WO2023168442A1

WO2023168442A1 - Methods for the coproduction of polyhydroxyalkanoates and indigoid derivatives from whey protein and lactose

Info

Publication number: WO2023168442A1
Application number: PCT/US2023/063731
Authority: WO
Inventors: Kobe Clark ROGERS; Alec Vincent BREWER; Simonne Josephine GUENETTE; George Howard MCARTHUR IV
Original assignee: Transfoam Llc D.B.A. Ourobio
Priority date: 2022-03-03
Filing date: 2023-03-03
Publication date: 2023-09-07

Abstract

Described herein are DNA constructs containing genes which enable co-production of polyhydroxyalkoanates and indigoid derivates in bacteria transformed with those DNA constructs. The DNA constructs described herein comprise genes which express a flavindependent monooxygenase and polyhydroxyalkoanates, a class of biodegradable polyesters. The resulting product is a natural polyester dyed with indigoid dyes

Description

METHODS FOR THE COPRODUCTION OF POLYHYDROXYALKANOATES AND

INDIGOID DERIVATIVES FROM WHEY PROTEIN AND LACTOSE

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This Application claims the benefit of U.S. Provisional Application No. 63/316,200, filed on March 3, 2022, which is incorporated herein by reference in its entirety.

REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA

EFS-WEB

[0002] The Sequence Listing submitted March 3, 2023 as an XML file named “2023-03- 03_Sequence Listing_OURO-00001-U-PCT-01 ,” created on March 3, 2023, and having a size of 69,019 bytes is hereby incorporated by reference pursuant to 37 C.F.R. § 1 .52(e)(5).

BACKGROUND

[0003] The environmental impact of accelerating human industrial activity is becoming increasingly clear. A recent report suggests that the production of geologically novel entities, such as plastics, has outpaced our societal ability to monitor and assess the safety of these materials and their associated production processes. The production of petroplastic goods and packaging accounts for over 1.5 gigatons CO₂ equivalents (CO2e)/year released into the atmosphere and over 80% of the 20 billion pounds of waste that makes its way into the ocean each year. The United States’ single digit recycling rates are not sufficient to confront these existential threats, and complications posed by contamination accumulated during product use and the complexity of consumer goods and packaging systems will continue to challenge closed-ioop recycling and decarbonization efforts even as new recycling infrastructure is developed.

[0004] There is an increasing emphasis in nearly all industries for the movement to more sustainable and ecologically sensitive methods of production of materials used in those industries. The dye industry is no exception, and there is a clear desire to shift production to highly sustainable methods for production of dyes used in foodstuffs, textiles, materials, and the like. Akin to the dye industry, the polymer industry is under increasing pressure to utilize sustainable and more ecologically benign methods of production, including production of biodegradable materials to ease the impact on the environment post-use. In addition, the reuse or utilization of waste streams from one production process in another production process is highly desired for mitigation production costs and maximum efficiencies in resource use.

[0005] The production of biodegradable plastic alternatives and additives is believed to provide a significant reduction in environmental and human toxicity, moreover such alternatives have great potential for the implementation of carbon capture technologies relative to their petroleum-derived counterparts. The need for a greater selection of biodegradable polymers and additives has become apparent as fully bio-based, biodegradable plastic products are currently only being offered a small section of products (i.e. , straws and cutlery) and often in only three shades - black, white, and “natural” (off- white). As more companies make the switch to biobased and biodegradable plastic alternatives, greater access to bio-based colorants will be needed to enable the production of low-footprint, brightly colored bioplastics that preserve the biodegradability of the finished product.

[0006] Production of dyes and polymers using bioreactors, e.g., recombinantly engineered cells for use in fermenters to produce either material, is highly desirable and would address industry needs as discussed above, there remain significant hurdles in the economical scaling of bioreactor production of dyes and polymers, much less co-production of a dye and a polymer.

[0007] Despite advances in research directed to sustainable production of either dyes or polymers, there remain a scarcity of suitable, economical, and scalable methods that can sustainably produce desired dyes or polymers, much less co-production of a dye and a polymer using a bioreactor. These needs and other needs are satisfied by the present disclosure.

SUMMARY

[0008] in accordance with the purpose(s) of the disclosure, as embodied and broadly described herein, the disclosure, in a further aspect, relates to methods and compositions comprising polyhydroxyalkanoates (PHAs) and indigoid dyes. In various aspects, the disclosed compositions pertain to recombinant bacteria engineered to comprise enzymes for biosynthesis of within the bacteria desired PHAs and indigoid dyes. In a further aspect, the disclosed methods pertain to co-production of PHAs and indigoid dyes in the disclosed recombinant bacteria using the disclosed bacteria. In a still further aspect, disclosed herein are methods of isolation and use of PHAs and indigoid dyes made using the disclosed methods with the disclosed recombinant bacteria.

[0009] Also disclosed herein are synthetic DNA sequences comprising an origin of replication; an antibiotic resistance gene; and one or more transgenes for co-production of at least one disclosed polyhydroxyalkanoate and at least one indigoid derivative.

[0010] Also disclosed herein are synthetic DNA sequences comprising an origin of replication; aann antibiotic resistance gene; a DNA encoding a flavin-dependent monooxygenase, operably linked to a promoter; and an expression cassette comprising a DNA encoding poly(3)hydroxyalkanoate polymerase (phaC), acetyl-CoA acetyltransferase (phaA), and acetoacetyl-CoA reductase (phaB), wherein the expression cassette is operably linked to a promoter for coordinate expression of poly(3)hydroxyalkanoate polymerase (phaC), acetyl-CoA acetyltransferase (phaA), and acetoacetyl-CoA reductase (phaB).

[0011] Also disclosed herein are DNA constructs, e.g., plasmid vectors and/or expression vectors, comprising the disclosed synthetic DNA sequences.

[0012] Also disclosed herein are recombinant cells comprising a host cell, e.g., a microbial cell, comprising a disclosed DNA construct for production of at least one disclosed polyhydroxyalkanoate and at least one indigoid derivative.

[0013] Also disclosed herein are processes for co-production of at least one disclosed polyhydroxyalkanoate and at least one indigoid derivative, the process comprising culturing a disclosed recombinant cell in a culture medium comprising at least tryptophan analogue and at least one sugar.

[0014] Also disclosed herein are processes for purification of at least one disclosed polyhydroxyalkanoate and at least one indigoid derivative produced using a disclosed process comprising culturing a disclosed recombinant cell in a culture medium comprising at least tryptophan analogue and at least one sugar

[0015] Also disclosed hheerreeiinn are products comprising at least one disclosed polyhydroxyalkanoate and at least one indigoid derivative produced by the disclosed processes.

[0016] Other systems, methods, features, and advantages of the present disclosure will be or become apparent to one with skill in the art upon examination of the following drawings and detailed description. It is intended that all such additional systems, methods, features, and advantages be included within this description, be within the scope of the present disclosure, and be protected by the accompanying claims. In addition, all optional and preferred features and modifications of the described aspects are usable in all aspects of the disclosure taught herein. Furthermore, the individual features of the dependent claims, as well as all optional and preferred features and modifications of the described aspects are combinable and interchangeable with one another.

BRIEF DESCRIPTION OF THE DRAWINGS

[0017] Many aspects of the present disclosure can be better understood with reference to the following drawings. The components in the drawings are not necessarily to scale, emphasis instead being placed upon clearly illustrating the principles of the present disclosure. Moreover, in the drawings, like reference numerals designate corresponding parts throughout the several views.

[0018] FIG. 1 shows a representative schematic depiction of biosynthetic pathways functioning in a cell, e.g., a bacterial cell, that comprises a disclosed synthetic DNA construct that provides for coproduction of PHAs and indigoid derivatives.

[0019] FIGs. 2A-3B show representative schematic depiction of disclosed synthetic DNA constructs. FIG. 2A shows a representative schematic depiction of a disclosed DNA construct. FIG. 2B representative schematic depiction a disclosed plasmid vector, pPHBIue plasmid, showing the direction and placement of various components of the disclosed plasmid vector.

[0020] FIGs. 3A-3B show representative data for macroelements and microelements found in representative whey compositions prior to further processing. FIG. 3A shows macroelements determined in the indicated whey compositions. FIG. 3B shows macroelements determined in the indicated whey compositions.

[0021] FIG. 4 shows representative data for carbon to nitrogen ratios in different whey compositions prior to further processing.

[0022] FIGs. 5A-5B show representative data for macroelements and microelements found in representative whey compositions after further processing. FIG. 5A shows macroelements determined in the indicated whey compositions after processing. FIG. SB shows macroelements determined in the indicated whey compositions after processing.

[0023] FIG. 6 shows representative data for carbon to nitrogen ratios in different whey compositions after further processing.

[0024] FIG. 7 shows representative data of a disclosed PHB-indigo composition compared to a PHB standard. The disclosed PHB-indigo composition was prepared using the disclosed processes.

[0025] FIG. 8 shows a representative photographic image of a disclosed PHB-indigo composition cast as a film.

[0026] FIGs. 9A-9F show representative scanning electron microscopy (SEM) images and elemental analysis of a PHB-indigo composition cast as a film such as shown in FIG. 8. FIG. 9A shows a representative scanning electron microscopy image of a PHB-indigo composition cast as a film such as shown in FIG. 8 (at SEM conditions as shown below the image). FIG. 9B shows a representative scanning electron microscopy image of a PHB- indigo composition cast as a film such as shown in FIG. 8 (at SEM conditions as shown below the image). FIG. 9C shows a representative scanning electron microscopy image of a PHB-indigo composition cast as a film such as shown in FIG. 8 (at SEM conditions as shown below the image). FIG. 9D shows carbon elemental analysis of a PHB-indigo composition cast as a film such as shown in FIG. 8. FIG. 9E shows nitrogen elemental analysis of a PHB- indigo composition cast as a film such as shown in FIG. 8. FIG. 9F shows oxygen elemental analysis of a PHB-indigo composition cast as a film such as shown in FIG. 8. Quantitation of the elemental analysis in FIGs. 9D-9F determined that the film was 74.61 wt% carbon; 2.23 wt% nitrogen; and 23.16 wt% oxygen.

[0027] Additional advantages of the disclosure will be set forth in part in the description which follows, and in part will be obvious from the description, or can be learned by practice of the disclosure. The advantages of the disclosure will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the disclosure, as claimed.

DETAILED DESCRIPTION

[0028] Before the present compounds, compositions, articles, devices, and/or methods are disclosed and described, it is to be understood that the aspects described below are not limited to specific compounds, synthetic methods, or uses, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and is not intended to be limiting.

[0029] In this specification and in the claims that follow, reference will be made to a number of terms that shall be defined to have the following meanings:

[0030] It must be noted that, as used in the specification and the appended claims, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a surfactant" includes mixtures of two or more such surfactants, and the like.

[0031] "Optional" or "optionally" means that the subsequently described event or circumstance can or cannot occur, and that the description includes instances where the event or circumstance occurs and instances where it does not. For example, the phrase "optionally includes a reporter protein" means that the reporter protein can or can not be present.

[0032] Ranges can be expressed herein as from "about" one particular value, and/or to "about" another particular value. Wien such a range is expressed, another aspect includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent "about," it will be understood that the particular value forms another aspect. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint.

[0033] Disclosed are materials and components that can be used for, can be used in conjunction with, can be used in preparation for, or are products of the disclosed compositions and methods. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combination and permutation of these compounds can not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a bacterium is disclosed and discussed and a number of different compatible bacterial plasmids are discussed, each and every combination and permutation of bacterium and bacterial plasmid that are possible are specifically contemplated unless specifically indicated to the contrary. For example, if a class of molecules A, B, and C are disclosed as well as a class of molecules D, E, and F and an example of a combination molecule, A-D is disclosed, then even if each is not individually recited, each is individually and collectively contemplated. Thus, in this example, each of the combinations A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C-F are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. Likewise, any subset or combination of these is also specifically contemplated and disclosed. Thus, for example, the sub-group of A-E, B-F, and C-E are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. This concept applies to all aspects of this disclosure including, but not limited to, steps in methods of making and using the disclosed compositions. Thus, if there are a variety of additional steps that can be performed it is understood that each of these additional steps can be performed with any specific aspect or combination of aspects of the disclosed methods, and that each such combination is specifically contemplated and should be considered disclosed.

I. Overview

[0034] Described herein are DNA constructs containing genes for co-production of polyhydroxyalkanoates (PHAs), a class of biodegradable polyesters, and indigoid dyes, in bacteria. Also described herein are microbial cells transformed with a DNA construct containing genes for co-producing PHAs and indigoid dyes. Methods for co-producing PHAs and indigoid dyes using transformed bacteria are also described herein.

[0035] The DNA constructs, transformed bacteria, and methods described herein provide for the sustainable production of dyed biopolymers using waste sources of protein and sugar. This will allow both the raw material costs and the downstream processing costs to be significantly reduced.

[0036] Described herein is a process for producing PHAs and indigoid dyes using microbial cells that includes (a) making a DMA construct containing genes for mFMO and pha CAB, (b) introducing the DMA construct into host microbial cells via transformation or transfection, and (c) culturing the microbial host cells to co-produce MFAs and indigoid dyes.

II. Polyhydroxyalkanoate Polymers

[0037] In various aspects, tthhee present disclosure relates to at least one polyhydroxyalkanoate that is produced using the disclosed processes, e.g., processes comprising use of disclosed recombinant cells comprising disclosed DNA constructs comprising disclosed synthetic DNA sequences. In aa further aspect, the polyhydroxyalkanoate is co-produced with an indigoid dye using the disclosed processes.

[0038] In a further aspect, the present disclosure pertains to polyhydroxyalkanoates (PHAs) co-produced in a host cell, e.g., a microbial cell, with an indigoid dye. PHAs are polyesters that be further classified as thermoplastic or elastomeric polymeric materials depending on their composition and structure. In various aspects, elastomeric means the disclosed polyhydroxyalkanoate behaves at room temperature as elastomers, i.e., providing a minimum elongation at break of 50%.

[0039] In a further aspect, PHAs of the present disclosure can be a compound having a structure represented by the formula:

wherein R is an alkyl group wherein the alkyl group is a C1-C50 alkyl group and wherein each of n is an integer such that the molecular weight of the PHA is from about 100 to about 1 ,000,000 KDa. In a still further aspect, PHAs of the present disclosure can be a compound having a structure represented by the formula:

wherein R is -(CH₂)_m-CH₃ or hydrogen; wherein each of m and n are integers such that the molecular weight of the PHA is from about 100 to about 1 ,000,000 KDa. In a yet further aspect, PHAs of the present disclosure can be a compound having a structure represented by the formula:

wherein each of m and n are integers such that the molecular weight of the PHA is from about 100 to about 1 ,000,000 KDa. In a still further aspect, PHAs of the present disclosure can be a compound having a structure represented by the formula:

wherein n is an integer such that the molecular weight of the PHA is from about 100 to about 1 ,000,000 KDa.

[0040] In aa ffuurrtthheerr aspect, tthhee present ddiisscclloossuurree pertains to modified polyhydroxyalkanoates (PHAs) co-produced in a host cell, e.g., a microbial cell, with an indigoid dye, wherein the PHA is modified within the cell.

[0041] In a ffuurrtthheerr aspect, the present ddiisscclloossuurree pertains to modified polyhydroxyalkanoates (PHAs) co-produced in a host cell, e.g., a microbial cell, with an indigoid dye, wherein the PHA is chemically modified following isolation from the ceils.

[0042] In a further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, and 10, wherein if m is 0, then the -(CH₂)_m- CH₃ group is -CH₃. In a still further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , 2, 3, 4, 5, 6, 7, 8, and 9, wherein if m is 0, then the -(CH₂)_m-CH₃ group is -CH₃. In a yet further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , 2, 3, 4, 5, 6, 7, and 8, wherein if m is 0, then the -(CH₂)_m-CH₃ group is -CH₃. In an even further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , 2, 3, 4, 5, 6, and 7, wherein if m is 0, then the -(CH₂)m-CH₃ group is -CH₃. In a still further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , 2, 3, 4, 5, and 6, wherein if m is 0, then the -(CH₂)_m-CH₃ group is -CH₃. In a yet further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , 2, 3, 4, and 5, wherein if m is 0, then the -(CH₂)m-CH₃ group is -CH₃. In an even further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , 2, 3, and 4, wherein if m is 0, then the -(CH₂)_m-CH₃ group is -CH₃. In a still further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , 2, and 3, wherein if m is 0, then the -(CH₂)m-CH₃ group is -CH₃. in a yet further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0, 1 , and 2, wherein if m is 0, then the - (CH₂)_m-CH₃ group is -CH₃. In an even further aspect, the PHA as disclosed herein above, as appropriate, m is an integer selected from 0 and 1 , wherein if m is 0, then the -(CH₂)_m- CH₃ group is -CH₃.

[0043] In a further aspect, the PHA as disclosed herein above, n is an integer selected from 1 , 2, 3, 4, 5, 6, 7, 8, 9, and 10. In a stili further aspect, the PHA as disclosed herein above, n is an integer selected from 1 , 2, 3, 4, 5, 6, 7, 8, and 9. In a yet further aspect, the PHA as disclosed herein above, n is an integer selected from 1 , 2, 3, 4, 5, 6, 7, and 8. In an even further aspect, the PHA as disclosed herein above, n is an integer selected from 1 , 2, 3, 4, 5, 6, and 7. In a still further aspect, the PHA as disclosed herein above, n is an integer selected from 1 , 2, 3, 4, 5, and 6. In a yet further aspect, the PHA as disclosed herein above, n is an integer selected from 1 , 2, 3, 4, and 5. In an even further aspect, the PHA as disclosed herein above, n is an integer selected from 1 , 2, 3, and 4. In a still further aspect, the PHA as disclosed herein above, n is an integer selected from 1 , 2, and 3 In a yet further aspect, the PHA as disclosed herein above, n is an integer selected from 1 and 2. lii. Indigoid Dyes

[0044] In various aspects, the present disclosure relates to at least one indigo dye, i.e., an indigoid dye, that is produced using the disclosed processes, e.g., processes comprising use of disclosed recombinant cells comprising disclosed DNA constructs comprising disclosed synthetic DNA sequences.

[0045] In a further aspect, the indigoid dye of the present disclosure comprises at least one compound selected from a compound having a structure represented by a formula:

and combinations thereof.

[0046] In a further aspect, the indigoid dye of the present disclosure comprises a compound having a structure represented by a formula:

IV. DNA Constructs

[0047] DNA constructs are provided herein for the co-production of PHAs and indigoid dyes. It is understood that one way to define the variants and derivatives of the genetic components and DNA constructs described herein is in terms of homology/identity to specific known sequences. Those of skill in the art readily understand how to determine the homology of two nucleic acids. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level. Another way of calculating homology can be performed according to published algorithms (see Zuker, M. Science 244:48-52, 1989; Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989; Jaeger et al. Methods Enzymol. 183:281-306, 1989, which are herein incorporated by reference for at least material related to nucleic acid alignment).

[0048] As used herein, "conservative" mutations are mutations that result in an amino acid change in the protein produced from a sequence of DNA. When a conservative mutation occurs, the new amino acid has similar properties as the wild type amino acid and generally does not drastically change the function or folding of the protein (e.g., switching isoleucine for valine is a conservative mutation since both are small, branched, hydrophobic amino acids). "Silent mutations," meanwhile, change the nucleic acid sequence of a gene encoding a protein but do not change the amino acid sequence of the protein.

[0049] It is understood that the description of mutations and homology can be combined together in any combination, such as aspects that have at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% homology to a particular sequence wherein the variants are conservative or silent mutations. It is understood that any of the sequences described herein can be a variant or derivative having the homology values listed above.

[0050] In a further aspect, a database such as, for example, GenBank, can be used to determine the sequences of genes and/or regulatory regions of interest, the species from which these elements originate, and related homologous sequences.

[0051] In a further aspect, the microorganisms are fungi or bacteria. In a further aspect, the fungi are yeasts such as, for example, Saccharomyces cerevisiae. In another aspect, the bacteria are Escherichia coli. In a further aspect, the DNA construct is incorporated as part of a vector for transfection into microbial cells. In a further aspect, the vector is a plasmid, a phagemid, a cosmid, a yeast artificial chromosome, a bacterial artificial chromosome, a virus, a phage, or a transposon.

[0052] Vectors capable of high levels of expression of recombinant genes and proteins are well known in the art. Vectors useful for the transformation of a variety of host cells are common and commercially available and include, for example, pWLneo, pSV2cat, pOG44, pXT1 , pSG, pSVK3, pBSK, pBR322, pYES, pYES2, pBSKII, pUC, pUC19, and pETDuet-1. The skilled practitioner will be able to choose a plasmid based on such factors as a) the amount of nucleic acid (i.e., number of genes and other elements) to be inserted, b) the host organism, c) culture conditions for the host organism, and other related factors.

[0053] In a further aspect, provided herein is a DNA construct comprising the following genetic components: a) a gene that expresses mFMO, a flavin-dependent monooxygenase; and b) one or more pha genes, e.g., selected from phaA, phaB, and phaC, or a homologue thereof.

Each component of the DNA construct is described in detail beiow.

[0054] In a further aspect, provided herein is a DNA construct comprising the following genetic components: c) a gene that expresses mFMO, a flavin-dependent monooxygenase from

Methylphaga sp. SK1 ; and d) one or more pha genes, e.g., selected from phaA, phaB, and phaC from Cupriavidus necator H16.

Each component of the DNA construct is described in detail beiow.

[0055] In a further aspect, the nucleic acids (e.g., genes that express mFMO or phaCAB used in the DNA constructs described herein can be amplified using polymerase chain reaction (FOR) prior to being ligated into a plasmid or other vector. Typically, PCR- ampiification techniques make uussee of primers, or short, chemically-synthesized oligonucleotides are complementary to regions on each respective strand flanking the DNA or nucleotide sequence to be amplified. A person having ordinary skill in the art will be able to design or choose primers based on the desired experimental conditions. In general, primers should be designed to provide for both efficient and faithful replication of the target nucleic acids. Two primers are required for the amplification of each gene, one for the sense strand (that is, the strand containing the gene of interest) and one for the antisense strand (that is, the strand complementary to the gene of interest). Pairs of primers should have similar melting temperatures that are close to the PCR reaction's annealing temperature. In order to facilitate the PCR reaction, the following features should be avoided in primers: mononucleotide repeats, complementarity with other primers in the mixture, selfcomplementarity, and internal hairpins and/or loops. Methods of primer design are known in the art; additionally, computer programs exist that can assist the skilled practitioner with primer design. Primers can optionally incorporate restriction enzyme recognition sites at their 5' ends to assist in later ligation into plasmids or other vectors.

[0056] PCR can be carried out using purified DNA, unpurified DNA that is integrated into a vector, or unpurified genomic DNA. The process for amplifying target DNA using PCR consists of introducing an excess of two primers having the characteristics described above to a mixture containing the sequence to be amplified, followed by a series of thermal cycles in the presence of a heat-tolerant or thermophilic DNA polymerase, such as, for example, any of Taq, Pfu, Pwo, Tfl, rTth, Tli, or Tma polymerases. A PCR "cycle" involves denaturation of the DNA through heating, followed by annealing of the primers to the target DNA, followed by extension of the primers using the thermophilic DNA polymerase and a supply of deoxynucleotide triphosphates (i.e., dCTP, dATP, dGTP, and TTP), along with buffers, salts, and other reagents as needed. In a further aspect, the DNA segments created by primer extension during the PCR process can serve as templates for additional PCR cycles. Many PCR cycles can be performed to generate a large concentration of target DNA or gene. PCR can optionally be performed in a device or machine with programmable temperature cycles for denaturation, annealing, and extension steps.

[0057] Further, PCR can be performed on multiple genes simultaneously in the same reaction vessel or microcentrifuge tube since the primers chosen will be specific to selected genes. PCR products can be purified by techniques known in the art such as, for example, gel electrophoresis followed by extraction from the gel using commercial kits and reagents.

[0058] In a further aspect, the plasmid can include an origin of replication, allowing it to use the cell's replication machinery to create copies of itself.

[0059] As used herein, "operably linked" refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one affects the function of another. For example, if sequences for multiple genes are inserted into a single plasmid, their expression can be operably linked. Alternatively, a promoter is said to be operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence.

[0060] As used herein, "expression" refers to transcription and/or accumulation of an mRNA derived from a gene or DNA fragment. Expression can also be used to refer to translation of mRNA into a peptide, polypeptide, or protein.

[0061] In a further aspect, the gene that expresses mFMO is isolated from Methylphaga sp. SK1. in a further aspect, the gene that expresses flavin-monooxygenase has the sequence shown beiow, or at least 70% homology thereof, at least 75% homology thereof, at least 80% homology thereof, at least 85% homology thereof, at least 90% homology thereof, or at least 95% homology thereof.

[0062] Other sequences expressing mFMO or related or homologous genes can be identified in a database such as, for example, GenBank.

[0063] In a further aspect, the genes that express pha (phaCAB) are isolated from Cupriavidus necator H16. In a further aspect, the pha genes have the sequences shown below, or at least 70% homology thereof. In a further aspect, the genes that express pha CAB have the sequences shown below or at least 70% homology thereof, at least 75% homology thereof, at least 80% homology thereof, at least 85% homology thereof, at least 90% homology thereof, or at least 95% homology thereof.

[0064] Other sequences expressing phaCAB or related or homologous genes can be identified in a database such as, for example, GenBank. In a further aspect, sequences useful herein include those with the Gl numbers listed below.

[0065] In another aspect, said construct further includes d) a promoter, e) a terminator or stop sequence, f) a gene that allows for selection upon transformation or transfection of a cell, e.g., confers resistance to an antibiotic (a "selective marker"), g) a reporter protein, or a combination thereof.

[0066] In another aspect, the DNA construct has the following genetic components: (1) a promoter, (2) a gene that mFMO, (3) a gene that expresses phaCAB, and (4) a terminator or stop sequence.

[0067] In a further aspect, the regulatory sequence is already incorporated into a vector such as, for example, a plasmid, prior to genetic manipulation of the vector. In another aspect, the regulatory sequence can be incorporated into the vector through the use of restriction enzymes or any other technique known in the art.

[0068] In a further aspect, the regulatory sequence is an operon such as, for example, the LAC operon. As used herein, an "operon" is a segment of DNA containing a group of genes wherein the group is controlled by a single promoter. Genes included in an operon are all transcribed together. In a further aspect, the operon is a LAC operon and can be induced when lactose crosses the cell membrane.

[0069] In a further aspect, the regulatory sequence is a promoter. The term "promoter" refers to a DNA sequence capable of controlling the expression of a coding sequence. In a further aspect, the coding sequence to be controlled is located 3’ to the promoter. In another aspect, the promoter is derived from a native gene. In an alternative aspect, the promoter is composed of multiple elements derived from different genes and/or promoters. A promoter can be assembled from elements found in nature, from artificial and/or synthetic elements, or from a combination thereof. It is understood by those skilled in the art that different promoters can direct the expression of a gene in different tissues or cell types, at different stages of development, in response to different environmental or physiological conditions, and/or in different species. In a further aspect, the promoter functions as a switch to activate the expression of a gene.

[0070] In a further aspect, the promoter is "constitutive." A constitutive promoter is a promoter that causes a gene to be expressed in most cell types at most times. In another aspect, the promoter is "regulated." A regulated promoter is a promoter that becomes active in response to a specific stimulus. A promoter can be regulated chemically, such as, for example, in response to the presence or absence of a particular metabolite (e.g., lactose or tryptophan), a metal ion, a molecule secreted by a pathogen, or the like. A promoter also can be regulated physically, such as, for example, in response to heat, cold, water stress, salt stress, oxygen concentration, illumination, wounding, or the like.

[0071] Promoters that are useful to drive expression of the nucleotide sequences described herein are numerous and familiar to those skilled in the art. Suitable promoters include, but are not limited to, the following: T3 promoter, T7 promoter, an iron promoter, and GAL1 promoter. In a further aspect, the promoter has the sequence shown below or at least 70% homology thereof of the plasmid pYES2. Variants of these promoters are also contemplated. The skilled artisan will be able to use site-directed mutagenesis and/or other mutagenesis techniques to modify the promoters to promote more efficient function. The promoter can be positioned, for example, from 10-100 nucleotides of a ribosomal binding site. In a further aspect, the promoter can be native to the vectors described herein. In another aspect, the promoter is positioned before the gene that expresses lipase, cellulose synthase, galactomannan galactosyltransferase, or a combination thereof.

[0072] In another aspect, the regulatory sequence is a terminator or stop sequence. As used herein, a terminator is a sequence of DNA that marks the end of a gene or operon to be transcribed. In a further aspect, the terminator is an intrinsic terminator or a Rho- dependent transcription terminator. As used herein, an intrinsic terminator is a sequence wherein a hairpin structure can form in the nascent transcript that disrupts the mRNA/DNA/RNA polymerase complex. As used herein, a Rho-dependent transcription terminator requires a Rho factor protein complex to disrupt the mRNA/DNA/RNA polymerase complex. In a further aspect, the terminator is a T7 terminator.

[0073] In a further aspect, the regulatory sequence includes both a promoter and a terminator or stop sequence. In a still further aspect, the regulatory sequence can include multiple promoters or terminators. Other regulatory elements, such as enhancers, are also contemplated. Enhancers can be located from about 1 to about 2000 nucleotides in the 5' direction from the start codon of the DNA to be transcribed, or can be located 3' to the DNA to be transcribed. Enhancers can be "cis-acting," that is, located on the same molecule of DNA as the gene whose expression they affect.

[0074] In another aspect, the vector contains one or more ribosomal binding sites. As used herein, a "ribosomal binding site" is a sequence of nucleotides located 5* to the start codon of an mRNA that recruits a ribosome to initiate protein translation. In a further aspect, the ribosomal binding site can be positioned before any or all genes in a DNA construct, or a before a subset of genes in a DNA construct.

[0075] In a further aspect, when the vector is a plasmid, the plasmid can also contain a multiple cloning site or polylinker. In a further aspect, the polylinker contains recognition sites for multiple restriction enzymes. The polylinker can contain up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, or more than 20 recognition sites for restriction enzymes. Further, restriction sites can be added, disabled, or removed as required, using techniques known in the art. In a further aspect, the plasmid contains restriction sites for any known restriction enzyme such as, for example, Hindlll, Kpnl, Sacl, BamHI, BstXI, EcoRI, BsaBI, Notl, Xhol, Sphl, Xbal, Apal, Sall, Clal, EcoRV, Pstl, Smal, Xmal, Spel, Eagl, Sacll, or any combination thereof. In a further aspect, the plasmid contains more than one recognition site for the same restriction enzyme.

[0076] In a further aspect, the restriction enzyme can cleave DNA at a palindromic or an asymmetrical restriction site. In a further aspect, the restriction enzyme cleaves DNA to leave blunt ends; in an alternative aspect, the restriction enzyme cleaves DNA to leave "sticky" or overhanging ends. In another aspect, the enzyme can cleave DNA a distance of from 20 bases to over 1000 bases away from the restriction site. A variety of restriction enzymes are commercially available and their recognition sequences, as well as instructions for use (e.g. amount of DNA needed, precise volumes of reagents, purification techniques, as well as information about salt concentration, pH, optimum temperature, incubation time, and the like) are provided by enzyme manufacturers.

[0077] In a further aspect, a plasmid with a polylinker containing one or more restriction sites can be digested with one restriction enzyme and a nucleotide sequence of interested can be ligated into the plasmid using a commercially-available DNA ligase enzyme. Several such enzymes are available, often as kits containing all reagents and instructions required for use. In another aspect, a plasmid with a polylinker containing two or more restriction sites can be simultaneously digested with two restriction enzymes and a nucleotide sequence of interest can be ligated into the plasmid using a DNA ligase enzyme. Using two restriction enzymes provides an asymmetric cut in the DNA, allowing for insertion of a nucleotide sequence of interest in a particular direction and/or on a particular strand of the double-stranded plasmid. Since RNA synthesis from a DNA template proceeds from 5' to 3', usually starting just after a promoter, the order and direction of elements inserted into a plasmid can be especially important. If a plasmid is to be simultaneously digested with multiple restriction enzymes, these enzymes must be compatible in terms of buffer, salt concentration, and other incubation parameters.

[0078] In some aspects, prior to ligation using a ligase enzyme, a plasmid that has been digested with a restriction enzyme is treated with an alkaline phosphatase enzyme to remove 5' terminal phosphate groups. This prevents self-ligation of the plasmid and thus facilitates ligation of heterologous nucleotide fragments into the plasmid.

[0079] In a further aspect, different genes can be ligated into a plasmid in one spot. In this aspect, the genes will first be digested with restriction enzymes. In certain aspects, the digestion of genes with restriction enzymes provides multiple pairs of matching 5' and 3' overhangs that will spontaneously assemble the genes in the desired order. In another aspect, the genes and components to be incorporated into a plasmid can be assembled into a single insert sequence prior to insertion into the plasmid. In a further aspect, a DNA ligase enzyme can be used to assist in the ligation process.

[0080] In another aspect, the ligation mix can be incubated in an electromagnetic chamber. In a further aspect, this incubation lasts for about 1 minute, about 2 minutes, about 5 minutes, about 10 minutes, about 15 minutes, about 20 minutes, about 30 minutes, or about 1 hour.

[0081] The DNA construct described herein can be part of a vector. In general, plasmid vectors containing replicon and control sequences that are derived from species compatible with the cell are used in connection with the hosts. The vector ordinarily carries a replication site as well as marking sequences that are capable of performing phenotypic selection in transformed cells. Plasmid vectors are well known and are commercially available. Such vectors include, but are not limited to, pWLneo, pSV2cat, pOG44, pXT1 , pSG (Strategene), pSVK3, pBSK, pBR322, pYES, pYES2, pBSKII, pUC, pUC19, and pETDuet-1 vectors.

[0082] Plasmids are double-stranded, autonomously-replicating, genetic elements that are not integrated into host cell chromosomes. Further, these genetic elements are usually not part of the cell's central metabolism. In bacteria, plasmids can range from 1 kilobase (kb) to over 200 kb. Plasmids can be engineered to encode a number of useful traits including the production of secondary metabolites, antibiotic resistance, the production of useful proteins, degradation of complex molecules and/or environmental toxins, and others. Plasmids have been the subject of much research in the field of genetic engineering, as plasmids are convenient expression vectors for foreign DNA in, for example, microorganisms. Plasmids generally contain regulatory elements such as promoters and terminators and also usually have independent replication origins. Ideally, plasmids will be present in multiple copies per host cell and can contain selectable markers (such as genes for antibiotic resistance) to allow the skilled artisan to select host cells that have been successfully transfected with the plasmids (for example, by growing the cells in a medium containing the antibiotic).

[0083] In certain aspects, the DNA construct includes a ribosomal binding site. In a further aspect, the ribosomal binding site in the DNA construct is AGGAGG or a derivative or variant thereof. In a further aspect, the ribosomal binding site is native to the vector used herein. In certain aspects, when the DNA construct further includes a ribosomal switch.

[0084] In another aspect, the DNA construct includes a terminator. In a further aspect, the terminator in the DNA construct is a known stop codon (TAA, TAG, TGA) or a derivative or variant thereof. In a further aspect, the terminator is native to the vector in which the DNA construct is incorporated. A terminator can be positioned after the mFMO gene, after the phaCAB genes, or both, from 5' to 3'.

[0085] In a further aspect, the vector encodes a selection marker. In a further aspect, the selection marker is a gene that confers resistance to an antibiotic. In certain aspects, during fermentation of host cells transformed with the vector, the cells are contacted with the antibiotic. For example, the antibiotic can be included in the culture medium. Cells that have not been successfully transformed cannot survive in the presence of the antibiotic; only cells containing the vector which confers antibiotic resistance can survive. Optimally, only cells containing the vector to be expressed will be cultured, as this will result in the highest production efficiency of the desired gene products (e.g., peptides). Cells that do not contain the vector would otherwise compete with transformed cells for resources. In a further aspect, the antibiotic is tetracycline, neomycin, kanamycin, ampicillin, hygromycin, chloramphenicol, amphotericin B, bacitracin, carbapenam, cephalosporin, ethambutol, fluoroquinolones, isonizid, methicillin, oxacillin, vancomycin, streptomycin, quinolines, rifampin, rifampicin, sulfonamides, cephalothin, erythromycin, spectinomycin, gentamycin, penicillin, other commonly-used antibiotics, or a combination thereof.

[0086] In certain aspects, the DNA construct can include a gene that expresses a reporter protein. The selection of the reporter protein can vary. For example, the reporter protein can be a yellow fluorescent protein, a red fluorescent protein, a green fluorescent protein, or a cyan fluorescent protein. The amount of fluorescence that is produced by the transformed cell can be correlated to the amount of DNA incorporated into the plant cells. The fluorescence produced by the transformed cell can be detected and quantified using techniques known in the art. For example, spectrofluorometers are typically used to measure fluorescence.

[0087] FIG. 2 provides a non-limiting example of a DNA construct as described herein. In this aspect, the construct is a plasmid having from 5* to 3' the following genetic components in the following order: (a) a promoter; (b) a gene that expresses mFMO; (c) an operon including the phaCAB genes; (d) a terminator or stop codon. Promoters and terminators are sourced from the Anderson promoters collection (http://parts.igem.org/Promoters/Catalog/Anderson). Suitable promoters include, but are not limited to, BBa_J23100 and BBa_J23119; suitable terminators include DT10 and U10 (BBa_1006).

[0088] In another aspect, the construct is a plasmid having from 5' to 3' the following genetic components in the following order: (a) a promoter; (b) a first ribosomal binding site; (c) a gene that expresses mFMO; (d) a terminator; (e) a promoter; (f) a second ribosomal binding site; (g) a gene that expresses phaC; (h) a third ribosomal binding site; (i) a gene that expresses phaA; (j) a fourth ribosomal binding site; (k) a gene that expresses phaB; and (I) a terminator.

[0089] In another aspect, the construct is a plasmid having from 5' to 3' the following genetic components in the following order: (a) a promoter having a promoter sequence shown below or at least 70% homology thereto; (b) a first ribosomal binding site; (c) a gene that expresses mFMO having the sequence shown below or at least 70% homology thereto; (d) a terminator or stop codon; (e) a promoter having the sequence shown below or at least 70% homology thereto; (f) a second ribosomal binding site; (g) a gene that expresses phaC having the sequence shown below or at least 70% homology thereto; (h) a third ribosomal binding site; (i) a gene that expresses phaA having the sequence shown below or at least 70% homology thereto; (j) a fourth ribosomal binding site; (k) a gene that expresses phaB having the sequence shown below or at least 70% homology thereto; and (I) a terminator or stop codon.

[0090] Exemplary methods for producing the DNA constructs described herein are provided in the Examples. Restriction enzymes and purification techniques known in the art can be used to assemble the DNA constructs. Backbone plasmids and synthetic inserts can be mixed together for ligation purposes at different ratios ranging from 1 :1 , 1 :2, 1 :3, 1 :4, and up to 1 :5. In a further aspect, the ratio of backbone plasmid to synthetic insert is 1 :4. After the vector comprising the DNA construct has been produced, the resulting vector can be incorporated into the cells using the methods described below.

V. Transformed Celis

[0091] In a further aspect, a "transformed cell" is formed when a microbial cell is transfected with the DNA construct described herein, in a further aspect, the DNA construct is carried by the expression vector into a cell and is separate from the cell's genome. In another aspect, the DNA construct is incorporated into the cell's genome. In still another aspect, incorporation of the DNA construct into the cell enables the cell to produce carbo sugars. "Heterologous" genes and proteins are genes and proteins that have been experimentally inserted into a cell that are not normally expressed by that cell. A heterologous gene can be cloned or derived from a different cell type or species than the recipient cell or organism. Heterologous genes can be introduced into cells by transduction or transformation.

[0092] An "isolated" nucleic acid is one that has been separated from other nucleic acid molecules and/or cellular material (peptides, proteins, lipids, saccharides, and the like) normally present in the natural source of the nucleic acid. An "isolated" nucleic acid can optionally be free of the flanking sequences found on either side of the nucleic acid as it naturally occurs. An isolated nucleic acid can be naturally occurring, can be chemically synthesized, or can be a cDNA molecule (i.e., is synthesized from an mRNA template using reverse transcriptase and DNA polymerase enzymes).

[0093] "Transformation" or "transfection" as used herein refers to a process for introducing heterologous DNA into a host cell. Transformation can occur under natural conditions or can be induced using various methods known in the art. Many methods for transformation are known in the art and the skilled practitioner will know how to choose the best transformation method based on the type of ceils being transformed. Methods for transformation include, for example, viral infection, electroporation, lipofection, chemical transformation, and particle bombardment. Cells can be stably transformed (i.e., the heterologous DNA is capable of replicating as an autonomous piasmid or as part of the host chromosome) or can be transiently transformed (i.e., the heterologous DNA is expressed only for a limited period of time).

[0094] "Competent cells" refers to microbial cells capable of taking up heterologous DNA. Competent cells can be purchased from a commercial source, or cells can be made competent using procedures known in the art.

[0095] The cells as referred to herein include their progeny, which are any and all subsequent generations formed by ceil division. It is understood that not all progeny can be identical due to deliberate or inadvertent mutations. A host cell can be "transfected" or

"transformed," which refers to a process by which exogenous nucleic acid is transferred or introduced into the cell.

[0096] A transformed cell includes the primary subject cell and its progeny. The cells can be naturally-occurring cells or "recombinant" cells. Recombinant cells are distinguishable from naturally-occurring cells in that naturally-occurring cells do not contain heterologous DNA introduced through molecular cloning procedures. In a further aspect, the cell is a prokaryotic cell such as, for example, Escherichia coli. In other aspects, the cell is a eukaryotic ceil such as, for example, the yeast Saccharomyces cerevisiae.

[0097] The DNA construct is first delivered into the cell. In a further aspect, the cells are naturally competent (i.e., able to take up exogenous DNA from the surrounding environment). In another aspect, cells must be treated to induce artificial competence. This delivery can be accomplished in vitro, using well-developed laboratory procedures for transforming cell lines. Transformation of bacterial cell lines can be achieved using a variety of techniques. One method involves calcium chloride. The exposure to the calcium ions renders the cells able to take up the DNA construct. Another method is electroporation. In this technique, a high-voltage electric field is applied briefly to cells, producing transient holes in the membranes of the cells through which the vector containing the DNA construct enters. Another method involves exposing intact yeast cells to alkali cations such as, for example, lithium. In a further aspect, this method includes exposing yeast to lithium acetate, polyethylene glycol, and single-stranded DNA such as, for example, salmon sperm DNA. Without wishing to be bound by theory, the single-stranded DNA is thought to bind to the cell wall of the yeast, thereby blocking plasmids from binding. The plasmids are then free to enter the yeast cell. Enzymatic and/or electromagnetic techniques can also be used alone, or in combination with other methods, to transform microbial cells. Exemplary procedures for transforming yeast and bacteria with specific DNA constructs are provided in the Examples. In certain aspects, two or more types of DNA can be incorporated into the cells. Thus, different metabolites can be produced from the same host cells at enhanced rates.

VI. Methods for Co-Preparation of PHAs and Indigoid Dyes

[0098] The transformed cell described herein are useful in methods for the co-production of at least one PHA and at least one indigoid dye. Once the DNA construct has been incorporated into a cell, e.g., by cell transformation or transfection techniques as known to the skilled artisan and/or described herein, the cells are cultured such that the cells multiply. A satisfactory microbiological culture contains available sources of hydrogen donors and acceptors, carbon, nitrogen, sulfur, phosphorus, inorganic salts, and, in certain cases, vitamins or other growth-promoting substances. For example, the addition of peptone provides a readily-available source of nitrogen and carbon. Furthermore, the use of different types of media results in different growth rates and different stationary phase densities; stationary phase is where secondary metabolite production occurs most frequently. A rich media results in a short doubling time and higher cell density at a stationary phase. Minimal media results in slow growth and low final cell densities. Efficient agitation and aeration increase final cell densities.

[0099] In a further aspect, the culture medium can contain tryptophan. Tryptophan is one of the 20 essential amino acids, primarily used in the translation of proteins. However, tryptophan is also capable of being metabolized and used as a carbon source. Many bacteria possess this pathway, starting with the enzyme tryptophanase. This enzyme cleaves tryptophan, creating indole, pyruvate, and ammonium. In some aspects, pyruvate can be a source of carbon from tryptophan and is further transformed into acetyl-CoA to fuel cellular respiration (Fig. 1). Indole is a byproduct of this reaction, accumulating in the growth medium and acting as a signal molecule of this pathway. When a monooxygenase, e.g., an aromatic monooxygenase, is expressed by the ceil, indole undergoes rapid oxidation to form indoxyl, an oxidized intermediate. Indoxyl is highly reactive with itself and undergoes spontaneous dimerization to form indigoid dyes. Indigo is one dye that can be formed by this process. Indirubin, often referred to as Indigo Red, will also form as a result of non-selective oxidation of the 3^rd and 2^nd carbons of indole. As used herein the term “indigoid dyes" and “indigoid derivatives” will be understood to be interchangeable and include, but are not limited to, Indigo and Indigo Red.

[00100] It should be noted that although the culture medium can contain tryptophan, this culture medium tryptophan is distinct from tryptophan that a cell produces via a biosynthetic pathway within the cell, included tryptophan biosynthetically produced in a cell via a pathway engineered into the cell as described herein.

[00101] In a further aspect, the culture medium can comprise a by-product or waste stream from another production process. In a further aspect, the culture medium can comprise a byproduct or waste stream from a food production process, a fermentation process, and combinations thereof. In a still further aspect, by-product or waste stream from another production process can be a whey. In a yet further aspect, the culture medium can comprise whey. Whey is a byproduct of the milk processing and production of cheese, casein, and yogurt. Whey typically contains 5% lactose, as well as minerals and lactalbumin. Whey also contains tryptophan, in lactalbumin; if desired, a whey-based culture medium can be supplemented with tryptophan and/or other nutrients. [00102] Any suitable source of whey can be used. The term "whey" ordinarily means the liquid remaining after the removal of the casein and fat from miik. Whey can be made from a variety of sources, including, but not limited to, skim milk, whole milk or buttermilk, or obtained as a waste or by-product stream from production of cheese, yogurt, and other products. In a further aspect, a whey can be a whey protein concentrate, a milk permeate, a cheese whey solid, a soluble modified whey solid, a delactosed whey solid, an untreated whey, a pre-treated whey, a raw cheese whey, a raw sweet cheese whey, whey cakes, whey powder, pasteurized sweet whey, pasteurized acid whey, non-pasteurized acid whey, and the like.

[00103] In various aspects, the whey can be further treated prior to use in a culture medium, e.g., pH treated by treatment with a suitable acid or base to adjust the pH of the whey, followed by isolation and/or neutralization.

[00104] Milk Permeate is a by-product of the Milk Protein Concentrate (MPC) production process, formed after ultrafiltration of milk to extract protein and fat. Milk Permeate powder is typically at least 80% lactose, with 3% protein, 9% ash, and trace amount of fat. Milk permeate powder may readily be obtained from a variety of commercial suppliers, such as, for example, Idaho Milk Products, Jerome, Id. USA. Lactose, a disaccharide derived from galactose and glucose, is a commercially-available white crystalline powder isolated from fresh, sweet whey (Glanbia Nutritionals, Inc., Twin Falls, Id. USA). It is soluble, has a bland flavor, and is colorless in solution. For the purposes of the present invention, either milk permeate or lactose may be used. Whey protein concentrates (WPC) are made by drying the retentate from the ultrafiltration of whey. They are also commercially available, and may be obtained from a variety of commercial suppliers, e.g., WPC products produced by Glanbia Nutritionals, Inc., Twin Falls, Id. USA (Avonlac® WPC).

[00105] In a further aspect, the culture medium can contain in addition to a source of carbon - for example glucose or other carbon source as discussed herein - can also contain buffers, salts, yeast extract, corn steep liquor, milk, milk byproducts, or similar materials, in addition to proteins such as casein, p-lactoglobulin and a-lactalbumin, as well as non-milk proteins, or hydrolysates of proteins.

[00106] In a further aspect, host cells can be cultured or fermented by any method known in the art. The skilled practitioner will be able to select a culture medium based on the species and/or strain of host cell selected. In certain aspects, the culture medium can contain at least one carbon source. A variety of carbon sources are contemplated, including, but not limited to: monosaccharides such as galactose, glucose and fructose, disaccharides such as lactose or sucrose, oligosaccharides, polysaccharides such as starch, or mixtures thereof. Unpurified mixtures extracted from feedstocks are also contemplated and include molasses, barley malt, crude glycerol, and related compounds and compositions. Other glycolytic and tricarboxylic acid cycle intermediates are also contemplated as carbon sources, as are one- carbon substrates such as carbon dioxide and/or methanol in the cases of compatible organisms. The carbon sources utilized are limited only by the particular organism being cultured.

[00107] In a further aspect, the culture medium can contain at least one nitrogen source.

[00108] Culturing or fermenting of host cells can be accomplished by any technique known in the art. In a further aspect, batch fermentation can be conducted. In batch fermentation, the composition of the culture medium is set at the beginning and the system is closed to future artificial alterations. In some aspects, a limited form of batch fermentation can be carried out, wherein factors such as oxygen concentration and pH are manipulated, but additional carbon is not added. Continuous fermentation methods are also contemplated. In continuous fermentation, equal amounts of a defined medium are continuously added to and removed from a bioreactor. In other aspects, microbial host cells are immobilized on a substrate. Fermentation can be carried out on any scale and can include methods in which literal "fermentation" is carried out as well as other culture methods which are non- fermentative.

[00109] In a further aspect, the method involves growing the transformed cells described herein for a sufficient time to co-produce PHAs and indigo. The ordinary artisan will be able to choose a culture medium and optimum culture conditions based on the biological identity of the cells. In a further aspect, a salt or electrolyte can optionally be added to the culture medium. In a further aspect, the salt is present in solution at about a 0.1%, 0.2%, 0.5%, 1%, 1.5%, 2%, 2.5%, 3%, or 5% concentration.

[00110] In certain aspects, after culturing the transformed cells to produce the mFMO and PHA, the cells can be lysed with one or more enzymes. In other aspects, the cells are sonicated and/or autoclaved to disrupt the cells.

[00111] In addition to enzymes, other components can be used to facilitate lysis of the cells, in a further aspect, chitosan can be used in combination with an enzyme to lyse the cells. Chitosan is generally composed of glucosamine units and N-acetyigiucosamine units and can be chemically or enzymatically extracted from chitin, which is a component of arthropod exoskeletons and fungal and microbial cell walls. In certain aspects, the chitosan can be acetylated to a specific degree of acetylation in order to enhance tissue growth during culturing as well as metabolite production. In a further aspect, the chitosan is from 60% to about 100%, 70% to 90%, 75% to 85%, or about 80% acetylated. The molecular weight of the chitosan can vary, as well. For example, the chitosan comprises about 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, or 20 glucosamine units and/or N-acetylglucosamine units. In another aspect, the chitosan includes 5 to 7 glucosamine units and/or N- acetylglucosamine units. In a further aspect, chitosan can be added until a concentration of 0.0015, 0.0025, 0.0050, 0.0075, 0.01 , 0.015, 0.02, 0.03, 0.04, or 0.05, where any value can be a lower and upper end-point of a range (e.g., 0.005 to 0.02, 0.0075 to 0.015, etc.) is achieved in the culture. Still further in this aspect, the chitosan is present at a concentration of 0.01%.

[00112] In a further aspect, the indigoid derivatives and PHAs can be collected, separated from the microbial cells (lysed or intact), and/or purified through any technique known in the art such as, for example, precipitation, centrifugation, filtration, and the like. In a further aspect, the indigoid derivatives and PHAs can be purified via microfiltration to remove impurities. In a further aspect, the microfilter has a pore size of 0.1 pm, 0.2 pm, 0.3 pm, 0.35 pm, 0.4 pm, 0.45 pm, 0.35 pm, 0.55 pm, 0.6 pm, 0.65 pm, 0.7 pm, or 0.8 pm, where any value can be a lower and upper end-point of a range (e.g., 0.3 pm to 0.5 pm). The Examples provide an exemplary procedure for producing and purifying the indigoid derivatives and PHAs described herein.

[00113] Particular examples of proteins, including a DMA encoding said protein, useful in the present disclosure, e.g., preparing DNA constructs that encode one or more these proteins, are given in Table 1 below.

Table 1 .

[00114] Exemplary oxygenases, including a DMA encoding said protein, useful in the present disclosure, e.g., preparing DMA constructs that encode one or more these proteins, are given in Table 2 below. Table 2.

[00115] Exemplary phaA proteins, including a DNA encoding said protein, useful in the present disclosure, e.g., preparing DNA constructs that encode one or more these proteins, are given in Table 3 below.

Table 3.

[00116] Exemplary alternatives for phaB proteins, including a DNA encoding said protein, useful in the present disclosure, e.g., preparing DNA constructs that encode one or more these proteins, are given in Table 4 below.

Table 4.

[00117] Exemplary alternatives for phaC protein, including a DNA encoding said protein, useful in the present disclosure, e.g., preparing DNA constructs that encode one or more these proteins, are given in Table 5 below. Table 5.

VII. Molecular Biological Methods

[00118] In various aspects, the disclosed DNA constructs encoding for various disclosed proteins, vectors, plasmids, transformation of cells, growth of cells can be carried out as described herein throughout. Various additional suitable methods, procedures, and processes applicable to the variations of the present disclosure, its use, and its practice can be realized from reference to the further specific molecular biological methods as disclosed herein.

VIII. Transformed Cells

[00119] In a further aspect, a "transformed cell" is formed when a microbial cell is transfected with the DNA construct described herein. In a further aspect, the DNA construct is carried by the expression vector into a cell and is separate from the cell's genome. In another aspect, the DNA construct is incorporated into the cell's genome. In still another aspect, incorporation of the DNA construct into the cell enables the cell to produce carbo sugars. "Heterologous" genes and proteins are genes and proteins that have been experimentally inserted into a cell that are not normally expressed by that cell. A heterologous gene can be cloned or derived from a different cell type or species than the recipient cell or organism. Heterologous genes can be introduced into cells by transduction or transformation.

[00120] It is understood that one way to define any known variants and derivatives or those that might arise, of the disclosed genes and proteins herein is through defining the variants and derivatives in terms of homology to specific known sequences. For example, the various specific sequences set forth by SEQ ID NO:1 - SEQ ID NO:38 as provided herein that set forth particular sequences of DNA sequences encoding proteins and/or set forth particular sequence of the protein encoded by these DNA sequences or the protein themselves. Specifically disclosed are variants of these and other genes and proteins herein disclosed which have at least, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 percent homology to the stated sequence. Those of skill in the art readily understand how to determine the homology of two proteins or nucleic acids, such as genes. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.

[00121] Another way of calculating homology can be performed by published algorithms. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. MoL Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wl), or by inspection.

[00122] The same types of homology can be obtained for nucleic acids by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989, Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger et al. Methods Enzymol. 183:281-306, 1989 which are herein incorporated by reference for at least material related to nucleic acid alignment.

[00123] It is understood that as discussed herein the use of the terms homology and identity mean the same thing as similarity . Thus, for example, if the use of the word homology is used between two non-natural sequences it is understood that this is not necessarily indicating an evolutionary relationship between these two sequences, but rather is looking at the similarity or relatedness between their nucleic acid sequences. Many of the methods for determining homology between two evolutionarily related molecules are routinely applied to any two or more nucleic acids or proteins for the purpose of measuring sequence similarity regardless of whether they are evolutionarily related or not.

[00124] In general, it is understood that one way to define any known variants and derivatives or those that might arise, of the disclosed genes and proteins herein, is through defining the variants and derivatives in terms of homology to specific known sequences. This identity of particular sequences disclosed herein is also discussed elsewhere herein. In general, variants of genes and proteins herein disclosed typically have at least, about 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to the stated sequence or the native sequence. Those of skill in the art readily understand how to determine the homology of two proteins or nucleic acids, such as genes. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.

[00125] Another way of calculating homology can be performed by published algorithms.

Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. MoL Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wl), or by inspection.

[00126] It is understood that any of the methods typically can be used and that in certain instances the results of these various methods may differ, but the skilled artisan understands if identity is found with at least one of these methods, the sequences would be said to have the stated identity, and be disclosed herein.

[00127] For example, as used herein, a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above. For example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using the Zuker calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by any of the other calculation methods. As another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using both the Zuker calculation method and the Pearson and Lipman calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by the Smith and Waterman calculation method, the Needleman and Wunsch calculation method, the Jaeger calculation methods, or any of the other calculation methods. As yet another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using each of calculation methods (although, in practice, the different calculation methods will often result in different calculated homology percentages).

[00128] There are a variety of molecules disclosed herein that are nucleic acid based, including for example the nucleic acids that encode the disclosed proteins, for example SEQ ID NO:1-SEQ ID NO:16 or any of the nucleic acids disclosed herein, for fragments thereof, as well as various functional nucleic acids. The disclosed nucleic acids are made up of for example, nucleotides, nucleotide analogs, or nucleotide substitutes. Non-limiting examples of these and other molecules are discussed herein. It is understood that for example, when a vector is expressed in a cell, that the expressed mRNA will typically be made up of A, C, G, and U. Likewise, it is understood that if, for example, an antisense molecule is introduced into a cell or cell environment through for example exogenous delivery, it is advantageous that the antisense molecule be made up of nucleotide analogs that reduce the degradation of the antisense molecule in the cellular environment.

[00129] A nucleotide is a molecule that contains a base moiety, a sugar moiety and a phosphate moiety. Nucleotides can be linked together through their phosphate moieties and sugar moieties creating an internucleoside linkage. The base moiety of a nucleotide can be adenin-9-yl (A), cytosin-1-yl (C), guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T). The sugar moiety of a nucleotide is a ribose or a deoxyribose. The phosphate moiety of a nucleotide is pentavalent phosphate. An non-limiting example of a nucleotide would be 3'- AMP (3'-adenosine monophosphate) or 5-GMP (5 -guanosine monophosphate). There are many varieties of these types of molecules available in the art and available herein.

[00130] A nucleotide analog is a nucleotide which contains some type of modification to either the base, sugar, or phosphate moieties. Modifications to nucleotides are well known in the art and would include for example, 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, and 2-aminoadenine as well as modifications at the sugar or phosphate moieties. There are many varieties of these types of molecules available in the art and available herein.

[00131] Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA). Nucleotide substitutes are molecules that will recognize nucleic acids in a Watson- Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid. There are many varieties of these types of molecules available in the art and available herein.

[00132] It is also possible to link other types of molecules (conjugates) to nucleotides or nucleotide analogs to enhance for example, cellular uptake. Conjugates can be chemically linked to the nucleotide or nucleotide analogs. Such conjugates include but are not limited to lipid moieties such as a cholesterol moiety. (Letsinger et al., Proc. Natl. Acad. Sci USA, 1989, 86, 6553-6556). There are many varieties of these types of molecules available in the art and available herein.

[00133] A Watson-Crick interaction is at least one interaction with the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute. The Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute includes the C2, N1 , and C6 positions of a purine based nucleotide, nucleotide analog, or nucleotide substitute and the C2, N3, C4 positions of a pyrimidine based nucleotide, nucleotide analog, or nucleotide substitute.

[00134] A Hoogsteen interaction is the interaction that takes place on the Hoogsteen face of a nucleotide or nucleotide analog, which is exposed in the major groove of duplex DNA. The Hoogsteen face includes the N7 position and reactive groups (NH2 or O) at the C6 position of purine nucleotides.

[00135] There are a variety of sequences related to the protein molecules involved in the signaling pathways disclosed herein, for example SEQ ID NO:1-SEQ ID NO:16 or any of the nucleic acids disclosed herein, or any of the nucleic acids disclosed herein for making a disclosed protein such as an oxygenase or phA, phaB, and/or phaC protein, all of which are encoded by nucleic acids or are nucleic acids. The sequences for the human analogs of these genes, as well as other analogs, and alleles of these genes, and splice variants and other types of variants, are available in a variety of protein and gene databases, including Genbank. Those of skill in the art understand how to resolve sequence discrepancies and differences and to adjust the compositions and methods relating to a particular sequence to other related sequences. Primers and/or probes can be designed for any given sequence given the information disclosed herein and known in the art.

[00136] Disclosed are compositions including primers and probes, which are capable of interacting with the disclosed nucleic acids, for example SEQ ID NO:1-SEQ ID NO:16 or any of the nucleic acids disclosed herein, or any of the nucleic acids disclosed herein for making a disclosed protein such as an oxygenase or phA, phaB, and/or phaC protein, all of which are encoded by nucleic acids or are nucleic acids. In certain aspects the primers are used to support DNA amplification reactions. Typically the primers will be capable of being extended in a sequence specific manner. Extension of a primer in a sequence specific manner includes any methods wherein the sequence and/or composition of the nucleic acid molecule to which the primer is hybridized or otherwise associated directs or influences the composition or sequence of the product produced by the extension of the primer. Extension of the primer in a sequence specific manner therefore includes, but is not limited to, PGR, DNA sequencing, DNA extension, DNA polymerization, RNA transcription, or reverse transcription. Techniques and conditions that amplify the primer in a sequence specific manner are preferred. In certain aspects the primers are used for the DNA amplification reactions, such as PGR or direct sequencing. It is understood that in certain aspects the primers can also be extended using non-enzymatic techniques, where for example, the nucleotides or oligonucleotides used to extend the primer are modified such that they will chemically react to extend the primer in a sequence specific manner. Typically the disclosed primers hybridize with the disclosed nucleic acids or region of the nucleic acids or they hybridize with the complement of the nucleic acids or complement of a region of the nucleic acids.

[00137] The size of the primers or probes for interaction with the nucleic acids in certain aspects can be any size that supports the desired enzymatic manipulation of the primer, such as DNA amplification or the simple hybridization of the probe or primer. A typical primer or probe would be at least 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46,

47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70,

71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94,

95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425,

450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3500, or 4000 nucleotides long.

[00138] In other aspects a primer or probe can be less than or equal to 6, 7, 8, 9, 10, 11 , 12 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36,

37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60,

61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84,

85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250,

275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3500, or 4000 nucleotides long.

[00139] The primers for disclosed nucleic acids, for example SEQ ID NO:1-SEQ ID NO:16 or any of the nucleic acids disclosed herein, or any of the nucleic acids disclosed herein for making a disclosed protein such as an oxygenase or phA, phaB, and/or phaC protein, all of which are encoded by nucleic acids or are nucleic acids gene typically will be used to produce an amplified DNA product that contains a region of the disclosed gene or the complete gene. In general, typically the size of the product will be such that the size can be accurately determined to within 3, or 2 or 1 nucleotides.

[00140] In certain aspects this product is at least 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30,

31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54,

55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78,

79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 100, 125,

150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3500, or 4000 nucleotides long.

[00141] In other aspects the product is less than or equal to 20, 21 , 22, 23, 24, 25, 26, 27,

28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 ,

52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75,

76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3500, or 4000 nucleotides long.

[00142] The nucleic acids that are delivered to ceils typically contain expression controlling systems. For example, the inserted genes in viral and retroviral systems usually contain promoters, and/or enhancers to help control the expression of the desired gene product. A promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. A promoter contains core elements required for basic interaction of RNA polymerase and transcription factors, and may contain upstream elements and response elements.

[00143] The promotor and/or enhancer may be specifically activated either by light or specific chemical events which trigger their function. Systems can be regulated by reagents such as tetracycline and dexamethasone. There are also ways to enhance viral vector gene expression by exposure to irradiation, such as gamma irradiation, or alkylating chemotherapy drugs.

[00144] In certain embodiments the promoter and/or enhancer region can act as a constitutive promoter and/or enhancer to maximize expression of the region of the transcription unit to be transcribed.

[00145] In some embodiments a DNA construct or plasmid can comprise a marker, e.g., a selectable marker. Examples of suitable selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin.

[00146] As discussed herein there are numerous variants of the disclosed proteins, e.g., oxygenases or proteins such as phaA, phaB, and/or phaC, are herein contemplated. Protein variants and derivatives can involve amino acid sequence modifications. For example, amino acid sequence modifications typically fall into one or more of three classes: substitutional, insertional or deletional variants. Insertions include amino and/or carboxyl terminal fusions as well as intrasequence insertions of single or multiple amino acid residues. Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues. Immunogenic fusion protein derivatives, such as those described in the examples, are made by fusing a polypeptide sufficiently large to confer immunogenicity to the target sequence by cross- linking in vitro or by recombinant cell culture transformed with DNA encoding the fusion. Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. Typically, no more than about from 2 to 6 residues are deleted at any one site within the protein molecule. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DMA encoding the protein, thereby producing DMA encoding the variant, and thereafter expressing the DMA in recombinant cell culture. Techniques for making substitution mutations at predetermined sites in DMA having a known sequence are well known, for example M13 primer mutagenesis and PCR mutagenesis. Amino acid substitutions are typically of single residues, but can occur at a number of different locations at once; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues. Deletions or insertions preferably are made in adjacent pairs, i.e. a deletion of 2 residues or insertion of 2 residues. Substitutions, deletions, insertions or any combination thereof may be combined to arrive at a final construct. The mutations must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure. Substitutional variants are those in which at least one residue has been removed and a different residue inserted in its place. Such substitutions generally are referred to as conservative substitutions, and can be made in accordance with the following Tables 6 and 7 below.

Table 6.

Amino Acid Abbreviations Amino Acid Abbreviations

TABLE 7.

Amino Acid Substitutions

[00147] Substantial changes in function or immunological identity are made by selecting substitutions that are less conservative than those in Table 2, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in the protein properties will be those in which (a) a hydrophilic residue, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine, in this case, (e) by increasing the number of sites for sulfation and/or glycosylation.

[00148] For example, the replacement of one amino acid residue with another that is biologically and/or chemically similar is known to those skilled in the art as a conservative substitution. For example, a conservative substitution would be replacing one hydrophobic residue for another, or one polar residue for another. The substitutions include combinations such as, for example, Gly, Ala; Vai, lie, Leu; Asp, Glu; Asn, Gin; Ser, Thr; Lys, Arg; and Rhe, Tyr. Such conservatively substituted variations of each explicitly disclosed sequence are included within the mosaic polypeptides provided herein.

[00149] Substitutional or deletional mutagenesis can be employed to insert sites for N- glycosylation (Asn-X-Thr/Ser) or O-glycosylation (Ser or Thr). Deletions of cysteine or other labile residues also may be desirable. Deletions or substitutions of potential proteolysis sites, e.g. Arg, is accomplished for example by deleting one of the basic residues or substituting one by glutaminyl or histidyl residues.

[00150] Certain post-translational derivatizations are the result of the action of recombinant host cells on the expressed polypeptide. Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and asparyl residues. Alternatively, these residues are deamidated under mildly acidic conditions. Other post- translational modifications include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the o-amino groups of lysine, arginine, and histidine side chains (T.E. Creighton, Proteins: Structure and Molecular Properties, W. H. Freeman & Co., San Francisco pp 79-86 [1983]), acetylation of the N- terminai amine and, in some instances, amidation of the C-terminal carboxyl.

[00151] It is understood that one way to define the variants and derivatives of the disclosed proteins, e.g., oxygenases or proteins such as phaA, phaB, and/or phaC, herein is through defining the variants and derivatives in terms of homology/identity to specific known sequences. Specifically disclosed are variants of the disclosed proteins, e.g., oxygenases or proteins such as phaA, phaB, and/or phaC, which have at least, 70% or 75% or 80% or 85% or 90% or 95% homology to the sequence as disclosed herein. Those of skill in the art readily understand how to determine the homology of two proteins. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.

[00152] Another way of calculating homology can be performed by published algorithms. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. MoL Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wl), or by inspection.

[00153] The same types of homology can be obtained for nucleic acids by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989, Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger et al. Methods Enzymol. 183:281-306, 1989. [00154] It is understood that the description of conservative mutations and homology can be combined together in any combination, such as embodiments that have at least 70% homology to a particular sequence wherein the variants are conservative mutations.

[00155] As the present disclosure discusses various proteins and protein sequences it is understood that the nucleic acids that can encode those protein sequences are also disclosed. This would include all degenerate sequences related to a specific protein sequence, i.e., all nucleic acids having a sequence that encodes one particular protein sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives of the protein sequences. Thus, while each particular nucleic acid sequence may not be written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed protein sequence. It is also understood that while no amino acid sequence indicates what particular DNA sequence encodes that protein within an organism, where particular variants of a disclosed protein are disclosed herein, the known nucleic acid sequence that encodes that protein from which that protein arises is also known and herein disclosed and described.

[00156] It is understood that there are numerous amino acid and peptide analogs which can be incorporated into the disclosed compositions. For example, there are numerous D amino acids or amino acids which have a different functional substituent then the amino acids shown in Table 1 and Table 2. The opposite stereo isomers of naturally occurring peptides are disclosed, as well as the stereo isomers of peptide analogs. These amino acids can readily be incorporated into polypeptide chains by charging tRNA molecules with the amino acid of choice and engineering genetic constructs that utilize, for example, amber codons, to insert the analog amino acid into a peptide chain in a site specific way.

[00157] Molecules can be produced that resemble peptides, but which are not connected via a natural peptide linkage. For example, linkages for amino acids or amino acid analogs can include CH₂NH-, -CH₂S-, -CH₂-CH₂ -, -CH=CH- (cis and trans), -COCH₂ -, - CH(OH)CH₂-, and -CHH₂SO — (These and others can be found in Spatola, A. F. in Chemistry and Biochemistry of Amino Acids, Peptides, and Proteins, B. Weinstein, eds., Marcel Dekker, New York, p. 267 (1983); Spatola, A. F., Vega Data (March 1983), Vol. 1 , Issue 3, Peptide Backbone Modifications (general review); Morley, Trends Pharm Sci (1980) pp. 463-468; Hudson, D. et al., Int J Pept Prat Res 14:177-185 (1979) (-CH₂NH-, CH₂CH₂- ); Spatola et al. Life Sci 38:1243-1249 (1986) (-CH H₂-S); Hann J. Chem. Soc Perkin Trans. I 307-314 (1982) (-CH-CH-, cis and trans); Almquist et al. J. Med. Chem. 23:1392- 1398 (1980) (-COCH₂-); Jennings-White et al. Tetrahedron Lett 23:2533 (1982) (-COCH₂- ); Szelke et al. European Appln, EP 45665 CA (1982): 97:39405 (1982) (-CH(OH)CH₂-); Holladay et al. Tetrahedron. Lett 24:4401-4404 (1983) (-C(OH)CH₂-); and Hruby Life Sci 31 :189-199 (1982) (--CH₂--S--); each of which is incorporated herein by reference. A particularly preferred non-peptide linkage is --CH₂NH-. It is understood that peptide analogs can have more than one atom between the bond atoms, such as b-alanine, g- aminobutyric acid, and the like.

[00158] Amino acid analogs and analogs and peptide analogs often have enhanced or desirable properties, such as, more economical production, greater chemical stability, enhanced pharmacological properties (half-life, absorption, potency, efficacy, etc.), altered specificity (e.g., a broad-spectrum of biological activities), reduced antigenicity, and others.

[00159] D-amino acids can be used to generate more stable peptides, because D amino acids are not recognized by peptidases and such. Systematic substitution of one or more amino acids of a consensus sequence with a D-amino acid of the same type (e.g., D-lysine in place of L-lysine) can be used to generate more stable peptides. Cysteine residues can be used to cyclize or attach two or more peptides together. This can be beneficial to constrain peptides into particular conformations.

IX. Aspects

[00160] The following listing of exemplary aspects supports and is supported by the disclosure provided herein.

[00161] Aspect 1. A synthetic DNA sequence comprising: an origin of replication; an antibiotic resistance gene; DNA encoding a flavin-dependent monooxygenase, operably linked to a promoter; and DNA encoding poly(3)hydroxyalkanoate polymerase (phaC), acetyl-CoA acetyltransferase (phaA), and acetoacetyl-CoA reductase (phaB), operably linked to a promoter.

[00162] Aspect 2. The synthetic DNA sequence of Aspect 1 , wherein the DNA encoding a flavin-dependent monooxygenase is from Methylphaga sp. SK1.

[00163] Aspect 3. The synthetic DNA sequence of Aspect 1 , wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC), acetyl-CoA acetyltransferase (phaA), and acetoacetyl-CoA reductase (phaB) are from Cupriavidus necator H16.

[00164] Aspect 4. A plasmid vector comprising the synthetic DNA sequence of Aspect 1.

[00165] Aspect 5. A bacterium transformed with the plasmid vector of Aspect 4.

[00166] Aspect 6. The bacterium of Aspect 5, wherein the bacterium is E. coli.

[00167] Aspect 7. The bacterium of Aspect 5, wherein the bacterium is E. coli K12 MG1655.

[00168] Aspect 8. A process for producing polyhydroxyalkanoates and indigoid derivatives comprising culturing bacteria according to Aspect 4 in a culture medium comprising tryptophan and a sugar.

[00169] Aspect 9. The process of Aspect 8 wherein the sugar is selected from the group consisting of galactose, glucose, sucrose, and lactose.

[00170] Aspect 10. The process of Aspect 8, wherein the culture medium comprises whey.

[00171] Aspect 11. The process of Aspect 9, wherein the whey is derived from one or more of cheese or yogurt.

[00172] Aspect 12. The process of Aspect 7, wherein the bacteria are E. coli.

[00173] Aspect 13. The process of Aspect 11 , wherein the bacteria are E. coli K12 MG1655.

[00174] Aspect 14. The process of Aspect 7, wherein PHB and Indigo are co-extracted from the bacteria in a single extraction process.

[00175] Aspect 15. The process of Aspect 13, wherein the single extraction process comprises the steps of solubilization of PHB and indigo using an organic solvent, and collecting PHB and indigo from the solvent by precipitation with an anti-solvent, followed by centrifugation or filtration.

[00176] From the foregoing, it will be seen that aspects herein are well adapted to attain all the ends and objects hereinabove set forth together with other advantages which are obvious and which are inherent to the structure.

[00177] While specific elements and steps are discussed in connection to one another, it is understood that any element and/or steps provided herein is contemplated as being combinable with any other elements and/or steps regardless of explicit provision of the same while still being within the scope provided herein.

[00178] It will be understood that certain features and subcombinations are of utility and can be employed without reference to other features and subcombinations. This is contemplated by and is within the scope of the claims.

[00179] Since many possible aspects can be made without departing from the scope thereof, it is to be understood that all matter herein set forth or shown in the accompanying drawings and detailed description is to be interpreted as illustrative and not in a limiting sense.

[00180] It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only, and is not intended to be limiting. The skilled artisan will recognize many variants and adaptations of the aspects described herein. These variants and adaptations are intended to be included in the teachings of this disclosure and to be encompassed by the claims herein. [00181] Now having described the aspects of the present disclosure, in general, the following Examples describe some additional aspects of the present disclosure. While aspects of the present disclosure are described in connection with the following examples and the corresponding text and figures, there is no intent to limit aspects of the present disclosure to this description. On the contrary, the intent is to cover all alternatives, modifications, and equivalents included within the spirit and scope of the present disclosure.

EXAMPLES

[00182] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, and methods described and claimed herein are made and evaluated, and are intended to be purely exemplary and are not intended to limit the scope of what the inventors regard as their invention. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperatures, etc.) but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in °C. or is at ambient temperature, and pressure is at or near atmospheric. Numerous variations and combinations of reaction conditions, e.g., component concentrations, desired solvents, solvent mixtures, temperatures, pressures, and other reaction ranges and conditions can be used to optimize the product purity and yield obtained from the described process. Only reasonable and routine experimentation will be required to optimize such processes and conditions.

Preparation of DNA Construct for Co-Production of PHAs and Indigoid Dyes.

[00183] The following DNA sequences were synthesized: a gene for expressing mFMO from Methylphaga sp. SK1 and an operon for expressing each of phaA gene, phaB, and phaC from Cupriavidus necator H16.

[00184] A plasmid vector was used to assemble a DNA construct, which also contains a promoter, and a terminator. The cloning of the DNA construct into the cells is performed as follows. Overlapping oligonucleotides are amplified by polymerase chain reaction. These oligonucleotides are then ligated using standard protocols to form an insert. The insert is cloned into cloning vector. Individual clones are sequenced and site-directed mutagenesis is used to correct mutations in the clones. Successful construction of the insert and ligation of the insert into the plasmid are confirmed using gel electrophoresis. Backbone plasmids at different ratios ranging from 1 :1 , 1 :2, 1 :3, 1 :4, and up to 1 :5 are evaluated.

[00185] Ligation of the insert occurred in one pot and is carried out using a kit and enzymes from Promega (Madison, Wis.). A 1 :2 molar ratio of vector/insert was used for most ligation reactions; a typical ligation reaction used 100-200 ng of vector DNA. To this mixture was added 8 pL of T4 DNA ligase and 124 of iigase buffer. In some reactions, the ligation mixture was incubated at room temperature for 5 minutes. In other reactions, the ligation mixture was introduced into an electromagnetic chamber for 15 minutes.

[00186] A schematic of the DNA construct is depicted in FIG. 2. DNA quantification is performed using a UV-Vis spectrophotometer and recording the ratio of the absorbance at 260 nm to the absorbance at 280 nm. Plasmids are then electrophoresed to verify the insertion of genes, then purified prior to further use.

Selection and Transformation of Microorganisms.

[00187] PHAs and indigo were produced using transfected bacteria (Escherichia coli MG1655).

[00188] Bacterial cells were transformed with the plasmid depicted in FIG. 3 using a standard heat shock protocol.

[00189] Cells are plated and cultured. Clones were selected and processed for full-length DNA sequencing. A clone with 100% DNA sequence accuracy for the target sequence was selected for further processing. This clone was used to obtain a high concentration of the desired plasmid construct using mid-scale plasmid purification level.

Comparison of macro- and microelements of different whey compositions before processing.

[00190] Elemental composition was evaluated using X-ray fluorescence (XRF) spectroscopy and inductively-coupled plasma (ICP) spectroscopy. Acid, sweet, and blended whey samples from both cow and goat were analyzed to quantify the concentration of elements critical to microbial growth. The data are shown in FIGs. 3A-3B: FIG. 3A shows macroelements determined in the indicated whey compositions; and FIG. 3B shows macroelements determined in the indicated whey compositions. These data show that the most abundant elements were potassium and chloride, which is consistent with previously reported whey data. Across different types of whey, acid whey from goats showed the most variability with a significantly higher calcium and zinc concentration compared to its counterparts. Of all the microelements, selenium was the only one present at significant concentrations.

Comparison of carbon to nitrogen ratios of different whey compositions before processing.

[00191] High carbon to nitrogen ratios are desired for optimal PHB production. The carbon and nitrogen content in whey samples were analyzed using an organic elemental analyzer (OEA). Samples were subjected to combustion and the resulting readout measured the percentage by weight of carbon and nitrogen. The ratio of carbon to nitrogen was then calculated. The data are shown in FIG. 4. From these results, sweet whey from goats had the highest carbon to nitrogen ratio, due to containing less soluble protein. However, sweet whey from cows contained the most total carbon content, which is consistent with previously reported data indicating that sweet whey from cows typically has the highest lactose concentration.

Comparison of macro- and microelements in different whey compositions after processing.

[00192] Whey was processed using HCI to adjust the pH in order to remove residual protein. Elemental composition was evaluated using X-ray fluorescence (XRF) spectroscopy and inductively-coupled plasma (ICP) spectroscopy. Acid, sweet, and blended whey samples from both cow and goat were analyzed to quantify the concentration of elements critical to microbial growth. The data are shown in FIGs. 5A-5B: FIG. 5A shows macroelements determined in the indicated whey compositions after processing; and FIG. SB shows macroelements determined in the indicated whey compositions after processing. These data indicate a significant increase in chloride concentration (due to the use of HCI for pH adjustment). The barium concentration of whey blend #1 was also significantly higher after processing, while no other blend saw an increase in barium. Other than a change in chloride and barium concentration, most elements remained at similar levels as the pre-processed whey.

Comparison of carbon to nitrogen ratios of different whey compositions after processing.

[00193] Whey samples were processed to remove residual protein as described above; and the carbon and nitrogen content in whey samples were analyzed using an organic elemental analyzer (OEA). Samples were subjected to combustion and the resulting readout measured the percentage by weight of carbon and nitrogen. The ratio of carbon to nitrogen was then calculated. The data are shown in FIG. 6. These data show that after processing to remove residual proteins, carbon to nitrogen ratios significantly increased. Blend #1 of whey permeate had the highest carbon to nitrogen ratio (70:1) while sweet whey permeate from cows contained the highest overall carbon content. These results indicate that processing whey to remove residual proteins is crucial for providing a substrate suitable for maximal PHB production.

Fourier Transform Infrared (FTIR) spectroscopic analysis of a disclosed PHB-indigo composition versus a PHB standard.

[00194] FTIR was performed using a ThermoFisher spectrometer. About 1 mg of a disclosed PHB-indigo composition was used to analyze and identify functional groups (O-H, C=O, N- H) and confirm the presence of indigo within the sample. The data are shown in FIG. 7. These data show a near identical spectroscopy profile for the disclosed PHB-indigo composition versus the PHB standard. However, as indicated in the figure, increased O-H stretching and N-H bond rocking was observed in the disclosed PHB-indigo composition, confirming the presence of indigo within the sample.

Solvent cast film using a disclosed PHB-indigo composition.

[00195] To prepare a film comprising a disclosed PHB-indigo composition, ~1 g of PHB containing 1% indigo was dissolved in 20 ml of chioroform by stirring for 3 hours at 50 °C. The dissolved solution was then poured into a glass petri dish and the solvent allowed to evaporate under ambient conditions. After evaporation, a blue PHB film remained attached to the glass petri dish. At only 1% indigo concentration, the film was slightly opaque but retained most of its transparency. The resulting film was brittle, which is not unexpected for a film comprising pure PHB without additional film additives. Washing with water, alcohol, and soap did not affect the color of the film, indicating the indigo pigment was well associated within the polymer matrix. The material properties for the film were as given in Table 8 below.

Table 8.

Melting Temp. (°C) 178.1

Glass Transition Temp. (°C) 1.1

Molecular Weight (g/mol) 5.3 x 105

Degradation Temp. (5% weight loss, °C) 249.5

% Crystallinity 60

[00196] These data show that a disclosed PHB-indigo composition sample was associated with a melting temperature of 178.1 °C. The glass transition temperature of the extracted sample is also much more apparent and shifted as compared to the standard (-0.5°C vs. ~4°C standard). The thermal decomposition temperature was defined as the temperature at which 5% loss was achieved; experimentally it was determined to be approximately 249.5°C, an improvement from the PHB standard (~220°C).

[00197] To obtain the foregoing data, the following methods were utilized: (a) Differential Scanning Calorimetry (DSC) was performed with a Q20 (TA Instruments, TX) using a heat/cool/heat method. The sample (~2-3mg) was heated to 200°C, cooled to -90°C, and reheated to 30°C; temperature ramps were 20°C/min. Melting (Tm), crystallization (Tc), and glass transition temperatures (Tg) were recorded; (b) Thermogravimetric Analysis (TGA) was performed with a Q500 (TA Instruments, TX). The sample was heated (20°C/min) from room temperature to 550°C under inert atmosphere (N2), then to 850°C under air. The thermal decomposition temperature was determined when the mass loss reached 5%; and (c) Molecular weight was measured using Gel Permeation Chromatography (GPC). PHB- indigo compound sample (1.5 mg) was dissolved in 1 mL chloroform before injection. 1OOpL of sample was injected into a column (Column Set: individual pore size 10^A3-4-4-5, 600mm) and run at 50°C with a flow rate of 1.00 mLVmin. The average molecular weight of the sample was calculated using polystyrene standards with known molecular weights.

Scanning electron microscopy and elemental analysis of a film comprising a disclosed PHB-indigo composition.

[00198] Surface morphology was analyzed using Scanning electron microscopy (SEM). Images were taken at 65X, 180X, and 322X magnification. Because PHB contains no nitrogen by itself, the presence of indigo within the film was evaluated using elemental analysis of the nitrogen content in the film. The data are shown in FIGs. 9A-9F. FIG. 9A shows a representative scanning electron microscopy image of a PHB-indigo composition cast as a film such as shown in FIG. 8 (at SEM conditions as shown below the image). FIG. 9B shows a representative scanning electron microscopy image of a PHB-indigo composition cast as a film such as shown in FIG. 8 (at SEM conditions as shown below the image). FIG. 9C shows a representative scanning electron microscopy image of a PHB- indigo composition cast as a film such as shown in FIG. 8 (at SEM conditions as shown below the image). FIG. 9D shows carbon elemental analysis of a PHB-indigo composition cast as a film such as shown in FIG. 8. FIG. 9E shows nitrogen elemental analysis of a PHB- indigo composition cast as a film such as shown in FIG. 8. FIG. 9F shows oxygen elemental analysis of a PHB-indigo composition cast as a film such as shown in FIG. 8. Quantitation of the elemental analysis in FIGs. 9D-9F determined that the film was 74.61 wt% carbon; 2.23 wt% nitrogen; and 23.16 wt% oxygen. The resulting images show that indigo did not significantly impact the surface morphology of the PHB film, but slightly decreased its porosity, suggesting that indigo is acting as a binding agent between polymer chains. A nitrogen concentration of 2.23 (% weight) was identified in the sample, confirming the presence of indigo dispersed throughout the film.

[00199] Disclosed sequences of the present disclosure are as provided in the co-filed sequence listing file, which are described in Table 9 below and full sequences included in full below.

[00200] It will be apparent to those skilled in the art that various modifications and variations can be made in the present disclosure without departing from the scope or spirit of the disclosure. Other aspects of the disclosure will be apparent to those skilled in the art from consideration of the specification and practice of the disclosure disclosed herein, It is intended that the specification and examples be considered as exemplary only, with a true scope and spirit of the disclosure being indicated by the following claims.

Table 9.

Disclosed Sequences

Claims

CLAIMS What is claimed is:

1. A DNA construct comprising a synthetic DNA sequence comprising: a first expression cassette comprising a DNA sequence encoding an oxygenase; and a second expression cassette comprising a DNA sequence encoding poly(3)hydroxyalkanoate polymerase (phaC); a third expression cassette comprising a DNA sequence encoding acetyl-CoA acetyltransferase (phaA); and a fourth expression cassette comprising a DNA sequence encoding acetoacetyl-CoA reductase (phaB).

2. The DNA construct of claim 1 , wherein the oxygenase is a co-factor dependent oxygenase.

3. The DNA construct of claim 1 or claim 2, wherein the DNA sequence encoding the oxygenase is selected from the group consisting of a DNA sequence encoding a nonheme iron oxygenase, a DNA sequence encoding a heme-containing oxygenase, DNA sequence encoding a flavin-dependent monooxygenase, and combinations thereof.

The DNA construct of any one of claims 1-3, wherein the DNA sequence encoding the oxygenase is a DNA sequence encoding a non-heme iron oxygenase.

5. The DNA construct of claim 4, wherein the DNA sequence encoding the non-heme iron oxygenase is a DNA sequence encoding a naphthalene dioxygenase.

6. The DNA construct of any one of claims 1-3, wherein the DNA sequence encoding the oxygenase is a DNA sequence encoding a heme-containing iron oxygenase.

7. The DNA construct of claim 6, wherein the DNA sequence encoding the hemecontaining iron oxygenase is a cytochrome P450.

8. The DNA construct of any one of claims 1-3, wherein the DNA sequence encoding the oxygenase is a DNA sequence encoding a flavin-dependent monooxygenase.

9. The DNA construct of claim 8, wherein the DNA sequence encoding the flavindependent monooxygenase is a DNA sequence encoding a Methylphaga sp. SK1 flavin-dependent monooxygenase.

10. The DNA construct of any one of claims 1-9, wherein the first expression cassette further comprises a first transcriptional promoter sequence operably linked to a DNA sequence encoding the flavin-dependent monooxygenase.

11. The DNA construct of claim 10, wherein the first transcriptional promoter sequence comprises SEQ ID NO:1.

12. The DNA construct of claim 10 or claim 11 , wherein the DNA sequence encoding the flavin-dependent monooxygenase is a DNA sequence is encoding a Methylphaga sp. SK1 flavin-dependent monooxygenase.

13. The DNA construct of claim 12, wherein the DNA sequence encoding the flavindependent monooxygenase is at least 80% homologous to SEQ ID NO:10.

14. The DNA construct of claim 12, wherein the DNA sequence encoding the flavindependent monooxygenase comprises a DNA sequence that is at least 90% homologous to SEQ ID NO:10.

15. The DNA construct of claim 12, wherein the DNA sequence encoding the flavindependent monooxygenase comprises a DNA sequence that is at least 95% homologous to SEQ ID NO:10.

16. The DNA construct of claim 12, wherein the DNA sequence encoding the flavindependent monooxygenase comprises a DNA sequence that is at least 97% homologous to SEQ ID NO:10.

17. The DNA construct of claim 12, wherein the DNA sequence encoding the flavindependent monooxygenase comprises a DNA sequence that is at least 98% homologous to SEQ ID NO:10.

18. The DNA construct of claim 12, wherein the DNA sequence encoding the flavindependent monooxygenase comprises a DNA sequence that is at least 99% homologous to SEQ ID NO:10.

19. The DNA construct of claim 12, wherein the DNA sequence encoding the flavindependent monooxygenase comprises SEQ ID NO:10.

20. The DNA construct of any one of claims 10-19, wherein the first expression cassette further comprises a first ribosome binding site that is 5' to an initiation codon of the DNA sequence encoding the flavin-dependent monooxygenase.

21. The DNA construct of any one of claims 10-20, wherein the first ribosome binding site comprises SEQ ID NO:4.

22. The DNA construct of any one of claims 1-21 , wherein the second expression cassette further comprises a second transcriptional promoter sequence operably linked to the DNA sequence encoding poly(3)hydroxyalkanoate polymerase (phaC).

23. The DNA construct of any one of claims 1-22, wherein the third expression cassette further comprises a third transcriptional promoter sequence operably linked to the DNA sequence encoding acetyl-CoA acetyltransferase (phaA).

24. The DNA construct of any one of claims 1-23, wherein the fourth expression cassette further comprises a fourth transcriptional promoter sequence operably linked to the DNA sequence encoding acetoacetyl-CoA reductase (phaB).

25. The method of claim 24, wherein the first transcriptional promoter sequence, the second transcriptional promoter sequence, the third transcriptional promoter sequence, and the fourth transcriptional promoter sequence are not the same.

26. The method of claim 24 or claim 25, wherein the first transcriptional promoter sequence, the second transcriptional promoter sequence, the third transcriptional promoter sequence, and the fourth transcriptional promoter sequence are independently selected from an inducible promoter and a constitutive promoter sequence.

27. The method of any one of claims 24-26, wherein the second transcriptional promoter sequence, the third transcriptional promoter sequence, and the fourth transcriptional promoter sequence are coordinately regulated.

28. The method of any one of claims 24-26, wherein the first transcriptional promoter sequence, the second transcriptional promoter sequence, the third transcriptional promoter sequence, and the fourth transcriptional promoter sequence are coordinately regulated.

29. The DNA construct of any one of claims 1-21 , wherein the second expression cassette, the third expression cassette, and the fourth expression cassette form a pha operon that is operably linked to a pha operon transcriptional promoter sequence.

30. The DNA construct of claim 29, wherein the pha operon transcriptional promoter sequence comprises SEQ ID NO:2.

31. The DNA construct of either claim 29 or claim 30, wherein the pha operon further comprises a pha transcriptional termination sequence following the 3’ end of the pha operon.

32. The DNA construct of any one of claims 29-31 , wherein order of expression cassettes in the pha operon is 5’ to 3’ from the pha operon transcriptional promoter sequence as follows: the second expression cassette, the third expression cassette, and the fourth expression cassette.

33. The DNA construct of any one of claims 29-32, wherein the pha operon comprises a second ribosome binding site sequence that is 5^' to an initiation codon of the DNA sequence encoding poly(3)hydroxyalkanoate polymerase (phaC); a third ribosome binding site sequence that is 5’ to an initiation codon of the DNA sequence encoding acetyl-CoA acetyltransferase (phaA); and a fourth ribosome binding site sequence that is 5’ to an initiation codon of the DNA sequence encoding acetoacetyl-CoA reductase (phaB).

34. The DNA construct of claim 33, wherein the second ribosome binding site is SEQ ID NO: 7.

35. The DNA construct of claim 33, wherein the third ribosome binding site is SEQ ID NO: 5.

36. The DNA construct of claim 33, wherein the fourth ribosome binding site is SEQ ID NO: 6.

37. The DNA construct of any one of claims 1-36, wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC) is a DNA sequence encoding a Cupriavidus necator H16 poly(3)hydroxyalkanoate polymerase (phaC).

38. The DNA construct of claim 37, wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC) is at least 80% homologous to SEQ ID NO: 13.

39. The DNA construct of claim 37, wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC) is at least 90% homologous to SEQ ID NO: 13.

40. The DNA construct of claim 37, wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC) is at least 95% homologous to SEQ ID NO: 13.

41. The DNA construct of claim 37, wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC) is at least 97% homologous to SEQ ID NO: 13.

42. The DNA construct of claim 37, wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC) is at least 98% homologous to SEQ ID NO: 13.

43. The DNA construct of claim 37, wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC) is at least 99% homologous to SEQ ID NO: 13.

44. The DNA construct of claim 37, wherein the DNA encoding poly(3)hydroxyalkanoate polymerase (phaC) comprises SEQ ID NO:13.

45. The DNA construct of any one of claims 1-44, wherein the DNA encoding acetyl-CoA acetyltransferase (phaA) is a DNA sequence encoding a Cupriavidus necator H16 acetyl-CoA acetyltransferase (phaA).

46. The DNA construct of claim 45, wherein the DNA encoding acetyl-CoA acetyltransferase (phaA) is at least 80% homologous to SEQ ID NO:11 .

47. The DNA construct of claim 45, wherein the DNA encoding acetyl-CoA acetyltransferase (phaA) is at least 90% homologous to SEQ ID NO:11 .

48. The DNA construct of claim 45, wherein the DNA encoding acetyl-CoA acetyltransferase (phaA) is at least 95% homologous to SEQ ID NO:11 .

49. The DNA construct of claim 45, wherein the DNA encoding acetyl-CoA acetyltransferase (phaA) is at least 97% homologous to SEQ ID NO:11 .

50. The DNA construct of claim 45, wherein the DNA encoding acetyl-CoA acetyltransferase (phaA) is at least 98% homologous to SEQ ID NO:11 .

51. The DNA construct of claim 45, wherein the DNA encoding acetyl-CoA acetyltransferase (phaA) is at least 99% homologous to SEQ ID NO:11 .

52. The DNA construct of claim 45, wherein the DNA encoding acetyl-CoA acetyltransferase (phaA) comprises SEQ ID NO:11 .

53. The DNA construct of any one of claims 1-52, wherein the DNA encoding acetoacetyl-CoA reductase (phaB) comprises SEQ ID NO:12.

54. The DNA construct of claim 53, wherein the DNA encoding acetoacetyl-CoA reductase (phaB) is at least 80% homologous to SEQ ID NO:12.

55. The DNA construct of claim 53, wherein the DNA encoding acetoacetyl-CoA reductase (phaB) is at least 90% homologous to SEQ ID NO:12.

56. The DNA construct of claim 53, wherein the DNA encoding acetoacetyl-CoA reductase (phaB) is at least 95% homologous to SEQ ID NO:12.

57. The DNA construct of claim 53, wherein the DNA encoding acetoacetyl-CoA reductase (phaB) is at least 97% homologous to SEQ ID NO:12.

58. The DNA construct of claim 53, wherein the DNA encoding acetoacetyl-CoA reductase (phaB) is at least 98% homologous to SEQ ID NO:12.

59. The DNA construct of claim 53, wherein the DNA encoding acetoacetyl-CoA reductase (phaB) is at least 99% homologous to SEQ ID NO:12.

60. The DNA construct of claim 53, wherein the DNA encoding acetoacetyl-CoA reductase (phaB) comprises SEQ ID NO:12.

61. A plasmid vector comprising the DNA construct of any one of claims 1-60.

62. The plasmid vector of claim 61 , further comprising a selectable marker.

63. The plasmid vector of claim 62, wherein the selectable marker is a selectable marker that confers resistance to an antibiotic.

64. The plasmid vector of any one of claims 61-63, wherein the plasmid vector is capable of integrating into a cell chromosome.

65. The plasmid vector of any one of claims 61-63, wherein the plasmid vector is capable of extrachromosomal replication in a cell.

66. A cell comprising the plasmid vector of any one of claims 61-65.

67. The cell of claim 66, wherein the cell is bacterial cell.

68. The cell of claim 67, wherein the bacterial cell is E. coli

69. The cell of claim 68, wherein the bacterial cell is E. coli K12 MG1655.

70. A process for co-producing at least one polyhydroxyalkanoate and at least one indigoid compound, the process comprising: culturing the cell of any one of claims 66-69 in a culture medium comprising a tryptophan and a sugar.

71. The process of claim 70, wherein the sugar is selected from the group consisting of galactose, glucose, sucrose, lactose, and combinations thereof.

72. The process of claim 70 or claim 71 , the culture medium further comprising a whey.

73. The process of any one of claims 70-72, wherein the whey comprises a cheese whey, a yogurt whey, or combination thereof.

74. The process of any one of claims 70-73, wherein the at least one polyhydroxyalkanoate and the at least one indigoid compound are co-extracted from the cell in a single extraction process.

75. The process of claim 74, wherein the single extraction process comprises the steps of: solubilization of the at least one polyhydroxyalkanoate and the at least one indigoid compound using an organic solvent thereby forming a solvent-polyhydroxyalkanoate- indigoid mixture; adding to the solvent-polyhydroxyalkanoate-indigoid mixture an anti-solvent, thereby forming a precipitate comprising the at least one polyhydroxyalkanoate and the at least one indigoid compound; and separating the precipitate from remaining non-precipitated material.

76. The process of claim 75, wherein the separating comprises filtration, centrifugation, or combinations thereof.

77. The process of any one of claims 70-76, wherein the at least one polyhydroxyalkanoate comprises polyhydroxybutyrate (PHB).

78. The process of any one of claims 70-77, wherein the at least one indigoid compound comprises indigo.