the signal-sequenceless version of AP from plasmid pAID135. It is clear from this data that in the context of the ssFdnG leader peptide, AP must be folded and oxidized prior to translocation by the Tat machinery. To the inventors knowledge, this is the first evidence that de n~vo disulfide bonds formed in the cytoplasm are stably maintained during Tat-dependent membrane translocation. Whether PhoA is translocated as a monomer (~48 kDa) or in its active homodimeric state (~96 kDa) is still unclear, although PhoA is known to fold rapidly into its highly stable, native dimeric state. Moreover, the notion that the large alkaline phosphatase dimer is compatible with the Tat machinery is supported previous studies demonstrating that the 142. kDa FdnGH subcomplex of E. coli formate dehydrogenase-N is transported by the Tat system.
E~~AMPLE 10 'Hitchhiker' strategy for Tat-mediated export of a folded anti-digoxin antibody fragment from the cytoplasm of E. coli.
A considerable portion of the proteins exported by the Tat pathway are enzymes that acquire cofactors in the cytoplasm prior to export and generally function in respiratory or electron transport processes (e.g., E. coli trimethlamine N oxide reductase). The acquisition of cofactors in the cytoplasm requires tertiary structure contacts that occur only after folding has been largely completed. Along these lines, it has been found that membrane targeting and the acquisition of nickel by HybC, the large subunit of the E. coli hydrogenase 2, is critically dependent on the export of the small subunit, HybO which contains a Tat-specific leader peptide. The model favored is that the small and large subunits of hydrogenase 2 first form a complex in the cytoplasm and the complex is then targeted to the membrane by virtue of the leader peptide of the small subunit.
Analogous to this naturally-occurring complex, it was tested whether a non-physiological heterodimeric antibody fragment could be exported via the Tat translocator when folded properly in the cytoplasm. Surprisingly, it was found that the Tat pathway could also export a disulfide linked heterodimer in which only one polypeptide chain was fused to the TorA leader peptide (see schematic, FIG. 6).
A Fab antibody fragment specific for the cardiac glycoside digoxin was used which consisted of two polypeptide chains, the heavy and light chains, linked together via a disulfide bond. In addition, the heavy and light chains each contained two intra-molecular disulfide bonds. The TorA leader peptide was fused only to the heavy chain (VH-CHl) which was co-expressed with the light chain (Vl-C~) from a dicistronic operon.
In this fashion, the TorA-heavy chain carries the light chain into the periplasm in a 'piggyback' fashion only if the interchain disulfide bridge is formed first in the cytoplasm prior to translocation.
In a mutant strain with an oxidizing cytoplasm (strain DR.A) and lacking elsbA, complete Fab protein was exported by the Tat pathway, but only a small fraction of Fab was localized (~15=20%) in the osmotic shock fraction as confirmed by Western blotting.
Earlier, it was reported that the folding yield of the anti-digoxin Fab in the cytoplasm is greatly increased by co-expressing a signal-sequenceless version of the periplasmic disulfide isomerase DsbC (~ssDsbC) or GroEL. In the present analysis, co-expression of ~ssDsbC resulted in a significant increase in the amount of Fab in the periplasm (~50% in the osmotic shock fraction). This may be due to co-expression of chaperones in the cytoplasm increasing the amount of protein competent for export presumably because it improved the yield of folded protein.
Fab was immunologically probed using a primary antibody that recognizes mouse light chain sequences. Therefore, the bands seen confirmed that the light chain was properly recruited by the heavy chain via intermolecular disulfide bond formation and subsequently delivered to the periplasmic space. The localization of the cytoplasmic marker protein GroEL and the periplasmic marker protein DsbC demonstrates that the subcellular fractionation was successful. The Fab protein in the periplasmic fraction of DRA cells was correctly folded and functional as evidenced by its ability to bind the antigen, digoxin in ELISA assays.
As with ssTorA-AP fusions, the appearance of Fab in the osmotic shock fraction was completely abolished in a tatB mutant, when the RR dipeptide in the TorA
leader was mutated to KID or in DHB4 cells having a reducing cytoplasm. Moreover, when incubated under conditions that increase the outer membrane permeability (Chen et al., 2001), intact cells expressing Fab antibodies exported into the periplasm via the Tat pathway could be specifically labeled with the fluorescent antigen digoxin-bodipy. The fluorescence of these cells was 5-fold higher than the background fluorescence observed in DIIA or DOD
control cells. Overall, these results indicate that: (i) the Tat pathway is capable of exporting a fully oxidized Fab across the membrane and (ii) the process is dependent on the assembly of the light and heavy chains and the formation of the intermolecular disulfide within the cytoplasm prior to export. The transport of oxidized, presumably fully folded, Fab molecules into the periplasm provides conclusive evidence for the hitchhiker mode of export suggested previously whereby a polypeptide containing a Tat leader peptide mediates the translocation of a second leaderless polypeptide with which it associates in the cytoplasm.

Table 7. Bacterial strains and plasmids used in this study.
E. coli strainRelevant phenotype Source DHB4 MC1000 phoR ~(phoA) PvuII ~(malF~3 F'[ZaclqZYABoyd et al.
pro] 1987 DHBA DHB4 dsbA::kan This work' DR473 DHB4 ~trxB gor552..TnlOTet ahpC*..TnlOCm(araCP~aGift trxB) DRA DR473 dsbA::kan This work FA113 DHB4 trxB gor552...TnlOtet' ahpC* Gift F-, araDl39 d(argF lac) U169 fIbB5301 Casabadan deoCl ptsF25 relAl and Col MC4100 rbsR22 rpsL150 thiA 1979 MCMTA MC4100 tatB::kan Gift DAD DR473 tatB::kan This work BUDDY MC4100 tatC: apec Gift FUDDY FA113 tatC: apec This work Plasmid name Relevant features Source pTrc99A trc promoter, ColEl ori, Ampr Amersham Pharma pTorA-AP E. coli TorA signal fused to PhoA(~2-22)This work cloned in pTrc99A

pKK-AP as pTorA-AP with R11K;R12K mutation in This work TorA signal peptide pFdnG-AP E. coli FdnG signal fused to PhoA(02-22)This work cloned in pTrc99A

pFdoG-AP E. coli FdoG signal fused to PhoA(~2-22)This work cloned in pTrc99A

pAID135 Signal sequenceless PhoA (42-22) controlled by tae promoter pTrc99-Fab Gene encoding anti-digoxin Fab in pTrc99A

E. coli torA signal fused to gene encoding~s work anti-digoxin Fab in pTorA-Fab Trc99A

pKK-Fab as pTorA-Fab with R11K;R12K mutation This work in TorA signal peptide pBADdsbC Gene encoding DsbC with optimized RBS
in pBAD33 pBAD~ssdsbC Gene encoding DsbC(02-20) with optimized RBS in pBAD33 TABLE 8: Amino acid sequence of leader peptides capable of Tat-dependent export of alkaline phosphatase AmiA* MSTFKPLKTLTSRRQVLKAGLAALTLSGMSQAIAK (SEQ ID

N0:33) DmsA MKTKIPDAVLAAEVSRRGLVKTTAIGGLAMASSALTLPFSRIAHAV
(SEQ

ID N0:43) FdnG MDVSRRQFFKICAGGMAGTTVAALGFAPKQALAQ (SEQ

ID N0:127) FdoG MQVSRRQFFKICAGGMAGTTAAALGFAPSVALAE (SEQ

ID N0:45) -HyaA* MNNEETFYQAMRRQGVTRRSFLKYCSLAATSLGLGAGMAPKIAWAL
(SEQ

ID N0:28) HybA MNRRNFIKAASCGALLTGALPSVSHAAA (SEQ ID

N0:36) Sufi MSLSRRQFIQASGIALCAGAVPLKASAA (SEQ ID

NO:38) TorA MNNNDLFQASRRRFLAQLGGLTVAGMLGPSLLTPRRATAA (SEQ

ID N0:128) YacK MQRRDFLKYSVALGVASALPLWSRAVFAA (SEQ ID

N0:29) YCbK MDKFDANRRKLLALGGVALGAAILPTPAFAT (SEQ ID

N0:30) Table 9. Periplasmic alkaline phosphatase (AP) activity obtained from fusions between putative Tat signal peptides of E. coli and leaderless E. coli alkaline phosphatase*
Leader __ ___~_ a Periplasmic AP activity dsbA
wildtype D2-20a trxB gor altpC
trxB gor ahpC dsbA
AmiAb trxB gor ahpC tatB
DmsA° trxB gor ahpC tatC
FdnG 1.0 (63) 1.3 FdoG

1.6 HyaA 1.3 1.3 HybAb 1.2 Sufl°
nd TorA° nd 0.2 YacK
0.2 YcbK nd 0.1 1.0 (35) 3.2 8.0 5.0 3.2 2.1 1.0 (32) 1.5 13.1 11.6 0.2 0.2 1.0 (55) 1.7 8.1 7.0 0.3 0.2 1.0 (7) 1.3 11.0 10.9 3.8 1.2 nd nd 0.2 0.1 nd 0.1 1.0 (75) 4.3 5.4 6.4 3.5 4.1 1.0 (42) 1.4 10.4 9.6 0.9 0.4 1.0 (25) 3.9 6.1 5.4 7.4 3.2 1.0 (21) 2.5 6.6 5.8 6.3 3.0 Relative alkaline phosphatase activity calculated by normalizing activity in sample to activity measured in DHA control strain. Reported values for alkaline phosphatase activity are the average of 3 separate measurements from 2 independent experiments (n=6). Standard error is less than 10% for all reported data. Values in parenthesis indicate the actual activity measured in the DHA
control strain.
aSignal-sequenceless AP construct bValues normalized to activity measured in DHA/ssHyaA-AP
°Signal sequence carries a c-region positive charge nd = not detectable *AmiA and HyaA are control Tat leader peptides. Both are incapable of exporting alkaline phosphatase under the conditions studies here.

REFERENCES
The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.
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Sambrook et al., Molecular Cloning: A Laboratory Manual, 3 ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2000.
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'70 Santini et al., J. Biol. Chern., 276:8159-8164, 2001.
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Thomas et al., Mol. Microbiol., 39:47-53, 2001.
Weiner et al., Cell, 93:93-101, 1998.
Yahr and Wickner, EMBO J., 20:2472-2479, 2001.
~1 SEQUENCE LISTING
<110> GEORGIOU, GEORGE

DELISA, MATTHEW

$

<120> ENGINEERING OF LEADER PEPTIDES FOR THE SECRETION
OF

RECOMBINANT PROTEINS IN BACTERIA

<130> CLFR:019W0 <140> UNKNOWN

<141> 2002-11-05 <150> 60/337,452 1$ <151> 2001-11-05 <160> 134 <170> PatentIn Ver. 2.1 <210> 1 <211> 6 <212> PRT

<213> Artificial Sequence 2$

<220>

<223> Description of Artificial Sequence: Synthetic Peptide <400> 1 Arg Arg Xaa Phe Leu Lys 3$ <210> 2 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 2 4$ Ser Arg Arg Arg Phe Leu Lys <210> 3 $0 <211> 7 <212> PRT
<213> Artificial Sequence <220>
$$ <223> Description of Artificial Sequence: Synthetic Peptide <400> 3 Ser Arg Arg Xaa Phe Leu Xaa 25227985.1 <210> 4 $ <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 4 Thr Arg Arg Xaa Phe Leu Xaa <210> 5 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 5 Ser Arg Arg Xaa Xaa Leu Lys <210> s <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 6 Ser Arg Arg Xaa Xaa Leu Ala <210> 7 <211> 7 <212> PRT
<213> Artificial Sequence so <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 7 Thr Arg Arg Xaa Xaa Leu Lys <210> 8 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> s Thr Arg Arg Xaa Xaa Leu Ala <210> 9 <211> 7 <2l2> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 9 2$ Ser Arg Arg Xaa Xaa Leu Thr <210> 10 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 10 Ser Arg Arg Xaa Xaa Ile Lys <210> 11 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 11 Ser Arg Arg Xaa Xaa Ile Ala <210> 12 <211> 7 <212> PRT

<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic $ Peptide <400> 12 Ser Arg Arg Xaa Phe Ile Xaa <210> 13 <211> 7 <212> PRT
1$ <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 13 Ser Arg Arg Xaa Phe Met Lys <210> 14 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide 3$ <400> 14 Ser Arg Arg Xaa Phe Val Lys <210> 15 <211> 7 <212> PRT
<213> Artificial Sequence 4$ <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 15 $0 Ser Arg Arg Xaa Phe Va1 Ala <210> 16 $$ <211> 7 <212> PRT
<213> Artificial Sequence <220>

<223> Description of Artificial Sequence: Synthetic Peptide <400> 16 Ser Arg Arg Gln Phe Leu Lys <210> 17 to <211> 6 <212> PRT
<2l3> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 17 Arg Arg Xaa Phe Leu Ala <210> 18 <211> 6 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 18 Arg Arg Xaa Phe Leu Lys <210> 19 <211> 30 <212> DNA
4~ <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 19 gcgatggagc tcttaaagag gagaaaggtc 30 5~ <210> 20 <211> 12 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 20 gcgatgtcta ga 12 <210> 2l $ <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 21 Ser Arg Arg Xaa Phe Met Lys 1$ 1 5 <210> 22 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic ~$ Peptide <400> 22 Ser Arg Arg Xaa Phe Val Lys <210> 23 <211> 7 <212> PRT
3$ <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 23 Ser Arg Arg Xaa Phe Val Ala 4$
<210> 24 <211> 7 <212> PRT
<213> Artificial Sequence $0 <220>
<223> Description of Artificial Sequence: Synthetic Peptide $$ <400> 24 Ser Arg Arg Gln Phe Leu Lys <210> 25 <211> 29 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 25 Met Pro Phe Lys Lys Leu Ser Arg Arg Thr Phe Leu Thr Ala Ser Ser Ala Leu Ala Phe Leu His Thr Pro Phe Ala Arg Ala Leu <210> 26 <211> 28 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 26 Met Thr Trp Ser Arg Arg Gln Phe Leu Thr Gly Val Gly Val Leu Ala 1 5 10 l5 Ala Val Ser Gly Thr Ala Gly Arg Val Val Ala Lys <210> 27 <211> 34 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 27 45. Met Lys Glu Ser Asn Ser Arg Arg Glu Phe Leu Ser Gln Ser Gly Lys Met Val Thr Ala A1a Ala Leu Phe Gly Thr Ser Val Pro Leu Ala His Ala Ala <210> 28 <211> 46 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 28 Met Asn Asn Glu Glu Thr Phe Tyr Gln Ala Met Arg Arg Gln Gly Val Thr Arg Arg Ser Phe Leu Lys Tyr Cys Ser Leu Ala Ala Thr Ser Leu Gly Leu Gly Ala Gly Met Ala Pro Lys Ile Ala Trp Ala Leu <210> 29 <211> 29 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 29 Met Gln Arg Arg Asp Phe Leu Lys Tyr Ser Val Ala Leu Gly Va1 Ala Ser Ala Leu Pro Leu Trp Ser Arg Ala Val Phe Ala Ala <210> 30 <211> 31 3$ <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 30 Met Asp Lys Phe Asp Ala Asn Arg Arg Lys Leu Leu Ala Leu Gly Gly Val Ala Leu Gly Ala Ala Ile Leu Pro Thr Pro Ala Phe Ala Thr $~ <210> 31 <211> 32 <212> PRT
<213> Artificial Sequence $5 <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 31 Met Arg His Ile Phe Gln Arg Leu Leu Pro Arg Arg Leu Trp Leu Ala Gly Leu Pro Cys Leu Ala Leu Leu Gly Cys Val Gln Asn His Asn Lys <210> 32 <211> 36 <212> PRT

<213> Artificial Sequence <220>

<223> Description of ArtificialSequence:
Synthetic Peptide 0 <400> 32 Met Gln Tyr Lys Asp Glu Val Asn Glu Pro.Ser Arg Asn Gly Arg Arg Leu Leu Lys Val Ile Gly Ala Leu Ala Gly Ser Pro Ala Leu Cys Val ~5 20 25 30 Ala His Ala Gln <210> 33 <211> 35 <212> PRT

<213> Artificial Sequence <220>

<223> Description of ArtificialSequence:
Synthetic Peptide 40 <400> 33 Met Ser Thr Phe Lys Pro Thr Leu Thr Ser Arg Gln Leu Lys Arg Val Leu Lys Ala Gly Leu Ala Thr Leu Ser Gly Met Gln Ala Leu Ser Ala t~.520 25 3 0 Ile Ala Lys <210> 34 <211> 45 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 34 Met Lys Lys Asn Gln Phe Leu Lys Glu Ser Asp Val Thr Ala Glu Ser $ Val Phe Phe Met Lys Arg Arg Gln Val Leu Lys Ala Leu Gly Ile Ser Ala Thr Ala Leu Ser Leu Pro His Ala Ala His Ala Asp <210> 35 <211> 31 <212> PRT
1$ <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 35 Met Ser Gly Leu Pro Leu Ile Ser Arg Arg Arg Leu Leu Thr Ala Met 2$ Ala Leu Ser Pro Leu Leu Trp Gln Met Asn Thr Ala His Ala Ala <210> 36 <211> 28 <212> PRT
<213> Artificial Sequence <220>
3$ <223> Description of Artificial Sequence: Synthetic Peptide <400> 36 Met Asn Arg Arg Asn Phe Ile Lys Ala Ala Ser Cys Gly Ala Leu Leu Thr Gly Ala Leu Pro Ser Val Ser His Ala Ala Ala $0 <210> 37 <211> 33 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide $$ <400> 37 Met Asp Arg Arg Arg Phe Ile Lys Gly Ser Met Ala Met Ala Ala Val Cys Gly Thr Ser Gly Ile Ala Ser Leu Phe Ser Gln Ala Ala Phe Ala Ala <210> 38 <211> 28 <212> PRT

1~ <213> Artificial Sequence <220>

<223> Description of Sequence:
Artificial Synthetic Peptide <400> 38 Met Ser Leu Ser Arg Arg PheIle G1nAla Ser Ile Ala Gln Gly Leu ~ Cys Ala Gly Ala Val Pro LysAla SerAla Ala Leu <210> 39 2$ <211> 49 <212> PRT

<213> Artificial Sequence <220>

<223> Description of Sequence:
Artificial Synthetic Peptide <400> 39 Met Ser Asn Gln Gly Glu ProGlu AspAsn Arg Gly Lys Tyr Va1 His Glu Pro.His Asp Leu Ser ThrArg ArgAsp Leu Lys Val Leu Ile Ser 4~ Ala Ala Thr Ala Ala Thr ValVal TyrPro His Thr Leu Ala Ser Ala Ala <210> 40 <211> 45 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 40 Met Ser Trp Ile Gly Trp Thr Val Ala Ala Thr Ala Leu Gly Asp Asn Gln Met Ser Phe Thr Arg Arg Lys Phe Val Leu Gly Met G1y Thr Val Ile Phe Phe Thr Gly Ser Ala Ser Ser Leu Leu Ala Asn $ 35 40 45 <210> 41 <211> 38 <212> PRT
<213> Artificial Sequence <220>

<223> Description ArtificialSequence: Synthetic of 1$ Peptide <400> 41 Met Thr Gly Asp Thr Leu His Ser His Gly Ile Asn Asn Ile Arg Arg Asp Phe Met Lys Cys Ala Leu Ala Ala Thr Met Gly Leu Ala Leu Ser Ser Lys Ala Ala Glu Ala 2$ 35 <210> 42 <211> 47 <212> PRT
<213> Artificial Sequence <220>

<223> Description ArtificialSequence:
of Synthetic 3$ Peptide <400> 42 Met Met Lys Ile Thr Thr Ala LeuMet Lys A1a Ile His Glu Glu Ser Arg Arg Ser Leu Lys Thr Ala LeuGly Ser Leu Leu Met Ser Ala Ala Ser Ser Ala Phe Leu Pro Ser GlnMet Val Arg Ala Thr Phe Ala 4$ 35 40 . 45 <210> 43 <211> 46 $0 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic $$ Peptide <400> 43 Met Lys Thr Lys Ile Pro Asp Ala Val Leu Ala Ala Glu Val Ser Arg Arg Gly Leu Val Lys Thr Thr Ala Ile Gly Gly Leu Ala Met Ala Ser Ser Ala Leu Thr Leu Pro Phe Ser Arg Ile Ala His Ala Val <210> 44 1O <211> 44 <212> PRT
<213> Artificial Sequence <220>

<223> Description ArtificialSequence:
of Synthetic Peptide <400> 44 Met Ser Lys Asn Arg Met Gly Ile Ser Arg Arg Thr Glu Val Leu Val Lys Ser Thr Ala Gly Ser Ala Leu Ala Ala Gly Gly Ile Leu Phe Ser ZS Leu Pro Phe Thr Arg Asn Ala Ala Ala Val Leu Ala <210> 45 ~ <211> 34 <212> PRT
<213> Artificial Sequence <220>
3$ <223> Description of Artificial Sequence: Synthetic Peptide <400> 45 Met Gln Val Ser Arg Arg Gln Phe Phe Lys Ile Cys Ala Gly Gly Met Ala Gly Thr Thr A1a Ala Ala Leu Gly Phe A1a Pro Ser Val Ala Leu 45 Ala Glu <210> 46 So <211> 62 <212> PRT
<213> Artificial Sequence <220>
55 <223> Description of Artificial Sequence: Synthetic Peptide <400> 46 Met Thr Asp Tyr Ala Ser Phe Ala Lys Val Ser Gly Gln Ile Ser Arg Leu Leu Val Thr Gln Leu Arg Phe Leu Leu Leu Gly Arg Gly Met Ser Gly Ser Asn Thr Ala Ile Ser Arg Arg Arg Leu Leu Gln Gly Ala Gly Ala Met Trp Leu Leu Ser Val Ser Gln Val Ser. Leu Ala Ala <210> 47 <211> 7 IS <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 47 Arg Arg Arg Gly Phe Leu Thr <210> 48 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 48 Gln Arg Arg Arg Ala Leu Thr <210> 49 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 49 Thr Arg Arg Glu Phe Ile Lys 5$ <210> 50 <211> 7 <2l2> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide $ <400> 50 Ser Arg Arg Ser Phe Met Lys <210> 51 <211> 7 <212> PRT
<213> Artificial Sequence 1$ <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 51 Gly Arg Arg Arg Phe Leu Arg <210> 52 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 52 Ser Arg Arg Gln Phe Phe Lys 3$ 1 5 <210> 53 <211> 7 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic 4$ Peptide <400> 53 Ser Arg Arg Arg Phe I,eu Gln $0 <210> 54 <211> 54 <212 > DNA
$$ <2l3> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 54 gcgatggagc tcttaaagag gagaaaggtc atgccattta aaaaactctc ccga 54 <210> 55 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer 1$ <400> 55 gcgatggagc tcttaaagag gagaaaggtc atgacctggt ctcgtcgc 48 <210> 56 <211> 48 <212> DNA
<213> Artificial Sequence <220>
2$ <223> Description of Artificial Sequence: Synthetic Primer <400> 56 gcgatggagc tcttaaagag gagaaaggtc atgaaagaaa gcaatagc 48 <210> 57 <211> 57 <212> DNA
3$ <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 57 gcgatggagc tcttaaagag gagaaaggtc atgaataacg aggaaacatt ttaccag 57 4$ <210> 58 <211> 48 <212> DNA
<213> Artificial Sequence $0 <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 58 $$ gcgatggagc tcttaaagag gagaaaggtc gtggggagac gacgcgga 48 <210> 59 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 59 gcgatggagc tcttaaagag gagaaaggtc atgcaacgtc gtgatttc 48 <210> 60 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 60 gcgatggagc tcttaaagag gagaaaggtc atgtcccggt cagcgaaa 48 <210> 61 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 61 3$ gcgatggagc tcttaaagag gagaaaggtc atggacaaat tcgacgct 48 <210> 62 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 62 gcgatggagc tcttaaagag gagaaaggtc atgcgacaca tttttcaa 48 <210> 63 <211> 53 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 63 gcgatggagc tcttaaagag gagaaaggtc atgcagtata aagatgaaaa cgg 53 <210> 64 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 64 gcgatggagc tcttaaagag gagaaaggtc atgagcactt ttaaacca 48 <210> 65 <211> 59 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 65 gcgatggagc tcttaaagag gagaaaggtc atgaaaaaga atcaattttt aaaagaatc 59 <210> 66 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 66 gcgatggagc tcttaaagag gagaaaggtc atgagcggct tacctctt 48 <210> 67 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 67 gcgatggagc tcttaaagag gagaaaggtc atgattcggc aacgtcgt 48 $5 <210> 68 <211> 48 <212> DNA

<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 68 gcgatggagc tcttaaagag gagaaaggtc atgatcaggg aggaagtt 48 1~
<210> 69 <211> 62 <212> DNA
<213> Artificial Sequence <2zo>
<223> Description of Artificial Sequence: Synthetic Primer ZO <400> 69 gcgatggagc tcttaaagag gagaaaggtc gtgaacagac gtaattttat taaagcagcc 60 tc 62 2$ <210> 70 <211> 48 <212> DNA
<213> Artificial Sequence 3O <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 70 35 gcgatggagc tcttaaagag gagaaaggtc atggatcgta gacgattt 48 <210> 71 <211> 48 4~ <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:. Synthetic 45 Primer <400> 71 gcgatggagc tcttaaagag gagaaaggtc atgtcactca gtcggcgt 48 <210> 72 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 72 gcgatggagc tcttaaagag gagaaaggtc atgagcaacc aaggcgaa 48 $ <210> 73 <2l1> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 73 gcgatggagc tcttaaagag gagaaaggtc atgtcatgga tagggtgg 48 <210> 74 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 74 gcgatggagc tcttaaagag gagaaaggtc atgactggag ataacacc 48 <210> 75 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 75 gcgatggagc tcttaaagag gagaaaggtc atgaaactca gtcgtcgt 48 <210> 76 4$ <211> 57 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 76 gcgatggagc tcttaaagag gagaaaggtc atgatgaaaa tccataccac agaggcg 57 <210> 77 <211> 52 <212> DNA

<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 77 gcgatggagc tcttaaagag gagaaaggtc atgaaaacga aaatccctga tg 52 <210> 7a <211> 54 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 7a gcgatggagc tcttaaagag gagaaaggtc atgtccaaaa atgaacgaat ggtg 54 <210> 79 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 79 gcgatggagc tcttaaagag gagaaaggtc atggacgtca gtcgcaga 48 <210> eo <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> ao gcgatggagc tcttaaagag gagaaaggtc atgcaggtca gcagaagg 48 $0 <210> 81 <211> 60 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 81 gcgatggagc tcttaaagag gagaaaggtc atgacagatt atgcgtcttt cgctaaagtt 60 <210> 82 $ <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 82 gcgatggagc tcttaaagag gagaaaggtc atgatttcac gccgccga 48 <210> 83 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 83 gcgatgtcta gagctttgtc gggcgggaag 30 3~ <210> 84 <211> 36 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 84 ~ gcgatgtcta gaattgatat tcaacgtttt cgccac 36 <210> 85 <211> 30 4$ <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic $~ Primer <400> 85 gcgatgtcta gatagggtgc cagctaccgc 30 <210> 86 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer S
<400> 86 gcgatgtcta gagcgcggtt tgttctccag 30 <210> 87 <211> 30 <212> DNA
<213> Artificial Sequence IS <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 87 gcgatgtcta gatacgcgcc cgatatggtt 30 <210> 88 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence. Synthetic Primer <400> 88 gcgatgtcta gataacgttg ggcgttctgc 30 <210> 89 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer 4S <400> 89 gcgatgtcta gagcgcaacc gcacgccaga 30 <210> 90 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 90 gcgatgtcta gagcgtgggg tagagagtgt 30 <210> 91 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<~223> Description of Artificial Sequence: Synthetic Primer <400> 91 gcgatgtcta gacgtatcaa tggctggctt 30 <210> 92 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 92 gcgatgtcta gacgcacttt gcgttttttg 30 <210> 93 <211> 32 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 93 gcgatgtcta gattttaaaa gttcgtcttt gg 32 <210> 94 <211> 30 <212> DNA
4$ <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer SO
<400> 94 gcgatgtcta gaaaaccagc taagcagatc 30 5$ <210> 95 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer $ <400> 95 gcgatgtcta gaattgggat caatagccgc 30 <2l0> 96 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 96 gcgatgtcta gagaatacag cgaccgtatg 30 <210> 97 <211> 30 <212> DNA
~5 <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 97 gcgatgtcta gatttaccgc ccttctcttc 30 <210> 98 <211> 30 <212> DNA
<213> Artificial Sequence 0 <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 98 gcgatgtcta gatggcgggc ggttttcagc 30 <210> 99 <211> 30 $0 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 99 gcgatgtcta gaggcaatat cagaatctgc 30 <210> 100 <211> 30 <212> DNA
S <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> loo gcgatgtcta gacggttgct gttgcccggc 30 <210> 10l <211> 30 <2l2> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 101 2$ gcgatgtcta gaagctgccg gaacgcttgc 30 <210> 102 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 102 gcgatgtcta gacttttctt gcctcgtgtt 30 <210> 103 <211> 30 <212> DNA
<213> Artificial Sequence .
<220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 103 gcgatgtcta gaaaccgatt cggccatctc 30 <210> 104 SS <211> 30 <212> DNA
<213> Artificial Sequence <220>

<223> Description of Artificial Sequence: Synthetic Primer <400> 104 gcgatgtcta gactgaccaa caacggcgcg 30 <210> 105 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic 1$ Primer <400> 105 gcgatgtcta gattctaccg gagcctctgc 30 <210> 106 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 106 gcgatgtcta gatggaatgg cgctatcgac 30 <210> 107 <211> 30 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 107 gcgatgtcta gatttttcgc gggcctgttg 30 <210> 108 <21l> 33 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer 5$
<400> 108 gcgatgtcta gataatttgt agtttcgcgc ctg 33 <210> 109 <211> 33 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer IO <400> l09 gcgatgtcta gacagtttat actgccgggt ttc 33 <210> 110 1$ <211> 30 <212> DNA
<213> Artificial Sequence <220>
ZO <223> Description of Artificial Sequence: Synthetic Primer <400> 110 gcgatgtcta gacgccacga cctggctg.ac 30 2$
<210> 111 <211> 30 <212> DNA
30 <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer 3$
<400> 111 gcgatgtcta gagctcgtgg ctatcgtcgc 30 4O <210> 112 <211> 36 <212> DNA
<213> Artificial Sequence 4$ <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 112 $O gcgatgtcta gaagtaaagg agaagaactt ttcact 3~
<210> 113 <211> 33 $$ <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 113 gcgatgaagc ttctatttgt atagttcatc cat 33 <210> 114 <211> 81 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer 1$
<400> 114 gcgatgaagc ttgcatgctt aagctgctaa agcgtagttt tcgtcgtttg ctgcgtcgac 60 tttgtatagt tcatccatgc c 81 <210> 115 <211> 60 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 115 gcgatggaat tcgagctctt aaagaggaga aaggtcatga acaataacga tctctttcag 60 <210> ll6 3$ <211> 36 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 116 gcgatgtcta gaagcgtcag tcgccgcttg cgccgc 36 <210> 117 <211> 60 <212> DNA
$0 <213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 117 gcgatggaat tcgagctctt aaagaggaga aaggtcgtga aacaaagcac tattgcactg 60 <210> 118 <211> 35 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 118 gcgatgaagc ttttatttca gccccagagc ggctt 35 <210> 119 1$ <211> 11 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 119 Ala Ala Asn Asp Glu Asn Tyr Ala Leu Ala Ala <210> 120 <211> 45 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 120 Met Asn Asn Asn Asp Leu Phe Gln A1a Ser Arg. Arg Arg Phe Leu Ala 1 5 ~ 10 15 Gln Leu Gly Gly Leu Thr Val Ala Gly Met Leu Gly Pro Ser Leu Leu Thr Pro Arg Arg Ala Thr Ala Ala Gln Ala Ala Thr Asp 35 40 . 45 <210> 121 <211> 46 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 121 Met Asn Asn Asn Asp Leu Phe Gln Thr Ser Arg Arg Arg Leu Leu Ala Gln Leu Gly Gly Leu Thr Val Ala Gly Met Leu Gly Pro Ser Leu Leu S Thr Pro Arg Arg Ala Thr Ala Ala Gln Ala Ala Thr Asp Ala <210> 122 1~ <211> 46 <212> PRT
<213> Artificial Sequence <220>
1$ <223> Description of Artificial Sequence: Synthetic Peptide <400> 122 Met Asn Asn Asn Asp Leu Phe Gln Thr Ser Arg Gln Arg Phe Leu Ala Gln Leu Gly Gly Leu Thr Val Ala Gly Met Leu Gly Pro Ser Leu Leu Thr Pro Arg Arg Ala Thr Ala Ala Gln Ala Ala Thr Asp Ala <210> 123 <211> 46 <212> PRT
<213> Artificial Sequence <220>

35 <223> Description ArtificialSequence:
of Synthetic Peptide <400> 123 Met Asn Asn Asn Ile Phe AlaSerArg Arg Arg Phe Leu Asp Gln Ala Gln Pro Gly Gly Thr Val GlyMetLeu Gly Pro Ser Leu Leu Ala Leu 4S Thr Pro Arg Arg Thr Ala GlnAlaAla Thr Asp A1a Ala Ala <210> 124 $~ <211> 46 <212> PRT
<213> Artificial Sequence <220>
55 <223> Description of Artificial Sequence: Synthetic Peptide <400> 124 Met Asn Asn Asn Glu Leu Phe Gln Ala Ser Arg Arg Arg Phe Leu Ala Gln Leu Gly Gly Leu Thr Val Ala Gly Met Leu Gly Pro Ser Leu Leu $
Thr Pro Arg Arg Ala Thr Ala Ala Gln Ala Ala Thr Asp Ala l~ <210> 125 <211> 46 <212> PRT

<213> Artificial Sequence 1$ <220>

<223> Description of Sequence:
Artificial Synthetic Peptide <400> 125 2o Met Asn Asn Asn Asp Leu GlnThr ThrArg Arg Arg Phe Leu Phe Ala Gln Leu Gly Gly Leu Thr AlaGly MetLeu Gly Pro Ser Leu Val Leu 2$

Thr Pro Arg Arg Ala Thr AlaGln AlaAla Thr Asp Ala Ala 3~ <210> 126 <211> 46 <212> PRT

<213> Artificial Sequence 3$<220>

<223> Description of Artificial Sequence:
Synthetic Peptide <400> 126 4~Met Asn Asn Asn Asp Ser GlnThrSer Arg Arg Arg Phe Phe Leu Ala Gln Leu Gly Gly Leu Thr AlaGlyMet Leu Gly Pro Ser Va1 Leu Leu 4$

Thr Pro Arg Arg Ala Thr AlaGlnAla Ala Thr Asp Ala Ala $~ <210> 127 <211> 34 <212> PRT
<2l3> Artificial Sequence $$ <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 127 Gly Cys Gly Ala Thr Gly Gly Ala Gly Cys Thr Cys Thr Thr Ala Ala Ala Gly Ala Gly Gly Ala Gly Ala Ala A1a Gly Gly Thr Cys Ala Thr $ 20 25 30 Gly Ala Ala Cys Ala Ala Thr Ala Ala Cys Gly Ala Thr Cys Thr Cys Thr Thr Thr Cys Ala Gly Gly Cys Ala Thr Cys Ala Ala Ala Gly Ala Ala Ala Cys Gly Thr Thr Thr Thr Cys Thr Gly Gly Cys Ala Cys Ala 1$
Ala Cys Thr Cys <210> 128 <211> 40 <212> PRT
<213> Artificial Sequence 2$ <220>
<223> Description of Artificial Sequence: Synthetic Peptide <400> 128 3~ Gly Cys Gly Cys Thr Gly Thr Thr Gly Cys Ala Gly Thr Thr Gly Ala Ala Cys Thr Thr Cys Gly Cys Thr Ala Gly Cys Ala Gly Cys Gly Thr 3$
Cys Ala Gly Thr Cys Gly Cys Cys Gly Cys Thr Thr Gly 40 <210> 129 <211> 84 <212> DNA
<213> Artificial Sequence 4$ <220>
<223> Description of Artificial Sequence: Synthetic Primer <400> 129 $0 gcgatggagc tcttaaagag gagaaaggtc atgaacaata acgatctctt tcaggcatca 60 aagaaacgtt ttctggcaca acts 84 <210> 130 $$ <211> 32 <212> DNA
<213> Artificial Sequence <220>

<223> Description of Artificial Sequence: Synthetic Primer <400> 130 $ gcgatgtcta gacggacacc agaaatgcct gt 32 <210> 131 <211> 35 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic 1$ Primer <400> 131 gcgatgaagc ttttatttca gccccagagc ggctt 35 <210> 132 <211> 27 <212> DNA

<213> Artificial Sequence 2$

<220>

<223> Description of ArtificialSequence:Synthetic Primer <400> 132 gctgctagcg aagttcaact gcaacag 27 <210> 133 3$ <211> 36 <212> DNA

<213> Artificial Sequence <220>

<223> Description of ArtificialSequence:Synthetic Primer <400> 133 gcgatgcccg ggggctttgt tagcagccggatctca 36 4$

<2l0> 134 <211> 45 <212> DNA

$0 <213> Artificial Sequence <220>

<223> Description of ArtificialSequence:Synthetic Primer $$

<400> 134 gcgctgttgc agttgaactt cgctagcagcgtcagtcgccgcttg 45

Claims (54)

WHAT IS CLAIMED IS:

1. A method of identifying a leader peptide that directs protein export in bacteria, comprising the steps of:
a) obtaining a library of nucleic acid sequences encoding mutated leader peptides;
b) constructing a plurality of expression cassettes comprising said nucleic acid sequences encoding mutated leader peptides upstream of a nucleic acid sequence encoding a short-lived reporter protein, wherein the short lived reporter protein is subject to degradation in the cytoplasm of bacteria;
c) expressing said plurality of expression cassettes in bacteria;
d) measuring expression of said reporter protein in said bacteria; and e) collecting bacteria cells having increased expression of said reporter protein relative to bacteria that do not express a peptide leader peptide that directs protein export of said short lived reporter protein, wherein the mutated leader peptide expressed in said cells that have increased expression of said reporter protein is a leader peptide that directs export from the cytoplasm, whereby said export rescues said short-lived reporter protein from degradation in the cytoplasm.

2. The method of claim 1, wherein said short-lived reporter protein is constructed by operably linking a cytoplasmic degradation sequence to the nucleic acid sequence encoding said reporter protein.

3. The method of claim 2, wherein said cytoplasmic degradation sequence is selected from the group consisting of SsrA, PEST, sequences recognized by LON, sequences recognized by ClpAP, sequences recognized by ClpXP, sequences recognized by Stsh and sequences recognized by HslUV.

4. The method of claim 2, wherein said cytoplasmic degradation sequence is attached to the N-terminal or the C-terminal end of said reporter protein.

5. The method of claim 1, wherein said reporter protein is selected from the group consisting of a fluorescent protein, an enzyme, a transport protein, an antibiotic resistance enzyme, a toxin immunity protein, a bacteriophage receptor protein and an antibody.

6. The method of claim 5, wherein said fluorescent protein is green fluorescent protein.

7. The method of claim 1, wherein said nucleic acid sequences encoding mutated leader peptides are generated by a method selected from the group consisting of random mutagenesis, error-prone PCR, site-directed mutagenesis and generation of random DNA
fragments.

8. The method of claim 1, wherein said leader peptide mediates protein secretion through a pathway selected from the group consisting of the general secretory (Sec) pathway, the signal recognition particle (SRP)-dependent pathway, the YidC-dependent pathway and the twin-arginine translocation (Tat) pathway.

9. The method of claim 1, further comprising the steps of:
f) cloning a selected nucleic acid sequence encoding a mutated leader peptide from collected bacteria cells having increased expression of said reporter protein compared to bacteria cells that express a wild type leader peptide, and g) constructing an expression cassette comprising said nucleic acid sequence encoding said mutated selected leader peptide upstream of a nucleic acid sequence encoding a heterologous polypeptide of interest.

10. The method of claim 9, still further comprising expressing said expression cassette in bacteria so that said leader peptide directs increased export of said heterologous polypeptide in bacteria.

11. The method of claim 1, wherein said bacteria are Gram negative bacteria.

12. A method of screening for a compound that inhibits or enhances protein export in bacteria, comprising the steps of:
a) constructing an expression cassette comprising a nucleic acid sequence encoding a mutated leader peptide that directs protein export in bacteria upstream of a nucleic acid sequence encoding a short-lived reporter protein, wherein the short lived reporter protein is subject to degradation in the cytoplasm of bacteria;

b) expressing said expression cassette in bacteria in the presence or absence of said compound; and c) measuring expression of said reporter protein in said bacteria, wherein increased expression of said reporter protein measured in the presence of said compound indicates said compound enhances protein export, and wherein decreased expression of said reporter protein measured in the presence of said compound indicates said compound inhibits protein export, whereby protein export rescues said short-lived reporter protein from degradation in the cytoplasm.

13. The method of claim 12, wherein said short-lived reporter protein is constructed by operably linking a cytoplasmic degradation sequence to the nucleic acid sequence encoding said reporter protein.

14. The method of claim 13, wherein said cytoplasmic degradation sequence is selected from the group consisting of SsrA, PEST, sequences recognized by LON, sequences recognized by ClpAP, sequences recognized by ClpXP, sequences recognized by Stsh and sequences recognized by HslUV.

15. The method of claim 13, wherein said cytoplasmic degradation sequence is attached to the N-terminal or the C-terminal of said reporter protein.

16. The method of claim 12, wherein said reporter protein is selected from the group consisting of fluorescent protein, an enzyme, a transport protein, an antibiotic resistance enzyme, a toxin immunity protein, a bacteriophage receptor protein and an antibody.

17. The method of claim 16, wherein said fluorescent protein is green fluorescent protein.

18. The method of claim 12, wherein said bacteria are Gram negative bacteria.

19. A method of identifying a leader peptide that directs increased protein export through the Twin Arginine Translocation pathway, comprising the steps of:
a) generating a library of nucleic acid sequences encoding mutated leader peptides specific for the Twin Arginine Translocation pathway;
b) constructing a plurality of expression cassettes comprising said nucleic acid sequences encoding mutated leader peptides upstream of a nucleic acid sequence encoding a short-lived reporter protein, wherein the short lived reporter protein is subject to degradation in the cytoplasm of bacteria;
c) expressing said expression cassettes in bacteria;
d) measuring the expression of said reporter protein in said bacteria; and e) collecting bacteria cells having increased expression of said reporter protein relative to bacteria that do not express a peptide leader peptide that directs protein export of said short lived reporter protein, wherein the mutated leader peptide expressed in said cells that exhibit increased expression of said reporter protein is a leader peptide that directs increased protein export from the cytoplasm through the Twin Arginine Translocation pathway, whereby said export rescues said short-lived reporter protein from degradation in the cytoplasm..

20. The method of claim 19, wherein said short-lived reporter protein is constructed by operably linking a cytoplasmic degradation sequence to the nucleic acid sequence encoding said reporter protein.

21. The method of claim 20, wherein said cytoplasmic degradation sequence is selected from the group consisting of SsrA, PEST, sequences recognized by LON, sequences recognized by ClpAP, sequences recognized by ClpXP, sequences recognized by Stsh and sequences recognized by HslUV.

22. The method of claim 20, wherein said cytoplasmic degradation sequence is attached to the N-terminal or the C-terminal of said reporter protein.

23. The method of claim 19, wherein said reporter protein is selected from the group consisting of fluorescent protein, an enzyme, a transport protein, an antibiotic resistance enzyme, a toxin immunity protein, a bacteriophage receptor protein and an antibody.

24. The method of claim 23, wherein said fluorescent protein is green fluorescent protein.

25. The method of claim 19, wherein said bacteria are Gram negative bacteria.

26. The method of claim 19, wherein said nucleic acid sequences encoding mutated leader peptides specific for the Twin Arginine Translocation pathway are generated by a method selected from the group consisting of random mutagenesis, error-prone PCR, site-directed mutagenesis and generation of random DNA fragments.

27. The method of claim 19, wherein said leader peptide comprises a sequence selected from the group consisting of SEQ ID NOs:120-128 or a sequence mutated therefrom.

28. A leader peptide that directs increased protein export through the Twin Arginine Translocation pathway prepared by the method of claim 19.

29. An isolated nucleic acid sequence encoding the leader peptide of claim 28.

30. A method of increasing export of heterologous polypeptide through the Twin Arginine Translocation pathway, comprising the steps of:
a) constructing an expression cassette comprising a nucleic acid sequence encoding a leader peptide that directs increased polypeptide export through the Twin Arginine Translocation pathway upstream of a nucleic acid sequence encoding a heterologous polypeptide of interest; and b) expressing said expression cassette in bacteria so that said leader peptide directs increased export of said heterologous polypeptide through the Twin Arginine Translocation pathway.

31. The method of claim 30, wherein said leader peptide comprises a sequence selected from the group consisting of SEQ ID NOs:120-128.

32. A method of screening for a compound that inhibits or enhances protein export through the Twin Arginine Translocation pathway, comprising the steps of:
a) constricting an expression cassette comprising a nucleic acid sequence encoding a leader peptide upstream of a nucleic acid sequence encoding a short-lived reporter protein, wherein the short lived reporter protein is subject to degradation in the cytoplasm of bacteria, and wherein said leader peptide directs protein export through the Twin Arginine Translocation pathway;
b) expressing said expression cassette in said bacteria in the presence or absence of said compound; and c) measuring expression of said reporter protein in said bacteria, wherein increased expression of said reporter protein measured in the presence of said compound indicates said compound enhances protein export through the Twin Arginine Translocation pathway, and decreased expression of said reporter protein measured in the presence of said compound indicates said compound inhibits protein export through the Twin Arginine Translocation pathway.

33. The method of claim 32, wherein said short-lived reporter protein is constructed by operably linking a cytoplasmic degradation sequence to the nucleic acid sequence encoding said reporter protein.

34. The method of claim 33, wherein said cytoplasmic degradation sequence is selected from the group consisting of SsrA, PEST, sequences recognized by LON, sequences recognized by ClpAP, sequences recognized by ClpXP, sequences recognized by Stsh and sequences recognized by HslUV.

35. The method of claim 33, wherein said cytoplasmic degradation sequence is attached to the N-terminal or the C-terminal of said reporter protein.

36. The method of claim 32, wherein said reporter protein is selected from the group consisting of fluorescent protein, an enzyme, a transport protein, an antibiotic resistance enzyme, a toxin immunity protein, a bacteriophage receptor protein and an antibody.

37. The method of claim 36, wherein said fluorescent protein is green fluorescent protein.

38. A method of producing a biologically-active heterologous polypeptide in a cell, comprising the steps of:
a) constructing an expression cassette comprising a nucleic acid sequence encoding a leader peptide that directs protein export through the Twin Arginine Translocation pathway upstream of a nucleic acid sequence encoding said heterologous polypeptide; and b) expressing said expression cassette in a bacterial cell, wherein said heterologous polypeptide is produced in a biologically-active form.

39. The method of claim 38, wherein the heterologous polypeptide comprises and antibody fragment.

40. The method of claim 38, wherein said leader peptide comprises a sequence selected from the group consisting of SEQ ID NOs: 25-46 and 120-128.

41. The method of claim 38, wherein said heterologous polypeptide is selected from the group consisting of a polypeptide secreted from said bacterial cell, a polypeptide isolatable from the periplasm of said bacterial cell, an integral membrane protein and a polypeptide isolatable from the culture supernatant of said bacterial cell.

42. The method of claim 38, wherein said heterologous polypeptide is a mammalian polypeptide.

43. The method of claim 42, wherein said mammalian polypeptide is selected from the group consisting of tissue plasminogen activator, pancreatic trypsin inhibitor, an antibody, an antibody fragment and a toxin immunity protein.

44. The method of claim 38, wherein said heterologous polypeptide is selected from the group consisting of a polypeptide in native conformation, a mutated polypeptide and a truncated polypeptide.

45. The method of claim 38, wherein said bacterial cell has an oxidizing cytoplasm.

46. The method of claim 38, wherein said heterologous polypeptide forms disulfide bonds in the cytoplasm of said bacterial cell

47. The method of claim 38, wherein a second heterologous polypeptide is expressed in the cytoplasm of said bacteria and associates in said cytoplasm with the heterologous polypeptide, wherein the second heterologous polypeptide lacks said leader peptide and wherein said leader peptide directs export of said second heterologous polypeptide associated with said heterologous polypeptide by protein export through the Twin Arginine Translocation pathway.

48. The method of claim 45, wherein said bacterial cell is a Gram negative bacteria.

49. The method of claim 45, wherein said bacterial cell is selected from the group consisting of an E. coli trxB mutant, E. coli gor mutant and E. coli trxB gor double mutant.

50. The method of claim 45, wherein said cell secretes at least one biologically-active heterologous polypeptide containing from about 2 to about 17 disulfide bonds.

51. The method of claim 50, wherein two of said heterologous polypeptides are linked by at least one disulfide bond.

52. An isolated leader peptide that directs protein secretion and export through the Twin Arginine Translocation pathway.

53. The isolated leader peptide of claim 52, wherein said leader peptide comprises a sequence selected from the group consisting of SEQ ID NOs:25-46 and 120-128.

54. A recombinant nucleic acid sequence encoding a leader peptide selected from the group consisting of SEQ ID NOs:25-46 and 120-128.