# Patent

## Title
Methods and compositions for production of blue pigment indigoidine

## Abstract

The present disclosure provides for an expression system for the production of blue pigment indigoidine. The system comprises a heterologous host cell, a DNA sequence encoding a Sc-IndB protein, and a DNA sequence encoding a Sc-IndC protein. The system may be configured for the co-expression of the Sc-IndB and Sc-IndC. DNA sequences encoding the Sc-IndB and Sc-IndC may be provided on at least one vector. Alternatively, the DNA sequences encoding the Sc-IndB and Sc-IndC may optionally be integrated into the genome of the heterologous host genome. The expression system may further comprise a sfp gene or a PPTase.

## Background
RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application No. 61/728,721, filed on Nov. 20, 2012.


BACKGROUND
Streptomyces is well-known for the production of structurally diverse natural products, including many industrially important bioactive molecules, such as oxytetracycline, chloramphenicol and bleomycin. Most of these bacterial secondary metabolites are produced by complex biosynthetic pathways encoded by physically clustered genes. Among characterized biosynthetic enzymes, polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are most commonly observed. The blue pigment indigoidine [5,5′-diamino-4,4′-dihydroxy-3,3′-diazadiphenoguinone-(2,2′)] was previously isolated from phytopathogenic Erwinia and other bacteria. It may be synthesized by condensation of two units of L-glutamine by a 4′-phosphopantetheinyl transferase (PPTase)-activated NRPS, such as IndC from Erwinia chrysanthemi and Streptomyces aureofaciens CCM 3239 and BpsA from Streptomyces lavendulae. Because of the presence in its structure of carbon-carbon double bonds conjugated with a carbonyl group, indigoidine is a powerful radical scavenger that enables phytopathogens to tolerate oxidative stress, organic peroxides and superoxides during the plant defense response. Recently, indigoidine has also been found to possess antimicrobial activity.
Streptomyces chromofuscus ATCC 49982 was previously isolated from soil collected from a stand of mixed woods from the Stepping Stone Falls Beach Pond State Park, R.I., USA.
Unfortunately, despite its various utilities, conventional methods for production of indigoidine provide for only limited production, which may limit the industrial use of this promising compound. Mere optimization of conventional methods is unlikely to provide meaningful increases in the production of indigoidine.
SUMMARY
In embodiments, the present disclosure provides an expression system for the production of blue pigment indigoidine [5,5′-diamino-4,4′-dihydroxy-3,3′-diazadiphenoguinone-(2,2′)], having a heterologous host cell, a DNA sequence encoding a Sc-IndB protein, and a DNA sequence encoding a Sc-IndC protein. Preferably, the expression system is configured for the co-expression of the Sc-IndB and Sc-IndC. The DNA sequences encoding the Sc-IndB and Sc-IndC proteins may be provided on at least one vector. In some examples, both sequences are provided on a single vector. Alternatively, the DNA sequences encoding the Sc-IndB and Sc-IndC may be integrated into the genome of the heterologous host genome.
In embodiments, expression systems related to the present disclosure may further comprise of a DNA sequence encoding a sfp gene or a PPTase. The sfp gene and PPTase may be endogenous to the host cell. Alternatively, the sfp or PPTase may be exogenous to the host cell.
In embodiments, DNA sequences encoding the Sc-IndB and Sc-IndC are operatively linked to at least one promoter. For example, the DNA sequences encoding the Sc-IndB and Sc-IndC may be operatively linked to a single promoter.
In embodiments, DNA sequences encoding a Sc-IndB protein may provide for a polypeptide having the amino acid sequence set forth in SEQ ID NO:2. For example, the DNA sequence may be the sequence set forth in SEQ ID NO:1.
In embodiments, DNA sequences encoding a Sc-IndC protein provides for a polypeptide having the amino acid sequence set forth in SEQ ID NO:4. For example, the DNA sequence may be the sequence set forth in SEQ ID NO:3.
In embodiments, the present disclosure provides methods for synthesizing a blue pigment indigoidine. Generally, the methods consist of co-expressing a Sc-IndB protein and a Sc-IndC protein in a heterologous host. For example, the host may be a bacterium. The heterologous host may have a nucleotide sequence that encodes a sfp gene and may expresses PPTase. For example, the host may have an exogenous sfp and PPTase. Alternatively, the sfp and PPTase may be exogenous.
In embodiments, the present disclosure provides methods for extracting blue pigment indigoidine from a fermentation broth. The methods may include centrifuging a blue pigment indigoidine fermentation broth by low-speed centrifugation to provide pelleted bacterial cells and a supernatant comprising blue pigment indigoidine, and centrifuging the supernatant at a speed sufficiently high to provide pelleted indigoidine pigments. The methods may further include treating the pelleted indigoidine pigment sequentially with water, methanol, ethyl acetate and hexanes to remove impurities to provide a substantially isolated, substantially pure indigoidine pigment.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A through 1H depict exemplary plasmids constructed for cloning and expression of biosynthetic genes. FIG. 1A shows the map of pJV1. pJV1 was constructed by cloning Sc-indA into the cloning vector pJET1.2. FIG. 1B shows the map of pJV2. pJV2 was constructed by cloning Sc-indB into the cloning vector pJET1.2. FIG. 1C shows the map of pJV3. pJV3 was constructed by cloning Sc-indC into the cloning vector pJET1.2. FIG. 1D shows the map of pDY49. pDY49 was constructed by ligating Sc-indC into pRM5. FIG. 1E shows the map of pJV6. pJV6 was constructed by ligating Sc-indC into pET28a. FIG. 1F shows the map of pDY52. pDY52 was constructed by ligating Sc-indA into pACYCDuet-1. FIG. 1G shows the map of pDY53. pDY53 was constructed by ligating Sc-indB into pACYCDuet-1. FIG. 1H shows the map of pDY54. pDY54 was constructed by ligating both Sc-indA and Sc-indB into pACYCDuet-1.
FIG. 2 depicts an exemplary indigoidine biosynthetic gene cluster in S. chromofuscus ATCC 49982. The structural organization of Sc-IndC and Sc-IndB is shown. A: adenylation; Ox: oxidation; T: thiolation; TE: thioesterase.
FIG. 3 depicts an exemplary reconstitution of indigoidine biosynthesis in S. coelicolor CH999. (A) Production of the blue pigment by S. coelicolor CH999/pDY49. The engineered strain was grown in a R5 medium supplemented with 50 μg/ml thiostrepton at 30° C. for 6 days. S. coelicolor CH999 harboring the blank shuttle vector was used as the vector control. All experiments were performed in triplicate, and a representative result was shown. (B) Indigoidine extracted from S. coelicolor CH999/pDY49 and dissolved in dimethyl sulfoxide. (C) HPLC analysis of the fermentation broth of S. coelicolor CH999/pDY49 at 600 nm. (D) UV spectrum of indigoidine.
FIG. 4 depicts an exemplary reconstitution of indigoidine biosynthesis in E. coli BAP1. (A) Production of indigoidine by E. coli BAP1/pJV6. The strain was grown in LB medium supplemented with 50 μg/mlkanamycin at 37° C. and induced with 200 μM IPTG at 25° C. for 13 hours. E. coli BAP1/pET28a was used as the vector control. (B) Effect of the OD600 values before induction on the yield of indigoidine. (C) Time-course analysis of indigoidine production at 18° C. and 25° C. (D) Effect of temperatures on the stability of indigoidine. The pigment was stored at room temperature (left) and 4° C. (right) in cell-free LB medium for 2 days. Experiments were performed in triplicate and presented as means±SD (n=3).
FIG. 5 depicts exemplary co-expression of Sc-IndC with Sc-IndA, with and without co-expression of Sc-IndB, in E. coli BAP1. (A) SDS-PAGE analysis of co-expression of Sc-IndA and/or Sc-IndB with Sc-IndC in E. coli BAP1. (B) The yield of indigoidine in E. coli BAP1 with or without co-expression of Sc-IndA and/or Sc-IndB. Experiments were performed in triplicate and presented as means±SD (n=3). C: Sc-IndC; AC: Sc-IndA and Sc-IndC; BC: Sc-IndB and Sc-IndC; ABC: Sc-IndA, Sc-IndB and Sc-IndC; S: soluble fraction; I: insoluble fraction.



DETAILED DESCRIPTION
The invention related to the present disclosure overcomes the problems associated with limited production, by providing methods and compositions useful for the increased production and extraction of the natural blue pigment indigoidine [5,5′-diamino-4,4′-dihydroxy-3,3′-diazadiphenoguinone-(2,2′)]. In the following description, numerous specific details are provided for a thorough understanding of specific preferred embodiments. However, those skilled in the art will recognize that embodiments can be practiced without one or more of the specific details, or with other methods, components, materials, etc. In some cases, well-known structures, materials, or operations are not shown or described in detail in order to avoid obscuring aspects of the preferred embodiments. Furthermore, the described features, structures, or characteristics may be combined in any suitable manner in a variety of alternative embodiments. Thus, the following more detailed description of the embodiments of the present invention, as illustrated in some aspects in the drawings, is not intended to limit the scope of the invention, but is merely representative of the various embodiments of the invention.
In this specification and the claims that follow, singular forms such as “a,” “an,” and “the” include plural forms unless the content clearly dictates otherwise. All ranges disclosed herein include, unless specifically indicated, all endpoints and intermediate values. In addition, “optional” or “optionally” refer, for example, to instances in which subsequently described circumstance may or may not occur, and include instances in which the circumstance occurs and instances in which the circumstance does not occur. The terms “one or more” and “at least one” refer, for example, to instances in which one of the subsequently described circumstances occurs, and to instances in which more than one of the subsequently described circumstances occurs.
Expression System Configured to Co-Express Sc-IndB and Sc-IndC
The genes were amplified from the genomic DNA of S. chromofuscus ATCC 49982 and ligated into a cloning vector such as pJET1.2 for sequencing. The Sc-indC was ligated into expression vectors such as pRM5 and pET28a to yield pDY49 and pJV6. Sc-indA and Sc-indB are ligated into an expression vector such as pACYCDuet-1 to yield pDY52, pDY53 and pDY54 (for plasmids constructed for cloning and expression of biosynthetic genes, see FIGS. 1A-1H).
In embodiments, the present disclosure provides for an expression system useful for the production of the blue pigment indigoidine. Components of the expression system may include a host cell, a Sc-IndC protein, a nucleotide sequence encoding the Sc-IndC, a Sc-IndB protein, and a nucleotide sequence encoding the Sc-IndB. The nucleotide sequences may be provided on a single vector or multiple vectors. The nucleotide sequences may be operatively linked to a promoter or promoters. For example, nucleotide sequences encoding Sc-IndC and Sc-IndB, and the promoter sequence, may be configured for the transcription of each gene to be driven by a single promoter. Alternatively, the genes may be configured such that different promoters drive the transcription of each gene.
In embodiments, the genes encoding Sc-IndC and Sc-IndB are provided on at least one vector. Preferably, the genes are provided on a single vector. Alternatively, the nucleotide sequences encoding the Sc-IndC and Sc-Ind B proteins may be incorporated in a host genome. Vectors may include pET28, pACYCDuet-1, pRM5 and other expression or integration vectors.
In embodiments, expression systems of the present disclosure include a heterologous host cell. Host cells may include bacteria, yeast, or mammalian cells. Preferably, host cells may have an endogenous PPTase that contributes to the activation of the T domain of Sc-IndC. Alternatively, an exogenous PPTase may be provided as part of the expression system. For example, PPTase may be provided on the same vector that provides for at least one of Sc-IndC or Sc-IndB, on a separate vector, or integrated into the host genome.
Polynucleotide and Polypeptide Sequences
It is an object of the present disclosure to provide nucleotide sequences that encode for polypeptides that function in the biosynthesis of blue pigment indigoidine. SEQ ID NO:1 is a DNA sequence that encodes for the polypeptide amino acid sequence SEQ ID NO:2. SEQ ID NO:2 is an amino acid sequence that serves as the primary structure of an exemplary Sc-IndB protein. SEQ ID NO:3 is a DNA sequence that encodes for the polypeptide amino acid sequence SEQ ID NO:4. SEQ ID NO:4 is an amino acid sequence that serves as the primary structure of an exemplary Sc-IndC protein.
It is a further object of this disclosure to provide functional equivalents of the listed isolated nucleic acid molecules and derivatives thereof. For example, the nucleic acid sequences depicted in SEQ ID NO:1 or SEQ ID NO:3 can be altered by substitutions, additions or deletions that provide for functionally equivalent molecules. Due to the degeneracy of nucleotide coding sequences, other DNA sequences which encode substantially the same amino acid sequence as depicted in SEQ ID NO:1 and SEQ ID NO:3 can be used in the practice of the present invention. These include but are not limited to nucleotide sequences comprising all or portions of the nucleic acid depicted in SEQ ID NO:1 and 3, which are altered by the substitution of different codons that encode the same amino acid residue, or a functionally equivalent amino acid residue within the sequence.
It is yet another object of the present disclosure to provide nucleotide sequence which result from the addition, deletion or substitution of at least one nucleotide to the 5′-end and/or the 3′-end of the nucleic acid formula shown in SEQ ID NO:1 and 3, or a derivative thereof. Any nucleotide or polynucleotide can be used in this regard, provided that its addition, deletion or substitution does not substantially alter the amino acid sequence of SEQ ID NO:2, or SEQ ID NO:4 which is encoded by the nucleotide sequence. Moreover, the nucleic acid molecule of the present invention can, as necessary, have restriction endonuclease recognition sites added to its 5′-end and/or 3′-end. Examples of 5′-end and 3′-end modifications include the introduction of additional nucleotides including ribosomal binding sites and various protein tags.
Further, it is possible to delete codons or to substitute one or more codons by codons other than degenerate codons to produce a structurally modified polypeptide, but one which has substantially the same utility or activity of the polypeptide produced by the unmodified nucleic acid molecule. As recognized in the art, the two polypeptides are functionally equivalent, as are the two nucleic acid molecules which give rise to their production, even though the differences between the nucleic acid molecules are not related to degeneracy of the genetic code.
As used herein, terms herein referring to nucleic acid molecules such as “isolated polynucleotide molecule,” “DNA sequence,” and “nucleotide sequence”, and the like, unless otherwise specified, include both single-stranded and double-stranded DNA molecules. Any reference to a “Sequence Listing” or a “SEQ ID NO” is intended to refer to both the DNA of the “Sequence Listing” includes sequences complementary to the DNA sequences.
References to sequences homologous to a sequence, or sequence listing, are to be understood to include sequences homologous to a sequence corresponding to the referenced sequence and sequences homologous to a sequence complementary to the referenced sequence.
Polynucleotide molecules of the present invention include both synthetic molecules and molecules obtained through recombinant techniques, such as by in vitro cloning and transcription.
For purposes of the present disclosure, the nucleotide sequence of a second polynucleotide molecule is “homologous” to the nucleotide sequence of a first polynucleotide molecule where the nucleotide sequence of the second polynucleotide molecule encodes the same polypeptide as the nucleotide sequence of the first polynucleotide molecule as based on the degeneracy of the genetic code, or when it encodes a polypeptide that is sufficiently similar to the polypeptide encoded by the nucleotide sequence of the first polynucleotide molecule so as to provide at least one in-vivo or in-vitro biological function that corresponds to a function of the polypeptide encoded by the nucleotide sequence of the first polynucleotide molecule and identified in the present disclosure. Generally, the nucleotide sequence of a second polynucleotide molecule is homologous to the nucleotide sequence of a first polynucleotide molecule if it has at least about 70% nucleotide sequence identity to the nucleotide sequence of the first polynucleotide molecule as based on the BLASTN algorithm (National Center for Biotechnology Information, otherwise known as NCBI, (Bethesda, Md., USA) of the United States National Institute of Health). Preferably, a homologous nucleotide sequence has at least about 75% nucleotide sequence identity, even more preferably at least about 85% nucleotide sequence identity. Since the genetic code is degenerate, a homologous nucleotide sequence can include any number of “silent” base changes, i.e. nucleotide substitutions that nonetheless encode the same amino acid. A homologous nucleotide sequence can further contain non-silent mutations, i.e. base substitutions, deletions, or additions resulting in amino acid differences in the encoded polypeptide, so long as the polypeptide sequence remains at least about 70% identical to the polypeptide encoded by the first nucleotide sequence or otherwise provides at least one in-vivo or in-vitro biological function that corresponds to a function of the polypeptide encoded by the nucleotide sequence of the first polynucleotide molecule.
Homologous nucleotide sequences can be determined by comparison of nucleotide sequences, for example by using BLASTN, above. Alternatively, homologous nucleotide sequences can be determined by hybridization under selected conditions. For example, the nucleotide sequence of a second polynucleotide molecule is homologous to SEQ ID NO:1 if it hybridizes to the complement of SEQ ID NO:1 under moderately stringent conditions, e.g., hybridization to filter-bound DNA in 0.5 M NaHPO.sub.4, 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65.degree. C., and washing in 0.2.times.SSC/0.1.degree./0 SDS at 42.degree. C., or conditions that will otherwise result in hybridization of sequences. In another embodiment, a second nucleotide sequence is homologous to SEQ ID NO:1 if it hybridizes to the complement of SEQ ID NO:1 under highly stringent conditions, e.g. hybridization to filter-bound DNA in 0.5 M NaHPO.sub.4, 7% SDS, 1 mM EDTA at 65.degree. C., and washing in 0.1.times.SSC/0.1% SDS at 68.degree. C.
Production of Indigoidine by Co-Expression of Sc-IndC and Sc-IndB
In one embodiment, the present disclosure provides methods of co-expressing Sc-IndC and Sc-IndB proteins to upregulate the production of a blue pigment indigoidine in a heterologous host. The methods are based, in part, on the unexpected discovery that co-expressing Sc-IndC and Sc-IndB proteins can greatly increase the yield of the blue pigment indigoidine. For example, the production of blue pigment indigoidine may be carried out by co-expressing Sc-IndC and Sc-IndB proteins in E. coli. Generally, the methods described herein provide for increased yield when compared to conventional methods. Preferably, the increased yield is higher than the yield observed for Sc-IndC or Sc-IndB expressed alone.
Exemplary fermentation conditions for the synthesis of the blue pigment indigoidine are provided herein. The exemplary fermentation conditions are provided in order to give guidance to those in the art who want to explore the broad concepts presented herein, and are not intended to limit the scope of the embodiments of the invention that are related to co-expressing Sc-IndC and Sc-IndB proteins.
Sequencing and Nucleotide Sequence Discovery
The present disclosure describes the discovery of a 9.4-kb biosynthetic gene cluster from S. chromofuscus ATCC 49982 that contains five open reading frames (ORFs), including a putative indigoidine synthase gene, designated Sc-indC. The Sc-indC gene and two other genes from the same gene cluster, Sc-indA and Sc-indB, were cloned. The identification of Sc-indB ultimately contributed to the discovery that co-expressing Sc-IndB and Sc-IndC, in a heterologous host, provides for the upregulation of the expression of the blue pigment indigoidine.
The present disclosure also provides for isolated, cDNA nucleotide sequences, related to SEQ ID NO: 1, which encode Sc-IndB proteins having an amino acid sequence related to SEQ ID NO: 2. SEQ ID NO: 1 is an exemplary sequence for providing an Sc-IndB protein, and is not necessarily intended to limit the scope to the present invention. Due to the degeneracy of the genetic code, various modifications to SEQ ID NO: 1 would result in the same polypeptide sequence of amino acids, and thus the same Sc-IndB protein, as provided by SEQ ID NO: 1. For the purpose of the present invention, it is sufficient that a nucleotide sequence encode for a Sc-IndB protein, or a functional sub-unit of a Sc-IndB protein. Preferably, the Sc-IndB protein comprises the polypeptide amino acid sequence shown in SEQ ID NO: 2.
Expression of Sc-IndC
Heterologous expression of Sc-IndC in S. coelicolor CH999 and E. coli BAP1 demonstrated that Sc-IndC is responsible, at least in part, for the synthesis of the blue pigment indigoidine. The fermentation conditions for indigoidine production in E. coli BAP1 were studied and optimized. The engineered E. coli BAP1 strain that expresses Sc-IndC may be grown in a fermentation medium such as LB medium. When the OD600 reaches 0.4 ̃1.0, an inducer such as isopropyl-1-thio-β-D-galactopyranoside (IPTG) and lactose will be added to induce protein expression and indigoidine production. The induced fermentation broth may be maintained at a temperature between 16 and 28° C. for 10 ̃20 hrs. Generally, any temperature suitable for fermentation may be used. Applicant has unexpectedly discovered, and the present disclosure provides, methods for production of blue pigment indigoidine comprising co-expressing Sc-IndC and Sc-IndB proteins that result in higher yields than those achieved with conventional methods.
Bacterial Strains, Vectors, and Culture Conditions
Any suitable bacterial strain, vector or culture condition may be used for the synthesis of the blue pigment indigoidine. By way of example, suitable bacterial strains include E. coli strains. Alternatively, any species or strain of Streptomyces may be used. Broadly, a suitable bacterial strain is any strain capable of expressing Sc-IndB and Sc-IndC proteins. There is no requirement that the mere expression of Sc-IndB and Sc-IndC proteins in a suitable bacterial strain result in the synthesis of the blue pigment indigoidine. It is acceptable that the suitable bacterial strain may require further engineering for the expression of Sc-IndB and Sc-IndC proteins to result in the synthesis of the blue pigment indigoidine. Preferably, the suitable bacterial strain may be pre-engineered to synthesize the blue pigment indigoidine when expression of Sc-IndB and Sc-IndC proteins are co-expressed. In some embodiments, Sc-IndB proteins and Sc-IndC proteins may be provided by a vector or vectors that encode for the proteins. The vector or vectors may be plasmids.
Extraction Methods
The present disclosure also provides a new, efficient and economical extraction and purification method for indigoidine. The first step is to remove E. coli cells from the fermentation broth by low-speed centrifugation. At a low centrifugation speed, the cells will be pelleted while indigoidine stays in the supernatant. The supernatant will be transferred into a new centrifugation tube and will be further centrifuged at a much higher speed to pellet indigoidine. This settled blue pigment will then successively be washed with water, methanol, ethyl acetate and hexanes to remove impurities to afford pure indigoidine.
The present disclosure also provides for the sequencing of a genome of S. chromofuscus ATCC 49982. Sequencing of the genome of S. chromofuscus ATCC 49982 led to the identification a noniterative type I polyketide biosynthetic gene cluster that is responsible for the biosynthesis of herboxidiene.
The present disclosure also provides for the discovery of a 9.4-kb biosynthetic gene cluster from S. chromofuscus ATCC 49982 that contains five open reading frames (ORFs), including a putative indigoidine synthase gene, designated Sc-indC. The Sc-indC gene and two other genes from the same gene cluster, Sc-indA and Sc-indB, were cloned.
The following examples are illustrative only and are not intended to limit the disclosure in any way. One skilled in the art would recognize various known methods and conditions for expressing or co-expressing proteins, for carrying out fermentation, and for extractions. Each of these various embodiments are within the scope of the invention.
EXAMPLES
The following material and methods may be used in carrying out the various embodiments of the invention.
Example 1
Bacterial Strains, Vectors, and Culture Conditions
S. chromofuscus ATCC 49982 was obtained from the American Type Culture Collection (ATCC). It was grown at 30° C. in YEME medium for the preparation of genomic DNA. S. coelicolor CH999 and E. coli BAP1 were obtained from Stanford University. S. coelicolor CH999 was grown in R5 medium at 30° C. The pRM5-derived plasmid pJX28 carrying the thiostrepton-resistance gene was used as an E. coli/Streptomyces shuttle vector to express Sc-IndC in S. coelicolor CH999. For the blue pigment synthesis, the engineered strain of S. coelicolor CH999 was cultured at 30° C. in R5 medium supplemented with 50 μg/ml thiostrepton.
E. coli XL1-Blue (Agilent) and pJET1.2 (Fermentas) were used for DNA cloning and sequencing. E. coli BAP1 and pET28a (Novagen) were used for protein expression and pACYCDuet-1 (Novagen) was used for the co-expression experiments. E. coli cells were grown in Luria-Bertani (LB) medium. When necessary, appropriate antibiotics were added at the following concentrations: ampicillin, 50 μg/ml; kanamycin, 50 μg/ml; and chloramphenicol, 25 μg/ml. For protein expression and product synthesis, 200 μM of IPTG was added into the E. coli BAP1 cultures for induction.
Example 2
DNA Manipulations
The genomic DNA of S. chromofuscus was isolated using standard methods. Plasmids in E. coli were extracted using a GeneJETTM Plasmid Miniprep Kit (Fermentas).
Example 3
Genome Sequencing and Homology Analysis of the Predicted Proteins
The genomic DNA of S. chromofuscus ATCC 49982 was sequenced using a 454 GS FLX+ next-generation DNA sequencer and annotated with RAST (Rapid Annotation using Subsystem Technology). The 9,457-kb indigoidine biosynthetic gene cluster was further analyzed through FramePlot and BLAST, and was deposited in GenBank under accession number JX499187.
Example 4
Expression of Sc-IndC in S. coelicolor CH999
The gene Sc-indC was amplified by PCR from the genome of S. chromofuscus ATCC 49982 with Phusion® Hot Start High-Fidelity DNA Polymerase (New England Biolabs) using a pair of primers, 5′-aaTTAATTAAGGAGGAGCCCATatgagcgtagagaccatccc-3′ (the PacI and NdeI sites are underlined) and a 5′-aaGCTAGCAAGCTTtcagtagttgggcgtcttgc-3′ (the NheI and HindIII sites are underlined). The amplified Sc-indC was ligated into the cloning vector pJET1.2 to yield pJV3 (Table 1).







TABLE 1







Description of plasmids constructed.










Plasmid
Description







pJV1
Sc-indA in pJET1.2



pJV2
Sc-indB in pJET1.2



pJV3
Sc-indC in pJET1.2



pDY49
Sc-indC in pRM5



pJV6
Sc-indC in pET28a



pDY52
Sc-indA pACYCDuet-1



pDY53
Sc-indB in pACYCDuet-1




Sc-indA and Sc-indB in



pDY54
pACYCDuet-1 under two




separated T7 promoters










The Sc-indC insert was excised from pJV3 with PacI and NheI and ligated into pJX28 between the same sites to generate pDY49 (Table 1). The plasmid was introduced into S. coelicolor CH999 by protoplast transformation, and confirmed transformants were selected on R5 agar containing 50 μg/ml thiostrepton after 5 ̃7 days of incubation at 30° C. The correct transformant was grown in 50 ml of R5 medium supplemented with 50 μg/ml thiostrepton, which was maintained at 30° C. with shaking at 250 rpm for 5 ̃7 days to produce indigoidine.
Example 5
Expression of Sc-IndC in E. coli BAP1
The Sc-indC gene was excised from pJV3 by digestion with NdeI and HindIII and inserted into the same sites of pET28a to generate pJV6 (Table 1). The plasmid was introduced into E. coli BAP1 and correct transformants were selected on LB agar supplemented with 50 μg/ml kanamycin. To reconstitute the biosynthesis of indigoidine, the correct transformant was grown in LB broth supplemented with 50 μg/ml kanamycin at 37° C. and 250 rpm. When the OD600 reached 0.4 ̃1.0, 200 μM of IPTG was added to induce the expression of Sc-IndC at a lower temperature (18° C. or 25° C.).
Example 6
Co-Expression of Sc-IndC with Sc-IndA and/or Sc-IndB in E. coli BAP1
The Sc-indA gene was amplified by PCR from the S. chromofuscus genome using 5′-aaCATatggacgatccccgccccccg-3′ (the NdeI site is underlined) and 5′-aatcactggtcttcctcgtc-3′. The amplified Sc-indA gene was ligated with the pJET1.2 vector to yield pJV1 (Table 1). The Sc-indA gene was excised from pJV1 by digestion with NdeI and XhoI (on pJET1.2) and inserted into MCS2 of the pACYCDuet-1 vector between the same sites to yield pDY52 (Table 1). The Sc-indB gene was amplified by PCR from the S. chromofuscus genome using 5′-aaGGATCCatgttcgacctggacggaac-3′ (the BamHI site is underlined) and 5′-aaAAGCTTtcagtcgaccgggggctgct-3′ (the HindIII site is underlined). The amplified Sc-indB gene was ligated with the pJET1.2 vector to yield pJV2 (Table 1). After gene sequencing, Sc-indB was excised from pJV2 by digestion with BamHI and HindIII and inserted into MCS1 of the pACYCDuet-1 vector between the same sites to yield pDY53 (Table 1). The Sc-indA gene was excised from pJV1 using NdeI and BglII (on pJET1.2) and ligated into MCS2 of pDY53 between the same sites to afford pDY54 (Table 1). Each of these pACYCDuet-1 derived plasmids (pDY52, pDY53 and pDY54) was introduced with pJV6 into E. coli BAP1. Co-expression experiments of Sc-indC with Sc-indA and/or Sc-indB in E. coli BAP1 were performed at 18° C.
Example 7
Extraction and Analysis of Indigoidine
To extract the blue pigment indigoidine, 1 ml of dark blue fermentation broth was taken into a 1.5-ml Eppendorf tube, which was centrifuged at 21,000×g for 10 minutes. The supernatant was discarded, and the pellet was washed with 1 ml of methanol three times with gentle vortexing to remove other metabolites from the cells. By centrifugation at 21,000×g for 10 minutes, the crude blue pigment was collected, dried in vacuo and dissolved in 1 ml of dimethyl sulfoxide by sonication. The dimethyl sulfoxide-insoluble components and cell debris were removed by centrifugation (850×g, 5 minutes). The solution of indigoidine in dimethyl sulfoxide was analyzed on an Agilent 1200 HPLC and 6130 Single Quad LC/MS (C18, 5 μm, 4.6×150 mm column), eluted with a linear gradient of 10-90% aqueous methanol over 25 minutes at a flow rate of 1 ml/min.
Example 8
Preparation of a Standard Curve for Indigoidine to Measure the Yields
To obtain pure indigoidine for a standard curve, the fermentation broth was centrifuged at 850×g for 5 minutes. At this speed, the cells were pelleted while indigoidine still remained in the supernatant. After removal of the cells, the supernatant was further centrifuged at a much higher speed (21,000×g) for 10 minutes to allow indigoidine to settle. This blue pigment was then successively washed twice with water, methanol, ethyl acetate and hexanes to remove impurities, which yielded pure indigoidine.
1 mg of purified indigoidine was dissolved in 1 ml of dimethyl sulfoxide. This solution was then serially diluted into six different concentrations (0.01, 0.025, 0.05, 0.10, 0.20 and 0.25 mg/ml). Each solution was measured for OD600 values on a Thermo Scientific GENESYS 20 Visible Spectrophotometer. The standard curve was established by the linear relationship between the absorbance and concentration.
Example 9
SDS-PAGE Analysis of Protein Expression
The engineered E. coli BAP1 strains were grown in 100 ml of LB medium supplemented with appropriate antibiotics and induced with 200 μM IPTG at 18° C. for 12 hours. The cells were collected by centrifugation at 2,700×g for 5 minutes and resuspended in 3 ml of lysis buffer (20 mM Tris-Cl, 500 mM NaCl, pH 7.9). After 10 minutes of ultrasonication (18 W, 30 s of interval), the resultant lysates were centrifuged at 21,000×g for 10 minutes. Insoluble proteins were dissolved in 8 M urea. Both soluble and insoluble fractions were analyzed by 12% SDS-PAGE.
Example 10
Analysis of a Putative Indigoidine Biosynthetic Gene Cluster
Referring now to FIG. 2, A 9.4-kb putative indigoidine biosynthetic gene cluster was found in the genome of S. chromofucus ATCC 49982 (Table 2). It contains five ORFs. The first ORF was named orf1, which encodes a putative transmembrane transporter. The second ORF Sc-indC encodes an indigoidine synthase that is homologous to IndC from E. chrysanthemi. IndC is a NRPS that synthesizes indigoidine in E. chrysanthemi. Further analysis of Sc-IndC showed that this protein contains an adenylation (A) domain, a thiolation (T) domain, a thioesterase (TE) domain, and an oxidation (Ox) domain that is embedded in the A domain. This structural organization is the same as other homologues such as BpsA from S. lavendulae ATCC 11924. Two conserved core motifs, DDFFELGGNSL (963-973) and GYSFG (1099-1103), were found in the T and TE domains, respectively. The A domain has the signature sequence DAWQFGLINK for recognition of L-glutamine, which is the precursor for indigoidine biosynthesis. This further suggested that Sc-IndC is an indigoidine synthase. The predicted protein product of the third ORF Sc-indA is similar to IndA that was previously found in the indigoidine biosynthetic pathway in E. chrysanthemi, although the function of IndA in indigoidine biosynthesis is still unclear. The fourth ORF Sc-indB in this gene cluster encodes a 614-aa protein. Interestingly, the N-terminal portion (1-221 aa) of this unusual protein is a homologue of IdgB from E. chrysanthemi, while the C-terminal part (217-614) resembles SclaA2—37635 of Streptomyces clavuligerus, which is a hypothetical protein without a known function. IndB and IdgB have been previously reported in the indigoidine biosynthetic pathway in different strains of E. chrysanthemi.







TABLE 2







Deduced functions of ORFs in the indigoidine biosynthetic gene cluster












No. of

% identity/



Gene
amino acids
Protein homologue (accession no.)
similarity
Proposed function














orf1
421
Transmembrane transporter of Streptomyces
55/68
Transmembrane




hygroscopicus ATCC 53653 (EFL27184)

transporter


Sc-indC
1,377
IndC of Erwinia chrysanthemi (CAB87990)
54/71
Indigoidine synthase


Sc-indA
317
IndA of E. chrysanthemi (CAB87988)
65/80
Hypothetical protein


Sc-indB
614
1-221
51/62
Predicted phosphatase




IdgB of E. chrysanthemi (AAF74780)




227-614
54/67
Hypothetical protein




SclaA2_37635 of Streptomyces clavuligerus




ATCC 27064 (ZP_08221604)


orf2
238
SanR of Streptomyces ansochromogenes
76/84
Phosphoribosyl




(AAG48136)

transferase-type I






domain









In this studied gene cluster, Sc-IndB appears to be a fusion protein of two proteins and it is unknown what role it plays in indigoidine biosynthesis in S. chromofucus ATCC 49982. The last ORF is named orf2, which encodes a phosphoribosyl transferase and is homologous to SanR of Streptomyces ansochromogenes (Table 2).
Example 11
Reconstitution of Sc-IndC and Indigoidine Biosynthesis in S. coelicolor CH999
Unexpectedly, although a putative indigoidine biosynthetic gene cluster was located in the genome of S. chromofucus ATCC 49982, no blue pigments were detected from the extract of this bacterium, which indicated that this gene cluster is silent in S. chromofucus ATCC 49982 under laboratory conditions. In order to identify the function of Sc-indC, this gene was ligated into an E. coli/Streptomyces shuttle vector to yield pDY49 (Table 1). This plasmid was introduced through protoplast transformation into S. coelicolor CH999.
Referring now to FIG. 3, the engineered strain of S. coelicolor CH999/pDY49 was grown in R5 medium supplemented with 50 μg/ml thiostrepton at 30° C. and was found to produce a blue pigment (FIG. 3A). The pigment was extracted and re-dissolved in dimethyl sulfoxide, which showed a bright blue color (FIG. 3B). LC-MS analysis of the extracted pigment at 600 nm showed a major peak at 9.64 min (FIG. 3C) that has a maximum UV absorption at 602 nm (FIG. 3D), which is consisted with that of indigoidine. ESI-MS spectrum of this compound showed a [M+H]+ peak at m/z 249, further confirming that this product is indigoidine. Thus, heterologous expression of Sc-indC confers the ability to synthesize indigoidine on S. coelicolor CH999. Accordingly, the function of Sc-IndC was characterized as an indigoidine synthase. A standard curve using purified indigoidine was established based on the absorbance at 600 nm and used to quantify the production of this pigment. In S. coelicolor CH999, the maximum yield of indigoidine achieved 593.5 mg/l after 6 days of cultivation.
Example 12
Reconstitution of Sc-IndC and Indigoidine Biosynthesis in E. coli BAP1
Compared with Streptomyces, E. coli possesses some advantages such as fast growth rate and high expression level for many heterologous proteins. E. coli is commonly used for heterologous expression of numerous enzymes including NRPSs and synthesis of their products. Because Sc-IndC is a NRPS, its T domain needs to be activated from the apo to holo form to be functional. Accordingly, a dedicated PPTase may be useful to transfer the phosphopantetheinyl group from coenzyme A to a conserved serine residue in the T-domain of Sc-IndC. E. coli BAP1 is an engineered strain of E. coli BL21(DE3) and harbors a sfp gene encoding a PPTase from Bacillus subtilis in the genome. The present disclosure provides for the use of E. coli BAP1 as a host to functionally reconstitute Sc-IndC. The Sc-indC gene was ligated into pET28a to yield pJV6 (Table 1), which was introduced into E. coli BAP1 for protein expression. As expected, the E. coli BAP1 cells transformed with pJV6 produced indigoidine (FIG. 4A). Compared to S. coelicolor CH999, the synthesis of this blue pigment in E. coli BAP1 is much faster. The blue color could be easily observed in the E. coli culture 30 minutes after IPTG induction.
Example 13
Production of Indigoidine in E. Coli BAP1
To optimize the production of indigoidine in E. coli BAP1, the fermentation conditions including the optimal OD600 value for IPTG induction, production temperature and fermentation time were investigated. E. coli BAP1/pJV6 was grown in four flasks containing 50 ml of LB medium supplemented with 50 μg/ml kanamycin at 37° C. The cultures were induced with 200 μM IPTG when the OD600 reached 0.4, 0.6, 0.8 and 1.0, respectively. The induced broths were maintained at 25° C. and 250 rpm for 13 hours, and then the yields of indigoidine were determined. As shown in FIG. 4B, induction of the fermentation broth at OD600 0.6 gave the best yield of the blue pigment.
By way of example, and without limiting the invention, the present disclosure provides for four different fermentation temperatures including 18° C., 25° C., 30° C. and 37° C. Almost no indigoidine synthesis was detected at 30° C. and 37° C., which might be attributed to the thermal instability and oxidability of indigoidine. Time course analysis was conducted to monitor the production of indigoidine at 18° C. and 25° C. As shown in FIG. 4C, the yield of indigoidine reached the highest (1.73 g/l) after 13 hours of IPTG induction at 25° C., while at 18° C. the best yield (2.78 g/l) was achieved at 28 hours. The yield of indigoidine dropped after the maximal point, suggesting that long fermentation or storage time may result in the degradation of this blue pigment.
Example 14
Investigation of the Stability of Indigoidine
Some antioxidants, such as ascorbic acid, are commonly used to stabilize indigoidine. It was previously reported indigoidine pigment was very stable in tetrahydrofuran and did not fade for over 1 month, but indigoidine was hardly dissolved in the solvent in our experiments. Instead, we found that dimethyl sulfoxide is a good solvent to dissolve the pigment. However, even in dimethyl sulfoxide, the blue color of indigoidine can fade at room temperature over months. Degradation of indigoidine is much faster in the fermentation broth, as seen in the time course of indigoidine production at 25° C. (FIG. 4C). We also tested the stability of indigoidine in the fermentation broth at room temperature and 4° C. As shown in FIG. 4D, indigoidine in cell-free LB medium was more stable at 4° C., while the color of the pigment at room temperature faded significantly after 2 days.
Example 15
Co-Expression of Sc-IndB and Sc-IndC Increases Indigoidine Biosynthesis
The Sc-indA and Sc-indB genes are present with Sc-indC in the same gene cluster in S. chromofucus ATCC 49982. To find out whether the Sc-indA and Sc-indB genes participate in indigoidine biosynthesis in S. chromofucus ATCC 49982, we constructed three plasmids using the pACYCDuet-1 vector, named pDY52, pDY53 and pDY54, which contain Sc-indA, Sc-indB, and Sc-indA and Sc-indB, respectively (Table 1). The plasmids were co-expressed in E. coli BAP1 with pJV6, separately. Both soluble and insoluble proteins of these strains were analyzed. SDS-PAGE analysis showed that Sc-IndA (33 kDa) and Sc-IndB (67 kDa) were co-expressed with Sc-IndC (150 kDa) in E. coli BAP1 cells at 18° C. (FIG. 5A). A comparison of the yield of indigoidine revealed that presence of Sc-IndB dramatically increased the production of indigoidine. As shown in FIG. 5B, E. coli BAP1/pJV6+pDY53 that expressed both Sc-IndC and Sc-IndB gave the highest yield of 3.93 g/l at 18° C. after 28 hours. Co-expression of Sc-IndA with Sc-IndC did not show any improvement in the production of the pigment. Instead, a slight decrease in the yield was observed. This is likely due to the extremely high expression level of Sc-IndA, which might have influenced the expression of other proteins in the cells. Similarly, a slightly lower yield of indigoidine than that in E. coli BAP1/pJV6+pDY53 was observed when Sc-IndC was co-expressed with both Sc-IndB and Sc-IndA (FIG. 5B).
Example 16
Production of the Blue Pigment Indigoidine
Indigoidine is a blue pigment that has been found in several different bacteria such as S. aureofaciens and E. chrysanthemi. It is a powerful radical scavenger for the producing strains. This pigment can be easily extracted and quantified. More and more useful properties of indigoidine have been discovered and utilized in recent years. In addition to the antimicrobial activity, the bright blue color of this natural product makes it a useful and sensitive indicator in biochemical studies. For instance, indigoidine has recently been developed into a versatile and universal reporter for bacteria and mammalian cells. The indigoidine synthase BpsA has also been used as a reporter for rapid and flexible measurement of PPTase activity. This system can be used for discovery and characterization of PPTase inhibitors.
The present disclosure provides for a new indigoidine biosynthetic gene cluster from the pharmaceutically important strain S. chromofucus ATCC 49982 which produces the anti-cholesterol compound herboxidiene, further expanding the spectrum of indigoidine-producing strains. This gene cluster is silent under laboratory conditions as no pigment formation was observed in the host. We were able to reconstitute this indigoidine biosynthetic pathway in two different heterologous hosts, S. coelicolor CH999 and E. coli BAP1. Sc-IndC is a single module NRPS that contains four domains (A, Ox, T and TE). It is proposed that the A domain selects and activates the substrate L-glutamine and transfers the precursor to the PPTase-activated T domain. The TE domain may hydrolyze the amino acid from the enzyme and catalyzes the cyclization to form 5-aminopiperidine-2,6-dione, which can be further oxidized and dimerized by the Ox domain to yield indigoidine. Thus, activation of Sc-IndC is critical to the biosynthesis of the pigment. Although no heterologous PPTase was introduced into S. coelicolor CH999, the strain appears to be an effective host for indigoidine biosynthesis. An endogenous PPTase may contribute to the activation of the T domain of Sc-IndC. The yield difference between S. coelicolor CH999 and E. coli BAP1 may be due to the efficiency of the PPTase and expression level of Sc-IndC.
A number of factors can affect the yield of indigoidine, such as fermentation time and temperature. In some embodiments, temperature may range from 18° C. and 25° C. Preferably, the temperature may be about 18° C. Low temperatures may attribute to the stability of the modular indigoidine synthase Sc-IndC and the product indigoidine. The yield of indigoidine drops after the maximum point, when the degradation rate is larger than the biosynthesis rate. This was revealed by the time course analysis at both 18° C. and 25° C. No pigment formation was observed at 30° C. and 37° C., suggesting that the production process prefers a lower temperature. The present disclosure provides for OD600 values useful in determining a suitable time to induce Sc-IndC in order to synthesize indigoidine. It is shown herein that OD600 values at which expression of Sc-IndC was induced with IPTG may influence the yield of indigoidine. Induction at four different OD600 values demonstrated that 0.6 appeared to be the best. Under the optimal fermentation conditions, the yield of indigoidine reached 2.78 g/l in E. coli BAP1.
Indigoidine is water-insoluble. The pigment precipitates during the fermentation, which provides a convenient way to harvest it by centrifugation. This compound is also not soluble in most organic solvents, and dimethyl sulfoxide appeared to be a suitable solvent for this pigment. Degradation of indigoidine is fast and it can be stored longer at lower temperatures.
Genes encoding IndA- and IndB-like proteins are often found in indigoidine biosynthetic pathways from different strains. However, the functions of these two proteins are still unknown. While IndA (or IdgA) is a hypothetical protein, IndB (or IdgB) is a putative phosphatase. A previous study has shown that an idgA mutant of E. chrysanthemi RA3B was deficient in the pigment production, while the idgB mutant produced only low level of indigoidine, suggesting that both IdgA and IdgB are involved in indigoidine biosynthesis in E. chrysanthemi RA3B. IndA- and IndB-like enzymes were also found in some other natural product biosynthetic pathways. For instance, AlnA and AlnB, which are homologous to IdgA and IdgB, respectively, have been found to be involved in the formation and attachment of the dioxan moiety in alnumycin biosynthesis in Streptomyces sp. CM020 through a gene disruption approach.
The present disclosure provides for a heterologous expression approach to investigate the functions of Sc-IndA and Sc-IndB. Sc-IndA had no obvious effects on the production of the blue pigment, while co-expression of Sc-IndB with Sc-IndC increased the yield of indigoidine by 41.4%. Sc-IndB is a unique fusion protein that has been for the first time found in an indigoidine biosynthetic pathway. Its N-terminal portion is similar to IdgB and other homologues, which is a putative phosphatase belonging to the family of haloacid dehalogenase-like hydrolases. However, Sc-IndB is nearly three times the size of IdgB and its homologues, as it has a large C-terminal domain without a known function. Although the exact function of Sc-IndB is still unknown, it is clear from this work that this unusual enzyme is involved in the biosynthesis of the blue pigment. Co-expression of this protein with Sc-IndC provides an effective way to significantly improve the production of indigoidine.
It will be appreciated that various of the above-disclosed and other features and functions, or alternatives thereof, may be desirably combined into many other different systems or applications. Also, various presently unforeseen or unanticipated alternatives, modifications, variations or improvements therein may be subsequently made by those skilled in the art, and are also intended to be encompassed by the following claims.

## Claims

1. An expression system for the production of blue pigment indigoidine, comprising:
(i) a heterologous host cell,
(ii) a DNA sequence encoding a Sc-IndB protein and having at least 85% identity to the amino acid sequence set forth in SEQ ID NO:2,
(iii) a DNA sequence encoding a Sc-IndC protein and having at least 85% identity to the amino acid sequence set forth in SEQ ID NO:4,
wherein the system is configured for the co-expression of the Sc-IndB and Sc-IndC.

2. The expression system of claim 1, wherein the DNA sequences encoding the Sc-IndB and Sc-IndC are provided on at least one vector.

3. The expression system of claim 2, wherein the DNA sequences are provided on a single vector.

4. The expression system of claim 1, wherein at least one of the DNA sequences encoding the Sc-IndB and Sc-IndC are integrated into the genome of the heterologous host genome.

5. The expression system of claim 1, further comprising a Bacillus subtilis-derived sfp gene.

6. The expression system of claim 1, further comprising a 4′-phosphopantetheinyl transferase (PPTase).

7. The expression system of claim 6, wherein the PPTase is an endogenous host PPTase.

8. The expression system of claim 6, wherein the PPTase is an exogenous PPTase.

9. The expression system of claim 1, wherein the DNA sequences encoding the Sc-IndB and Sc-IndC are operatively linked to at least one promoter.

10. The expression system of claim 9, wherein the DNA sequences encoding the Sc-IndB and Sc-IndC are operatively linked to a single promoter.

11. The expression system of claim 1, wherein the DNA sequence encoding the Sc-IndB protein is a sequence at least 85% identical to the sequence set forth in SEQ ID NO:1.

12. The expression system of claim 1, wherein the DNA sequence encoding the Sc-IndC protein is a sequence at least 85% identical to the sequence set forth in SEQ ID NO:3.

13. A method for synthesizing a blue pigment indigoidine, the method comprising:
co-expressing a Sc-IndB protein and a Sc-IndC protein in a heterologous host cell,
wherein the Sc-IndB protein has at least 85% identity to the amino acid sequence set forth in SEQ ID NO:2, and the Sc-IndC protein has at least 85% identity to the amino acid sequence set forth in SEQ ID NO:4.

14. The method of claim 13, wherein the heterologous host is a bacterium.

15. The method of claim 13, wherein the heterologous host further comprises a nucleotide sequence that encodes a Bacillus subtilis-derived sfp gene.

16. The method of claim 13, wherein the heterologous host expresses a phosphopantetheinyl transferase (PPTase).

17. The expression system of claim 1, wherein:
the Sc-IndB protein is encoded by the amino acid sequence set forth in SEQ ID NO:2, and
the Sc-IndC protein is encoded by the amino acid sequence set forth in SEQ ID NO:4.

18. The expression system of claim 1, wherein:
the DNA sequence encoding the Sc-IndB protein is the sequence set forth in SEQ ID NO:1, and
the DNA sequence encoding the Sc-IndC protein is the sequence set forth in SEQ ID NO:3.