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Martín JF, Liras P, Sánchez S. Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes. Front Microbiol 2021; 12:630694. [PMID: 33796086 PMCID: PMC8007912 DOI: 10.3389/fmicb.2021.630694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. There are two types of phosphorylations involved in the control of transcriptional factors: (1) phosphorylation of sensor kinases and transfer of the phosphate group to the receiver domain of response regulators, which alters the expression of regulator target genes. (2) Phosphorylation systems involving promiscuous serine/threonine/tyrosine kinases that modify proteins at several amino acid residues, e.g., the phosphorylation of the global nitrogen regulator GlnR. Another post-translational modification is the acetylation at the epsilon amino group of lysine residues. The protein acetylation/deacetylation controls the activity of many short and long-chain acyl-CoA synthetases, transcriptional factors, key proteins of bacterial metabolism, and enzymes for the biosynthesis of non-ribosomal peptides, desferrioxamine, streptomycin, or phosphinic acid-derived antibiotics. Acetyltransferases catalyze acetylation reactions showing different specificity for the acyl-CoA donor. Although it functions as acetyltransferase, there are examples of malonylation, crotonylation, succinylation, or in a few cases acylation activities using bulky acyl-CoA derivatives. Substrates activation by nucleoside triphosphates is one of the central reactions inhibited by lysine acetyltransferases. Phosphorylation/dephosphorylation or acylation/deacylation reactions on global regulators like PhoP, GlnR, AfsR, and the carbon catabolite regulator glucokinase strongly affects the expression of genes controlled by these regulators. Finally, a different type of post-translational protein modification is the phosphopantetheinylation, catalized by phosphopantetheinyl transferases (PPTases). This reaction is essential to modify those enzymes requiring phosphopantetheine groups like non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. Up to five PPTases are present in S. tsukubaensis and S. avermitilis. Different PPTases modify substrate proteins in the PCP or ACP domains of tacrolimus biosynthetic enzymes. Directed mutations of genes encoding enzymes involved in the post-translational modification is a promising tool to enhance the production of bioactive metabolites.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Paloma Liras
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, Mexico
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Cook TB, Pfleger BF. Leveraging synthetic biology for producing bioactive polyketides and non-ribosomal peptides in bacterial heterologous hosts. MEDCHEMCOMM 2019; 10:668-681. [PMID: 31191858 PMCID: PMC6540960 DOI: 10.1039/c9md00055k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/06/2019] [Indexed: 12/14/2022]
Abstract
Bacteria have historically been a rich source of natural products (e.g. polyketides and non-ribosomal peptides) that possess medically-relevant activities. Despite extensive discovery programs in both industry and academia, a plethora of biosynthetic pathways remain uncharacterized and the corresponding molecular products untested for potential bioactivities. This knowledge gap comes in part from the fact that many putative natural product producers have not been cultured in conventional laboratory settings in which the corresponding products are produced at detectable levels. Next-generation sequencing technologies are further increasing the knowledge gap by obtaining metagenomic sequence information from complex communities where production of the desired compound cannot be isolated in the laboratory. For these reasons, many groups are turning to synthetic biology to produce putative natural products in heterologous hosts. This strategy depends on the ability to heterologously express putative biosynthetic gene clusters and produce relevant quantities of the corresponding products. Actinobacteria remain the most abundant source of natural products and the most promising heterologous hosts for natural product discovery and production. However, researchers are discovering more natural products from other groups of bacteria, such as myxobacteria and cyanobacteria. Therefore, phylogenetically similar heterologous hosts have become promising candidates for synthesizing these novel molecules. The downside of working with these microbes is the lack of well-characterized genetic tools for optimizing expression of gene clusters and product titers. This review examines heterologous expression of natural product gene clusters in terms of the motivations for this research, the traits desired in an ideal host, tools available to the field, and a survey of recent progress.
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Affiliation(s)
- Taylor B Cook
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
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3
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Sucipto H, Pogorevc D, Luxenburger E, Wenzel SC, Müller R. Heterologous production of myxobacterial α-pyrone antibiotics in Myxococcus xanthus. Metab Eng 2017; 44:160-170. [PMID: 29030273 DOI: 10.1016/j.ymben.2017.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/01/2017] [Accepted: 10/05/2017] [Indexed: 11/17/2022]
Abstract
Myxopyronins (MXN) and corallopyronins (COR) are structurally related α-pyrone antibiotics from myxobacteria that represent a highly promising compound class for the development of broad-spectrum antibacterial therapeutic agents. Their ability to inhibit RNA polymerase through interaction with the "switch region", a novel target, distant from previously characterized RNA polymerase inhibitors (e.g. rifampicin), makes them particularly promising candidates for further research. To improve compound supply for further investigation of MXN, COR and novel derivatives of these antibacterial agents, establishment of an efficient and versatile microbial production platform for myxobacterial α-pyrone antibiotics is highly desirable. Here we describe design, construction and expression of a heterologous production and engineering platforms for MXN and COR to facilitate rational structure design and yield improvement approaches in the myxobacterial host strain Myxococcus xanthus DK1622. Optimization of the cultivation medium yielded significantly higher production titers of MXN A at around 41-fold increase and COR A at around 25-fold increase, compared to the standard CTT medium.
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Affiliation(s)
- Hilda Sucipto
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Domen Pogorevc
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Eva Luxenburger
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Silke C Wenzel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany.
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
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4
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Affiliation(s)
- Silke C. Wenzel
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
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5
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Molecular Mechanisms of Signaling in Myxococcus xanthus Development. J Mol Biol 2016; 428:3805-30. [DOI: 10.1016/j.jmb.2016.07.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/30/2016] [Accepted: 07/08/2016] [Indexed: 11/19/2022]
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Characterization of Discrete Phosphopantetheinyl Transferases in Streptomyces tsukubaensis L19 Unveils a Complicate Phosphopantetheinylation Network. Sci Rep 2016; 6:24255. [PMID: 27052100 PMCID: PMC4823652 DOI: 10.1038/srep24255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/23/2016] [Indexed: 11/08/2022] Open
Abstract
Phosphopantetheinyl transferases (PPTases) play essential roles in both primary metabolisms and secondary metabolisms via post-translational modification of acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs). In this study, an industrial FK506 producing strain Streptomyces tsukubaensis L19, together with Streptomyces avermitilis, was identified to contain the highest number (five) of discrete PPTases known among any species thus far examined. Characterization of the five PPTases in S. tsukubaensis L19 unveiled that stw ACP, an ACP in a type II PKS, was phosphopantetheinylated by three PPTases FKPPT1, FKPPT3, and FKACPS; sts FAS ACP, the ACP in fatty acid synthase (FAS), was phosphopantetheinylated by three PPTases FKPPT2, FKPPT3, and FKACPS; TcsA-ACP, an ACP involved in FK506 biosynthesis, was phosphopantetheinylated by two PPTases FKPPT3 and FKACPS; FkbP-PCP, an PCP involved in FK506 biosynthesis, was phosphopantetheinylated by all of these five PPTases FKPPT1-4 and FKACPS. Our results here indicate that the functions of these PPTases complement each other for ACPs/PCPs substrates, suggesting a complicate phosphopantetheinylation network in S. tsukubaensis L19. Engineering of these PPTases in S. tsukubaensis L19 resulted in a mutant strain that can improve FK506 production.
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Genetic engineering and heterologous expression of the disorazol biosynthetic gene cluster via Red/ET recombineering. Sci Rep 2016; 6:21066. [PMID: 26875499 PMCID: PMC4753468 DOI: 10.1038/srep21066] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/18/2016] [Indexed: 11/08/2022] Open
Abstract
Disorazol, a macrocyclic polykitide produced by the myxobacterium Sorangium cellulosum So ce12 and it is reported to have potential cytotoxic activity towards several cancer cell lines, including multi-drug resistant cells. The disorazol biosynthetic gene cluster (dis) from Sorangium cellulosum (So ce12) was identified by transposon mutagenesis and cloned in a bacterial artificial chromosome (BAC) library. The 58-kb dis core gene cluster was reconstituted from BACs via Red/ET recombineering and expressed in Myxococcus xanthus DK1622. For the first time ever, a myxobacterial trans-AT polyketide synthase has been expressed heterologously in this study. Expression in M. xanthus allowed us to optimize the yield of several biosynthetic products using promoter engineering. The insertion of an artificial synthetic promoter upstream of the disD gene encoding a discrete acyl transferase (AT), together with an oxidoreductase (Or), resulted in 7-fold increase in disorazol production. The successful reconstitution and expression of the genetic sequences encoding for these promising cytotoxic compounds will allow combinatorial biosynthesis to generate novel disorazol derivatives for further bioactivity evaluation.
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The substrate promiscuity of a phosphopantetheinyl transferase SchPPT for coenzyme A derivatives and acyl carrier proteins. Arch Microbiol 2016; 198:193-7. [PMID: 26748983 DOI: 10.1007/s00203-015-1179-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/24/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
Phosphopantetheinyl transferases (PPTases) catalyze the posttranslational modification of acyl carrier proteins (ACPs) in fatty acid synthases (FASs), ACPs in polyketide synthases, and peptidyl carrier proteins (PCPs) in nonribosomal peptide synthetases (NRPSs) in all organisms. Some bacterial PPTases have broad substrate specificities for ACPs/PCPs and/or coenzyme A (CoA)/CoA analogs, facilitating their application in metabolite production in hosts and/or labeling of ACPs/PCPs, respectively. Here, a group II PPTase SchPPT from Streptomyces chattanoogensis L10 was characterized to accept a heterologous ACP and acetyl-CoA. Thus, SchPPT is a promiscuous PPTase and may be used on polyketide production in heterologous bacterial host and labeling of ACPs.
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Oßwald C, Zipf G, Schmidt G, Maier J, Bernauer HS, Müller R, Wenzel SC. Modular construction of a functional artificial epothilone polyketide pathway. ACS Synth Biol 2014; 3:759-72. [PMID: 23654254 DOI: 10.1021/sb300080t] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Natural products of microbial origin continue to be an important source of pharmaceuticals and agrochemicals exhibiting potent activities and often novel modes of action. Due to their inherent structural complexity chemical synthesis is often hardly possible, leaving fermentation as the only viable production route. In addition, the pharmaceutical properties of natural products often need to be optimized for application by sophisticated medicinal chemistry and/or biosynthetic engineering. The latter requires a detailed understanding of the biosynthetic process and genetic tools to modify the producing organism that are often unavailable. Consequently, heterologous expression of complex natural product pathways has been in the focus of development over recent years. However, piecing together existing DNA cloned from natural sources and achieving efficient expression in heterologous circuits represent several limitations that can be addressed by synthetic biology. In this work we have redesigned and reassembled the 56 kb epothilone biosynthetic gene cluster from Sorangium cellulosum for expression in the high GC host Myxococcus xanthus. The codon composition was adapted to a modified codon table for M. xanthus, and unique restriction sites were simultaneously introduced and others eliminated from the sequence in order to permit pathway assembly and future interchangeability of modular building blocks from the epothilone megasynthetase. The functionality of the artificial pathway was demonstrated by successful heterologous epothilone production in M. xanthus at significant yields that have to be improved in upcoming work. Our study sets the stage for future engineering of epothilone biosynthesis and production optimization using a highly flexible assembly strategy.
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Affiliation(s)
- Corina Oßwald
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken,
Germany
| | | | | | - Josef Maier
- IStLS, Information Services to Life Science, Oberndorf a.N., Germany
| | | | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken,
Germany
| | - Silke C. Wenzel
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken,
Germany
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10
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Wang YY, Li YD, Liu JB, Ran XX, Guo YY, Ren NN, Chen X, Jiang H, Li YQ. Characterization and evolutionary implications of the triad Asp-Xxx-Glu in group II phosphopantetheinyl transferases. PLoS One 2014; 9:e103031. [PMID: 25036863 PMCID: PMC4103896 DOI: 10.1371/journal.pone.0103031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/25/2014] [Indexed: 01/11/2023] Open
Abstract
Phosphopantetheinyl transferases (PPTases), which play an essential role in both primary and secondary metabolism, are magnesium binding enzymes. In this study, we characterized the magnesium binding residues of all known group II PPTases by biochemical and evolutionary analysis. Our results suggested that group II PPTases could be classified into two subgroups, two-magnesium-binding-residue-PPTases containing the triad Asp-Xxx-Glu and three-magnesium-binding-residue-PPTases containing the triad Asp-Glu-Glu. Mutations of two three-magnesium-binding-residue-PPTases and one two-magnesium-binding-residue-PPTase indicate that the first and the third residues in the triads are essential to activities; the second residues in the triads are non-essential. Although variations of the second residues in the triad Asp-Xxx-Glu exist throughout the whole phylogenetic tree, the second residues are conserved in animals, plants, algae, and most prokaryotes, respectively. Evolutionary analysis suggests that: the animal group II PPTases may originate from one common ancestor; the plant two-magnesium-binding-residue-PPTases may originate from one common ancestor; the plant three-magnesium-binding-residue-PPTases may derive from horizontal gene transfer from prokaryotes.
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Affiliation(s)
- Yue-Yue Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu-Dong Li
- Department of Bioengineering, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Jian-Bo Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin-Xin Ran
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuan-Yang Guo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ni-Ni Ren
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hui Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang, China
- * E-mail: (HJ); (YQL)
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang, China
- * E-mail: (HJ); (YQL)
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Gemperlein K, Rachid S, Garcia RO, Wenzel SC, Müller R. Polyunsaturated fatty acid biosynthesis in myxobacteria: different PUFA synthases and their product diversity. Chem Sci 2014. [DOI: 10.1039/c3sc53163e] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Beld J, Sonnenschein EC, Vickery CR, Noel JP, Burkart MD. The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life. Nat Prod Rep 2014; 31:61-108. [PMID: 24292120 PMCID: PMC3918677 DOI: 10.1039/c3np70054b] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: up to 2013. Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from identification, characterization, structure determination, mutagenesis, inhibition, and engineering in synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of enzymes that post-translationally install a 4'-phosphopantetheine arm on various carrier proteins.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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Improvement of natamycin production by engineering of phosphopantetheinyl transferases in Streptomyces chattanoogensis L10. Appl Environ Microbiol 2013; 79:3346-54. [PMID: 23524668 DOI: 10.1128/aem.00099-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Phosphopantetheinyl transferases (PPTases) are essential to the activities of type I/II polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) through converting acyl carrier proteins (ACPs) in PKSs and peptidyl carrier proteins (PCPs) in NRPSs from inactive apo-forms into active holo-forms, leading to biosynthesis of polyketides and nonribosomal peptides. The industrial natamycin (NTM) producer, Streptomyces chattanoogensis L10, contains two PPTases (SchPPT and SchACPS) and five PKSs. Biochemical characterization of these two PPTases shows that SchPPT catalyzes the phosphopantetheinylation of ACPs in both type I PKSs and type II PKSs, SchACPS catalyzes the phosphopantetheinylation of ACPs in type II PKSs and fatty acid synthases (FASs), and the specificity of SchPPT is possibly controlled by its C terminus. Inactivation of SchPPT in S. chattanoogensis L10 abolished production of NTM but not the spore pigment, while overexpression of the SchPPT gene not only increased NTM production by about 40% but also accelerated productions of both NTM and the spore pigment. Thus, we elucidated a comprehensive phosphopantetheinylation network of PKSs and improved polyketide production by engineering the cognate PPTase in bacteria.
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Hornung C, Poehlein A, Haack FS, Schmidt M, Dierking K, Pohlen A, Schulenburg H, Blokesch M, Plener L, Jung K, Bonge A, Krohn-Molt I, Utpatel C, Timmermann G, Spieck E, Pommerening-Röser A, Bode E, Bode HB, Daniel R, Schmeisser C, Streit WR. The Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and L. pneumophila LqsA autoinducer synthases. PLoS One 2013; 8:e55045. [PMID: 23405110 PMCID: PMC3566124 DOI: 10.1371/journal.pone.0055045] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/18/2012] [Indexed: 01/13/2023] Open
Abstract
Janthinobacteria commonly form biofilms on eukaryotic hosts and are known to synthesize antibacterial and antifungal compounds. Janthinobacterium sp. HH01 was recently isolated from an aquatic environment and its genome sequence was established. The genome consists of a single chromosome and reveals a size of 7.10 Mb, being the largest janthinobacterial genome so far known. Approximately 80% of the 5,980 coding sequences (CDSs) present in the HH01 genome could be assigned putative functions. The genome encodes a wealth of secretory functions and several large clusters for polyketide biosynthesis. HH01 also encodes a remarkable number of proteins involved in resistance to drugs or heavy metals. Interestingly, the genome of HH01 apparently lacks the N-acylhomoserine lactone (AHL)-dependent signaling system and the AI-2-dependent quorum sensing regulatory circuit. Instead it encodes a homologue of the Legionella- and Vibrio-like autoinducer (lqsA/cqsA) synthase gene which we designated jqsA. The jqsA gene is linked to a cognate sensor kinase (jqsS) which is flanked by the response regulator jqsR. Here we show that a jqsA deletion has strong impact on the violacein biosynthesis in Janthinobacterium sp. HH01 and that a jqsA deletion mutant can be functionally complemented with the V. cholerae cqsA and the L. pneumophila lqsA genes.
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Affiliation(s)
- Claudia Hornung
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Anja Poehlein
- Laboratorium für Genomanalyse, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Frederike S. Haack
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Martina Schmidt
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Andrea Pohlen
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laure Plener
- Center for integrated Protein Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Center for integrated Protein Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Andreas Bonge
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Ines Krohn-Molt
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Christian Utpatel
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Gabriele Timmermann
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Eva Spieck
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Andreas Pommerening-Röser
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Edna Bode
- Molekulare Biotechnologie, Institut für Molekulare Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Molekulare Biotechnologie, Institut für Molekulare Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Rolf Daniel
- Laboratorium für Genomanalyse, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Christel Schmeisser
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Wolfgang R. Streit
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
- * E-mail:
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15
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Heterologous Expression and Genetic Engineering of the Tubulysin Biosynthetic Gene Cluster Using Red/ET Recombineering and Inactivation Mutagenesis. ACTA ACUST UNITED AC 2012; 19:361-71. [DOI: 10.1016/j.chembiol.2012.01.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 12/22/2011] [Accepted: 01/02/2012] [Indexed: 11/18/2022]
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Nair DR, Ghosh R, Manocha A, Mohanty D, Saran S, Gokhale RS. Two functionally distinctive phosphopantetheinyl transferases from amoeba Dictyostelium discoideum. PLoS One 2011; 6:e24262. [PMID: 21931666 PMCID: PMC3171403 DOI: 10.1371/journal.pone.0024262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 08/03/2011] [Indexed: 12/16/2022] Open
Abstract
The life cycle of Dictyostelium discoideum is proposed to be regulated by expression of small metabolites. Genome sequencing studies have revealed a remarkable array of genes homologous to polyketide synthases (PKSs) that are known to synthesize secondary metabolites in bacteria and fungi. A crucial step in functional activation of PKSs involves their post-translational modification catalyzed by phosphopantetheinyl transferases (PPTases). PPTases have been recently characterized from several bacteria; however, their relevance in complex life cycle of protozoa remains largely unexplored. Here we have identified and characterized two phosphopantetheinyl transferases from D. discoideum that exhibit distinct functional specificity. DiAcpS specifically modifies a stand-alone acyl carrier protein (ACP) that possesses a mitochondrial import signal. DiSfp in contrast is specific to Type I multifunctional PKS/fatty acid synthase proteins and cannot modify the stand-alone ACP. The mRNA of two PPTases can be detected during the vegetative as well as starvation-induced developmental pathway and the disruption of either of these genes results in non-viable amoebae. Our studies show that both PPTases play an important role in Dictyostelium biology and provide insight into the importance of PPTases in lower eukaryotes.
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Affiliation(s)
- Divya R Nair
- National Institute of Immunology, New Delhi, India
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Furusawa G, Dziewanowska K, Stone H, Settles M, Hartzell P. Global analysis of phase variation in Myxococcus xanthus. Mol Microbiol 2011; 81:784-804. [PMID: 21722202 PMCID: PMC3192537 DOI: 10.1111/j.1365-2958.2011.07732.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Myxococcus xanthus can vary its phenotype or 'phase' to produce colonies that contain predominantly yellow or tan cells that differ greatly in their abilities to swarm, survive and develop. Yellow variants are proficient at swarming (++) and tend to lyse in liquid during stationary phase. In contrast, tan variants are deficient in swarming (+) and persist beyond stationary phase. The phenotypes and transcriptomes of yellow and tan variants were compared with mutants affected in phase variation. Thirty-seven genes were upregulated specifically in yellow variants including those for production of the yellow pigment, DKxanthene. A mutant in DKxanthene synthesis produced non-pigmented (tan) colonies but still phase varied for swarming suggesting that pigmentation is not the cause of phase variation. Disruption of a gene encoding a HTH-Xre-like regulator, highly expressed in yellow variants, abolished pigment production and blocked the ability of cells to switch from a swarm ++ to a swarm (+) phenotype, showing that HTH-Xre regulates phase variation. Among the four genes whose expression was increased in tan variants was pkn14, which encodes a serine-threonine kinase that regulates programmed cell death in Myxococcus via the MrpC-MazF toxin-antitoxin complex. High levels of phosphorylated Pkn14 may explain why tan cells enjoy enhanced survival.
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Affiliation(s)
- Gou Furusawa
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3052
| | | | - Hannah Stone
- Program in Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID 83844-3052
| | - Matthew Settles
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3052
| | - Patricia Hartzell
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3052
- Program in Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID 83844-3052
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Buntin K, Irschik H, Weissman KJ, Luxenburger E, Blöcker H, Müller R. Biosynthesis of Thuggacins in Myxobacteria: Comparative Cluster Analysis Reveals Basis for Natural Product Structural Diversity. ACTA ACUST UNITED AC 2010; 17:342-56. [DOI: 10.1016/j.chembiol.2010.02.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 01/22/2010] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
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Wenzel SC, Müller R. Myxobacteria--'microbial factories' for the production of bioactive secondary metabolites. MOLECULAR BIOSYSTEMS 2009; 5:567-74. [PMID: 19462013 DOI: 10.1039/b901287g] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this article, we briefly review the potential of myxobacteria as 'natural product factories' by highlighting results from the recently sequenced myxobacterial model strain Myxococcus xanthus. We will focus on the production of polyketides, non-ribosomally-made peptides, and their hybrids, and discuss the evaluation of biosynthetic potential using genome-based methods, as well as biosynthetic process engineering.
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Affiliation(s)
- Silke C Wenzel
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
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