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Wan M, Gan L, Li Z, Wang M, Chen J, Chen S, Hu J, Li J. Enhancement of fungichromin production of Streptomyces sp. WP-1 by genetic engineering. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12672-4. [PMID: 37417973 DOI: 10.1007/s00253-023-12672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Fungichromin is a polyene macrolide antibiotic with potent killing activity against a broad range of agricultural pathogens and filamentous fungi and a wide range of potential applications. The production of fungichromin is still hampered by poor fermentation yield and high cost. In this study, the whole genome sequencing of fungichromin-producing Streptomyces sp. WP-1 was conducted, and the fungichromin biosynthetic gene cluster was identified. Comparative analysis revealed that the fungichromin biosynthetic gene cluster contains two regulatory genes, ptnF, and ptnR. The roles of ptnF and ptnR were determined through knockout and complementation. The yield of fungichromin was increased by overexpressing these two regulatory genes, as well as the crotonyl CoA reductase/carboxylase gene ptnB in Streptomyces sp. WP-1. The yield of fungichromin was increased to 8.5 g/L using a combination of genetic engineering and a medium optimization strategy, which is the highest fermentation titer recorded. KEY POINTS: • Confirmation of the positive regulation of ptnF and ptnR on fungichromin. • Improvement of fungichromin production by the construction of ptnF, ptnR, and ptnB overexpression strains. • Improvement of fungichromin production by the addition of soybean oil and copper ions at optimal concentration.
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Affiliation(s)
- Miyang Wan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Lu Gan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhenxin Li
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Mengran Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jingtao Chen
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Shaoxin Chen
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Jinfeng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiyang Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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System-Wide Analysis of the GATC-Binding Nucleoid-Associated Protein Gbn and Its Impact on
Streptomyces
Development. mSystems 2022; 7:e0006122. [PMID: 35575488 PMCID: PMC9239103 DOI: 10.1128/msystems.00061-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large part of the chemical space of bioactive natural products is derived from
Actinobacteria
. Many of the biosynthetic gene clusters for these compounds are cryptic; in others words, they are expressed in nature but not in the laboratory.
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KasQ an Epimerase Primes the Biosynthesis of Aminoglycoside Antibiotic Kasugamycin and KasF/H Acetyltransferases Inactivate Its Activity. Biomedicines 2022; 10:biomedicines10020212. [PMID: 35203422 PMCID: PMC8869731 DOI: 10.3390/biomedicines10020212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/07/2022] Open
Abstract
Kasugamycin (KSM), an aminoglycoside antibiotic, is composed of three chemical moieties: D-chiro-inositol, kasugamine and glycine imine. Despite being discovered more than 50 years ago, the biosynthetic pathway of KSM remains an unresolved puzzle. Here we report a structural and functional analysis for an epimerase, KasQ, that primes KSM biosynthesis rather than the previously proposed KasF/H, which instead acts as an acetyltransferase, inactivating KSM. Our biochemical and biophysical analysis determined that KasQ converts UDP-GlcNAc to UDP-ManNAc as the initial step in the biosynthetic pathway. The isotope-feeding study further confirmed that 13C, 15N-glucosamine/UDP-GlcNH2 rather than glucose/UDP-Glc serves as the direct precursor for the formation of KSM. Both KasF and KasH were proposed, respectively, converting UDP-GlcNH2 and KSM to UDP-GlcNAc and 2-N’-acetyl KSM. Experimentally, KasF is unable to do so; both KasF and KasH are instead KSM-modifying enzymes, while the latter is more specific and reactive than the former in terms of the extent of resistance. The information gained here lays the foundation for mapping out the complete KSM biosynthetic pathway.
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Woods C, Humphreys CM, Rodrigues RM, Ingle P, Rowe P, Henstra AM, Köpke M, Simpson SD, Winzer K, Minton NP. A novel conjugal donor strain for improved DNA transfer into Clostridium spp. Anaerobe 2019; 59:184-191. [PMID: 31269456 PMCID: PMC6866869 DOI: 10.1016/j.anaerobe.2019.06.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/29/2022]
Abstract
Clostridium encompasses species which are relevant to human and animal disease as well as species which have industrial potential, for instance, as producers of chemicals and fuels or as tumour delivery vehicles. Genetic manipulation of these target organisms is critical for advances in these fields. DNA transfer efficiencies, however, vary between species. Low efficiencies can impede the progress of research efforts. A novel conjugal donor strain of Escherichia coli has been created which exhibits a greater than 10-fold increases in conjugation efficiency compared to the traditionally used CA434 strain in the three species tested; C. autoethanogenum DSM 10061, C. sporogenes NCIMB 10696 and C. difficile R20291. The novel strain, designated 'sExpress', does not methylate DNA at Dcm sites (CCWGG) which allows circumvention of cytosine-specific Type IV restriction systems. A robust protocol for conjugation is presented which routinely produces in the order of 105 transconjugants per millilitre of donor cells for C. autoethanogenum, 106 for C. sporogenes and 102 for C. difficile R20291. The novel strain created is predicted to be a superior conjugal donor in a wide range of species which possess Type IV restriction systems.
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Affiliation(s)
- Craig Woods
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Christopher M Humphreys
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Raquel Mesquita Rodrigues
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Patrick Ingle
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Peter Rowe
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anne M Henstra
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michael Köpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2RD, UK.
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5
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Yan Q, Fong SS. Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing. Front Microbiol 2017; 8:2060. [PMID: 29123506 PMCID: PMC5662904 DOI: 10.3389/fmicb.2017.02060] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/09/2017] [Indexed: 12/26/2022] Open
Abstract
Metabolic diversity in microorganisms can provide the basis for creating novel biochemical products. However, most metabolic engineering projects utilize a handful of established model organisms and thus, a challenge for harnessing the potential of novel microbial functions is the ability to either heterologously express novel genes or directly utilize non-model organisms. Genetic manipulation of non-model microorganisms is still challenging due to organism-specific nuances that hinder universal molecular genetic tools and translatable knowledge of intracellular biochemical pathways and regulatory mechanisms. However, in the past several years, unprecedented progress has been made in synthetic biology, molecular genetics tools development, applications of omics data techniques, and computational tools that can aid in developing non-model hosts in a systematic manner. In this review, we focus on concerns and approaches related to working with non-model microorganisms including developing molecular genetics tools such as shuttle vectors, selectable markers, and expression systems. In addition, we will discuss: (1) current techniques in controlling gene expression (transcriptional/translational level), (2) advances in site-specific genome engineering tools [homologous recombination (HR) and clustered regularly interspaced short palindromic repeats (CRISPR)], and (3) advances in genome-scale metabolic models (GSMMs) in guiding design of non-model species. Application of these principles to metabolic engineering strategies for consolidated bioprocessing (CBP) will be discussed along with some brief comments on foreseeable future prospects.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, United States
| | - Stephen S. Fong
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, United States
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
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6
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Petrus MLC, Vijgenboom E, Chaplin AK, Worrall JAR, van Wezel GP, Claessen D. The DyP-type peroxidase DtpA is a Tat-substrate required for GlxA maturation and morphogenesis in Streptomyces. Open Biol 2016; 6:150149. [PMID: 26740586 PMCID: PMC4736821 DOI: 10.1098/rsob.150149] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The filamentous bacterium Streptomyces lividans depends on the radical copper oxidase GlxA for the formation of reproductive aerial structures and, in liquid environments, for the formation of pellets. Incorporation of copper into the active site is essential for the formation of a cross-linked tyrosyl-cysteine cofactor, which is needed for enzymatic activity. In this study, we show a crucial link between GlxA maturation and a group of copper-related proteins including the chaperone Sco and a novel DyP-type peroxidase hereinafter called DtpA. Under copper-limiting conditions, the sco and dtpA deletion mutants are blocked in aerial growth and pellet formation, similarly to a glxA mutant. Western blot analysis showed that GlxA maturation is perturbed in the sco and dtpA mutants, but both maturation and morphology can by rescued by increasing the bioavailability of copper. DtpA acts as a peroxidase in the presence of GlxA and is a substrate for the twin-arginine translocation (Tat) translocation pathway. In agreement, the maturation status of GlxA is also perturbed in tat mutants, which can be compensated for by the addition of copper, thereby partially restoring their morphological defects. Our data support a model wherein a copper-trafficking pathway and Tat-dependent secretion of DtpA link to the GlxA-dependent morphogenesis pathway.
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Affiliation(s)
- Marloes L C Petrus
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Erik Vijgenboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Amanda K Chaplin
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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7
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Fujimoto M, Chijiwa M, Nishiyama T, Takano H, Ueda K. Developmental defect of cytochrome oxidase mutants of Streptomyces coelicolor A3(2). MICROBIOLOGY-SGM 2016; 162:1446-1455. [PMID: 27384768 DOI: 10.1099/mic.0.000332] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To study the link between energy metabolism and secondary metabolism/morphological development in Streptomyces, knockout mutants were generated with regard to the subunits of the cytochrome oxidase supercomplex (CcO) in Streptomyces coelicolor A3(2). All mutants exhibited an identical phenotype: viable but defective in antibiotic production and cell differentiation when grown in both complex and minimal media. The growth yield of the CcO mutant was about half of that of the WT strain on glucose medium while both strains grew similarly on maltose medium. Intracellular ATP measurement demonstrated that the CcO mutant exhibited high intracellular ATP level. A similar elevation of intracellular ATP level was observed with regard to the WT strain cultured in the presence of BCDA, a copper-chelating agent. Reverse transcriptase PCR analysis demonstrated that the transcription of ATP synthase operon is upregulated in the CcO mutant. Addition of carbonylcyanide m-chlorophenylhydrazone, an inhibitor of ATP synthesis, promoted antibiotic production and aerial mycelia formation in the CcO mutant and BCDA-treated WT cells. We hypothesize that the deficiency of CcO causes accumulation of intracellular ATP, and that the high ATP level inhibits the onset of development in S. coelicolor.
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Affiliation(s)
- Masahiro Fujimoto
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880 Fujisawa, Japan
| | - Masato Chijiwa
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880 Fujisawa, Japan
| | - Tatsuya Nishiyama
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880 Fujisawa, Japan
| | - Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880 Fujisawa, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880 Fujisawa, Japan
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8
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Locatelli FM, Goo KS, Ulanova D. Effects of trace metal ions on secondary metabolism and the morphological development of streptomycetes. Metallomics 2016; 8:469-80. [DOI: 10.1039/c5mt00324e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Structural and mechanistic insights into an extracytoplasmic copper trafficking pathway in Streptomyces lividans. Biochem J 2014; 459:525-38. [PMID: 24548299 DOI: 10.1042/bj20140017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In Streptomyces lividans an extracytoplasmic copper-binding Sco protein plays a role in two unlinked processes: (i) initiating a morphological development switch and (ii) facilitating the co-factoring of the CuA domain of CcO (cytochrome c oxidase). How Sco obtains copper once secreted to the extracytoplasmic environment is unknown. In the present paper we report on a protein possessing an HX₆MX₂₁HXM motif that binds a single cuprous ion with subfemtomolar affinity. High-resolution X-ray structures of this extracytoplasmic copper chaperone-like protein (ECuC) in the apo- and Cu(I)-bound states reveal that the latter possesses a surface-accessible cuprous-ion-binding site located in a dish-shaped region of β-sheet structure. A cuprous ion is transferred under a favourable thermodynamic gradient from ECuC to Sco with no back transfer occurring. The ionization properties of the cysteine residues in the Cys⁸⁶xxxCys⁹⁰ copper-binding motif of Sco, together with their positional locations identified from an X-ray structure of Sco, suggests a role for Cys⁸⁶ in initiating an inter-complex ligand-exchange reaction with Cu(I)-ECuC. Generation of the genetic knockouts, Δsco, Δecuc and Δsco/ecuc, and subsequent in vivo assays lend support to the existence of a branched extracytoplasmic copper-trafficking pathway in S. lividans. One branch requires both Sco and to a certain extent ECuC to cofactor the CuA domain, whereas the other uses only Sco to deliver copper to a cuproenzyme to initiate morphological development.
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10
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Proteomic Analysis of theStreptomyces griseusRibosomal Fraction. Biosci Biotechnol Biochem 2014; 76:2267-74. [DOI: 10.1271/bbb.120556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Lin W, Wang Y, Han X, Zhang Z, Wang C, Wang J, Yang H, Lu Y, Jiang W, Zhao GP, Zhang P. Atypical OmpR/PhoB subfamily response regulator GlnR of actinomycetes functions as a homodimer, stabilized by the unphosphorylated conserved Asp-focused charge interactions. J Biol Chem 2014; 289:15413-25. [PMID: 24733389 DOI: 10.1074/jbc.m113.543504] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The OmpR/PhoB subfamily protein GlnR of actinomycetes is an orphan response regulator that globally coordinates the expression of genes related to nitrogen metabolism. Biochemical and genetic analyses reveal that the functional GlnR from Amycolatopsis mediterranei is unphosphorylated at the potential phosphorylation Asp(50) residue in the N-terminal receiver domain. The crystal structure of this receiver domain demonstrates that it forms a homodimer through the α4-β5-α5 dimer interface highly similar to the phosphorylated typical response regulator, whereas the so-called "phosphorylation pocket" is not conserved, with its space being occupied by an Arg(52) from the β3-α3 loop. Both in vitro and in vivo experiments confirm that GlnR forms a functional homodimer via its receiver domain and suggest that the charge interactions of Asp(50) with the highly conserved Arg(52) and Thr(9) in the receiver domain may be crucial in maintaining the proper conformation for homodimerization, as also supported by molecular dynamics simulations of the wild type GlnR versus the deficient mutant GlnR(D50A). This model is backed by the distinct phenotypes of the total deficient GlnR(R52A/T9A) double mutant versus the single mutants of GlnR (i.e. D50N, D50E, R52A and T9A), which have only minor effects upon both dimerization and physiological function of GlnR in vivo, albeit their DNA binding ability is weakened compared with that of the wild type. By integrating the supportive data of GlnRs from the model Streptomyces coelicolor and the pathogenic Mycobacterium tuberculosis, we conclude that the actinomycete GlnR is atypical with respect to its unphosphorylated conserved Asp residue being involved in the critical Arg/Asp/Thr charge interactions, which is essential for maintaining the biologically active homodimer conformation.
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Affiliation(s)
- Wei Lin
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Ying Wang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology, the State Key Laboratory of Genetic Engineering, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaobiao Han
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Zilong Zhang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Chengyuan Wang
- State Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jin Wang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Huaiyu Yang
- the Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yinhua Lu
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Weihong Jiang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Guo-Ping Zhao
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology, the State Key Laboratory of Genetic Engineering, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China, the Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China, the Department of Microbiology and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China, and
| | - Peng Zhang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China,
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13
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Tan BG, Vijgenboom E, Worrall JAR. Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans. Nucleic Acids Res 2013; 42:1326-40. [PMID: 24121681 PMCID: PMC3902906 DOI: 10.1093/nar/gkt902] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. The copper sensitive operon repressor (CsoR) family is widely distributed in bacteria and controls the expression of copper efflux systems. CsoR operator sites consist of G-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. Here, we use a structurally characterized CsoR from Streptomyces lividans (CsoRSl) together with three specific operator targets to reveal the salient features pertaining to the mechanism of DNA binding. We reveal that CsoRSl binds to its operator site through a 2-fold axis of symmetry centred on a conserved 5′-TAC/GTA-3′ inverted repeat. Operator recognition is stringently dependent not only on electropositive residues but also on a conserved polar glutamine residue. Thermodynamic and circular dichroic signatures of the CsoRSl–DNA interaction suggest selectivity towards the A-DNA-like topology of the G-tracts at the operator site. Such properties are enhanced on protein binding thus enabling the symmetrical binding of two CsoRSl tetramers. Finally, differential binding modes may exist in operator sites having more than one 5′-TAC/GTA-3′ inverted repeat with implications in vivo for a mechanism of modular control.
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Affiliation(s)
- Benedict G Tan
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK and Molecular Biotechnology, Institute of Biology Leiden, Sylvius Laboratory, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands
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14
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Blundell KLIM, Wilson MT, Svistunenko DA, Vijgenboom E, Worrall JAR. Morphological development and cytochrome c oxidase activity in Streptomyces lividans are dependent on the action of a copper bound Sco protein. Open Biol 2013; 3:120163. [PMID: 23345541 PMCID: PMC3603459 DOI: 10.1098/rsob.120163] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Copper has an important role in the life cycle of many streptomycetes, stimulating the developmental switch between vegetative mycelium and aerial hyphae concomitant with the production of antibiotics. In streptomycetes, a gene encoding for a putative Sco-like protein has been identified and is part of an operon that contains two other genes predicted to handle cellular copper. We report on the Sco-like protein from Streptomyces lividans (ScoSl) and present a series of experiments that firmly establish a role for ScoSl as a copper metallochaperone as opposed to a role as a thiol-disulphide reductase that has been assigned to other bacterial Sco proteins. Under low copper concentrations, a Δsco mutant in S. lividans displays two phenotypes; the development switch between vegetative mycelium and aerial hyphae stalls and cytochrome c oxidase (CcO) activity is significantly decreased. At elevated copper levels, the development and CcO activity in the Δsco mutant are restored to wild-type levels and are thus independent of ScoSl. A CcO knockout reveals that morphological development is independent of CcO activity leading us to suggest that ScoSl has at least two targets in S. lividans. We establish that one ScoSl target is the dinuclear CuA domain of CcO and it is the cupric form of ScoSl that is functionally active. The mechanism of cupric ion capture by ScoSl has been investigated, and an important role for a conserved His residue is identified.
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Affiliation(s)
- Katie L I M Blundell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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15
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Guss AM, Olson DG, Caiazza NC, Lynd LR. Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:30. [PMID: 22559230 PMCID: PMC3536630 DOI: 10.1186/1754-6834-5-30] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/29/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Industrial production of biofuels and other products by cellulolytic microorganisms is of interest but hindered by the nascent state of genetic tools. Although a genetic system for Clostridium thermocellum DSM1313 has recently been developed, available methods achieve relatively low efficiency and similar plasmids can transform C. thermocellum at dramatically different efficiencies. RESULTS We report an increase in transformation efficiency of C. thermocellum for a variety of plasmids by using DNA that has been methylated by Escherichia coli Dam but not Dcm methylases. When isolated from a dam+dcm+E. coli strain, pAMG206 transforms C. thermocellum 100-fold better than the similar plasmid pAMG205, which contains an additional Dcm methylation site in the pyrF gene. Upon removal of Dcm methylation, transformation with pAMG206 showed a four- to seven-fold increase in efficiency; however, transformation efficiency of pAMG205 increased 500-fold. Removal of the Dcm methylation site from the pAMG205 pyrF gene via silent mutation resulted in increased transformation efficiencies equivalent to that of pAMG206. Upon proper methylation, transformation efficiency of plasmids bearing the pMK3 and pB6A origins of replication increased ca. three orders of magnitude. CONCLUSIONS E. coli Dcm methylation decreases transformation efficiency in C. thermocellum DSM1313. The use of properly methylated plasmid DNA should facilitate genetic manipulation of this industrially relevant bacterium.
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Affiliation(s)
- Adam M Guss
- Thayer School of Engineering, Dartmouth College, 8000 Cummings Hall, Hanover, NH 03755, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, 8000 Cummings Hall, Hanover, NH 03755, USA
- Mascoma Corporation, 67 Etna Rd, Suite 300, Lebanon, NH 03755, USA
| | - Nicky C Caiazza
- Mascoma Corporation, 67 Etna Rd, Suite 300, Lebanon, NH 03755, USA
- Current address: Synthetic Genomics Inc, La Jolla, CA 92037, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, 8000 Cummings Hall, Hanover, NH 03755, USA
- Mascoma Corporation, 67 Etna Rd, Suite 300, Lebanon, NH 03755, USA
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Farkašovská J, Godány A. Analysis of the Site-Specific Integration System of the Streptomyces aureofaciens Phage μ1/6. Curr Microbiol 2011; 64:226-33. [DOI: 10.1007/s00284-011-0054-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/07/2011] [Indexed: 10/14/2022]
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17
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Fujimoto M, Yamada A, Kurosawa J, Kawata A, Beppu T, Takano H, Ueda K. Pleiotropic role of the Sco1/SenC family copper chaperone in the physiology of Streptomyces. Microb Biotechnol 2011; 5:477-88. [PMID: 22117562 PMCID: PMC3815325 DOI: 10.1111/j.1751-7915.2011.00319.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Antibiotic production and cell differentiation in Streptomyces is stimulated by micromolar levels of Cu(2+) . Here, we knocked out the Sco1/SenC family copper chaperone (ScoC) encoded in the conserved gene cluster 'sco' (the S treptomycescopper utilization) in Streptomyces coelicolor A3(2) and S. griseus. It is known that the Sco1/SenC family incorporates Cu(2+) into the active centre of cytochrome oxidase (cox). The knockout caused a marked delay in antibiotic production and aerial mycelium formation on solid medium, temporal pH decline in glucose-containing liquid medium, and significant reduction of cox activity in S. coelicolor. The scoC mutant produced two- to threefold higher cellular mass of the wild type exhibiting a marked cox activity in liquid medium supplied with 10 µM CuSO(4) , suggesting that ScoC is involved in not only the construction but also the deactivation of cox. The scoC mutant was defective in the monoamine oxidase activity responsible for cell aggregation and sedimentation. These features were similarly observed with regard to the scoC mutant of S. griseus. The scoC mutant of S. griseus was also defective in the extracellular activity oxidizing N,N'-dimethyl-p-phenylenediamine sulfate. Addition of 10 µM CuSO(4) repressed the activity of the conserved promoter preceding scoA and caused phenylalanine auxotrophy in some Streptomyces spp. probably because of the repression of pheA; pheA encodes prephenate dehydratase, which is located at the 3' terminus of the putative operon structure. Overall, the evidence indicates that Sco is crucial for the utilization of copper under a low-copper condition and for the activation of the multiple Cu(2+) -containing oxidases that play divergent roles in the complex physiology of Streptomyces.
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Affiliation(s)
- Masahiro Fujimoto
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Japan
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Zhang H, Boghigian BA, Armando J, Pfeifer BA. Methods and options for the heterologous production of complex natural products. Nat Prod Rep 2011; 28:125-51. [PMID: 21060956 PMCID: PMC9896020 DOI: 10.1039/c0np00037j] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This review will detail the motivations, experimental approaches, and growing list of successful cases associated with the heterologous production of complex natural products.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, Medford, MA 02155, USA.
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19
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Petrícek M, Petrícková K, Havlícek L, Felsberg J. Occurrence of two 5-aminolevulinate biosynthetic pathways in Streptomyces nodosus subsp. asukaensis is linked with the production of asukamycin. J Bacteriol 2006; 188:5113-23. [PMID: 16816183 PMCID: PMC1539946 DOI: 10.1128/jb.01919-05] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the results of cloning genes for two key biosynthetic enzymes of different 5-aminolevulinic acid (ALA) biosynthetic routes from Streptomyces. The genes encode the glutamyl-tRNAGlu reductase (GluTR) of the C5 pathway and the ALA synthase (ALAS) of the Shemin pathway. While Streptomyces coelicolor A3(2) synthesizes ALA via the C5 route, both pathways are operational in Streptomyces nodosus subsp. asukaensis, a producer of asukamycin. In this strain, the C5 route produces ALA for tetrapyrrole biosynthesis; the ALA formed by the Shemin pathway serves as a precursor of the 2-amino-3-hydroxycyclopent-2-enone moiety (C5N unit), an antibiotic component. The growth of S. nodosus and S. coelicolor strains deficient in the GluTR genes (gtr) is strictly dependent on ALA or heme supplementation, whereas the defect in the ALAS-encoding gene (hemA-asuA) abolishes the asukamycin production in S. nodosus. The recombinant hemA-asuA gene was expressed in Escherichia coli and in Streptomyces, and the encoded enzyme activity was demonstrated both in vivo and in vitro. The hemA-asuA gene is situated within a putative cluster of asukamycin biosynthetic genes. This is the first report about the cloning of genes for two different ALA biosynthetic routes from a single bacterium.
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Affiliation(s)
- Miroslav Petrícek
- Institute of Microbiology AS CR, Vídenská 1083, 142 20 Prague 4, Czech Republic.
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20
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Zhou X, He X, Li A, Lei F, Kieser T, Deng Z. Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66. Appl Environ Microbiol 2005; 70:7110-8. [PMID: 15574907 PMCID: PMC535201 DOI: 10.1128/aem.70.12.7110-7118.2004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Streptomyces lividans ZX1 has become a preferred host for DNA cloning in Streptomyces species over its progenitor, the wild-type strain 66 (stock number 1326 from the John Innes Center collection), especially when stable DNA is crucial for in vitro electrophoresis, because DNA from strain 66 contains a novel modification that makes it sensitive to oxidative double-strand cleavage during electrophoresis. Detailed analysis of this modification-deficient mutant (ZX1) revealed that it has several additional phenotypic traits associated with a chromosomal deletion of ca. 90 kb, which was cloned and mapped by using a cosmid library. Comparative sequence analysis of two clones containing the left and right deletion ends originating from strain 66 and one clone with the deletion and fused sequence cloned from strain ZX1 revealed a perfect 15-bp direct repeat, which may have mediated deletion and fusion to yield strain ZX1 by site-specific recombination. Analysis of AseI linking clones in the deleted region in relation to the published AseI map of strain ZX1 yielded a complete AseI map for the S. lividans 66 genome, on which the relative positions of a cloned phage phiHAU3 resistance (phiHAU3r) gene and the dnd gene cluster were precisely localized. Comparison of S. lividans ZX1 and its progenitor 66, as well as the sequenced genome of its close relative, Streptomyces coelicolor M145, reveals that the ca. 90-kb deletion in strain ZX1 may have originated from an insertion from an unknown source.
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Affiliation(s)
- Xiufen Zhou
- Bio-X Life Science Research Center, School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, People's Republic of China
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21
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Paradkar A, Trefzer A, Chakraburtty R, Stassi D. Streptomyces genetics: a genomic perspective. Crit Rev Biotechnol 2003; 23:1-27. [PMID: 12693442 DOI: 10.1080/713609296] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Streptomycetes are gram-positive, soil-inhabiting bacteria of the order Actinomycetales. These organisms exhibit an unusual, developmentally complex life cycle and produce many economically important secondary metabolites, such as antibiotics, immunosuppressants, insecticides, and anti-tumor agents. Streptomyces species have been the subject of genetic investigation for over 50 years, with many studies focusing on the developmental cycle and the production of secondary metabolites. This information provides a solid foundation for the application of structural and functional genomics to the actinomycetes. The complete DNA sequence of the model organism, Streptomyces coelicolor M145, has been published recently, with others expected to follow soon. As more genomic sequences become available, the rational genetic manipulation of these organisms to elucidate metabolic and regulatory networks, to increase the production of commercially important compounds, and to create novel secondary metabolites will be greatly facilitated. This review presents the current state of the field of genomics as it is being applied to the actinomycetes.
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Affiliation(s)
- Ashish Paradkar
- Small Molecule Discovery, Diversa Corporation, 4955 Directors Place, San Diego, CA 92121, USA
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22
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Yeung MK. Molecular and genetic analyses of Actinomyces spp. CRITICAL REVIEWS IN ORAL BIOLOGY AND MEDICINE : AN OFFICIAL PUBLICATION OF THE AMERICAN ASSOCIATION OF ORAL BIOLOGISTS 2000; 10:120-38. [PMID: 10759417 DOI: 10.1177/10454411990100020101] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Members of the genus Actinomyces are predominant primary colonizers of the oral cavity and play an important role in initiating plaque development. These bacteria have evolved unique mechanisms that favor colonization and persistence in this micro-environment. The expression of cell-surface fimbriae is correlated with the ability of these bacteria to adhere to specific receptors on the tooth and mucosal surfaces, and to interact with other plaque bacteria. The elaboration of sialidase is thought to enhance fimbriae-mediated adherence by unmasking the fimbrial receptors on mammalian cells. The presence of certain cell-associated or extracellular enzymes, including those involved in sucrose or urea metabolism, may provide the means for these bacteria to thrive under conditions when other growth nutrients are not available. Moreover, these enzyme activities may influence the distribution of other plaque bacteria and promote selection for Actinomyces spp. in certain ecological niches. The recent development of a genetic transfer system for Actinomyces spp. has allowed for studies the results of which demonstrate the existence of multiple genes involved in fimbriae synthesis and function, and facilitated the construction of allelic replacement mutants at each gene locus. Analyses of these mutants have revealed a direct correlation between the synthesis of assembled fimbriae and the observed adherence properties. Further genetic analysis of the various enzyme activities detected from strains of Actinomyces should allow for an assessment of the role of these components in microbial ecology, and their contribution to the overall success of Actinomyces spp. as a primary colonizer and a key player in oral health and disease.
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Affiliation(s)
- M K Yeung
- Department of Pediatric Dentistry, University of Texas Health Science Center at San Antonio, 78284, USA
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Kim HJ, Calcutt MJ, Schmidt FJ, Chater KF. Partitioning of the linear chromosome during sporulation of Streptomyces coelicolor A3(2) involves an oriC-linked parAB locus. J Bacteriol 2000; 182:1313-20. [PMID: 10671452 PMCID: PMC94417 DOI: 10.1128/jb.182.5.1313-1320.2000] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/1999] [Accepted: 12/13/1999] [Indexed: 11/20/2022] Open
Abstract
Candidate partitioning genes (parA and parB) for the linear chromosome of Streptomyces coelicolor were identified by DNA sequencing in a series of seven genes located between rnpA and trxA near the chromosomal replication origin. The most likely translation start point of parB overlapped the parA stop codon, suggestive of coregulation, and transcription analysis suggested that the two genes formed an operon. Deletion of part of parB had no effect on the growth or appearance of colonies but caused a deficiency in DNA partitioning during the multiple septation events involved in converting aerial hyphae into long chains of spores. At least 13% of spore compartments failed to inherit the normal DNA allocation. The same phenotype was obtained with a deletion removing a segment of DNA from both parA and parB. Reinforcing the idea of a special role for the par locus during sporulation, the stronger of two parAB promoters was greatly upregulated at about the time when sporulation septation was maximal in colonies. Three copies of a 14-bp inverted repeat (GTTTCACGTGAAAC) were found in or near the parAB genes, and at least 12 more identical copies were identified within 100 kb of oriC from the growing genome sequence database. Only one perfect copy of the 14-bp sequence was present in approximately 5 Mb of sequence available from the rest of the genome. The 14-bp sequence was similar to sequences identified as binding sites for Spo0J, a ParB homologue from Bacillus subtilis believed to be important for DNA partitioning (D. C.-H. Lin and A. D. Grossman, Cell 92:675-685, 1998). One of these sites encompassed the transcription start point of the stronger parA promoter.
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Affiliation(s)
- H J Kim
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom
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24
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Aínsa JA, Parry HD, Chater KF. A response regulator-like protein that functions at an intermediate stage of sporulation in Streptomyces coelicolor A3(2). Mol Microbiol 1999; 34:607-19. [PMID: 10564501 DOI: 10.1046/j.1365-2958.1999.01630.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
whiI is one of several loci originally described as essential for sporulation in Streptomyces coelicolor A3(2). We have characterized whiI at the molecular level. It encodes an atypical member of the response regulator family of proteins, lacking at least two of the residues strongly conserved in the conventional phosphorylation pocket. It is not adjacent to a potential sensor kinase gene. Fifteen mutant alleles of whiI were sequenced, revealing, among others, six mutations affecting conserved amino acids, several frameshift mutations and one mutation in the promoter. The whiI promoter is specifically transcribed by the sporulation-specific sigmaWhiG-containing form of RNA polymerase. Transcription of whiI is temporally controlled, reaching a maximum level coincident with the formation of spores. Further transcriptional studies suggested that WhiI is involved directly or indirectly in repressing its own expression and that of another sigmaWhiG-dependent sporulation-specific regulatory gene, whiH.
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Affiliation(s)
- J A Aínsa
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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25
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Flärdh K, Findlay KC, Chater KF. Association of early sporulation genes with suggested developmental decision points in Streptomyces coelicolor A3(2). MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 9):2229-2243. [PMID: 10517576 DOI: 10.1099/00221287-145-9-2229] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cytological analysis of a series of Streptomyces coelicolor A3(2) mutants with disruptions of early sporulation (whi, for white aerial mycelium) genes in an isogenic background has provided new information about the role of whiH, and confirmed and extended previous knowledge about whiG, whiA and whiB. The characteristic straight aerial hyphae of whiG mutants contained normally spaced vegetative-like septa, while mutants in whiA or whiB had abnormally long and coiled aerial hyphae almost devoid of septation. whiG, whiA and whiB were all absolutely required for sporulation septation, and for all visible signs of nucleoid condensation and partitioning and other changes associated with later stages of sporulation. On the other hand, whiH appeared to enhance low basal levels of these processes. Thus, whiH mutant aerial hyphae were divided into loosely coiled fragments of variable sizes by what appeared to be a few sporulation septa. These fragments showed some spore-like characteristics and contained condensed and aberrantly partitioned nucleoids. whiG, whiA and whiB were epistatic to whiH on the criterion that they prevented such fragments from forming in double mutants. These spore-like features and the synthesis of clearly detectable levels of the whiE-directed grey spore pigment were not due to any residual activity of previously studied whiH alleles since they were retained by a constructed whiH null mutant. A model is presented that explains the mutant phenotypes by proposing two early developmental decision points involved in commitment to sporulation septation, one requiring whiG and the other requiring whiA and whiB.
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Affiliation(s)
- Klas Flärdh
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK1
| | - Kim C Findlay
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK1
| | - Keith F Chater
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK1
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26
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Flett F, de Mello Jungmann-Campello D, Mersinias V, Koh SL, Godden R, Smith CP. A 'gram-negative-type' DNA polymerase III is essential for replication of the linear chromosome of Streptomyces coelicolor A3(2). Mol Microbiol 1999; 31:949-58. [PMID: 10048037 DOI: 10.1046/j.1365-2958.1999.01237.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Streptomyces coelicolor dnaE gene, encoding the catalytic alpha-subunit of DNA polymerase III (pol III) was isolated by genetic complementation of a temperature-sensitive DNA replication mutant, S. coelicolor ts-38. The deduced protein sequence (1179 residues) is highly similar to the Escherichia coli-type pol III alpha-subunit, rather than to the PolC-type alpha-subunit that is known to be essential for replication in the 'low G + C' Gram-positive bacteria such as Bacillus subtilis. The dnaE gene is able to restore replication to a 'slow stop' mutant (ts-38) and a 'fast stop' mutant (ts-114); the dnaE gene of ts-38 carries a single amino acid substitution (Glu-802 to Lys), and the mutation in ts-114 has been mapped between codons 697 and 1062 of dnaE. Mutant ts-38 is considered to be defective in assembly of the multisubunit pol III holoenzyme and, hence, in initiation of replication, whereas ts-114 is defective in chain elongation. This study provides the first evidence that a DnaE-type pol III is essential for replication in a Gram-positive bacterium. In addition, the complementation studies suggest that the C-terminal 117 residues are not essential for DnaE function in S. coelicolor. When integrated at a distant site on the chromosome, a fragment containing the 3' half of dnaE(codons 697-1179) is capable of rescuing ts-38 (but not ts-114) at the restrictive temperature; it was demonstrated that homogenotization was responsible for this phenomenon.
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Affiliation(s)
- F Flett
- Department of Biomolecular Sciences, UMIST, Manchester, UK
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27
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Tan H, Yang H, Tian Y, Wu W, Whatling CA, Chamberlin LC, Buttner MJ, Nodwell J, Chater KF. The Streptomyces coelicolor sporulation-specific sigma WhiG form of RNA polymerase transcribes a gene encoding a ProX-like protein that is dispensable for sporulation. Gene 1998; 212:137-46. [PMID: 9661673 DOI: 10.1016/s0378-1119(98)00152-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the non-motile mycelial organism Streptomyces coelicolor A3(2), the sporulation gene whiG encodes a protein that closely resembles RNA polymerase sigma factors such as sigma D of Bacillus subtilis, which mainly control motility and chemotaxis genes. Here, we show that the whiG gene product, purified from an Escherichia coli strain carrying an expression construct, could activate E. coli core RNA polymerase in vitro to transcribe a sigma D-dependent motility-related promoter from B. subtilis. Such RNA polymerase holoenzyme preparations could also transcribe from an S. coelicolor promoter, PTH4, previously shown to require an intact whiG gene for in-vivo transcription. The in-vivo dependence on whiG was therefore shown to be direct. Unusually, the initiation of PTH4 transcription in vitro depended on the provision of appropriate dinucleotides. The whiG-dependent PTH4 transcription unit consisted of a single gene, orfTH4. Sequence comparisons suggested that the gene product was a member of a small group of proteins that include the B. subtilis and E. coli ProX proteins. Though none of these proteins shared more than about 30% of extended primary sequence identity, they had similar size and hydropathy profiles, and could be aligned end to end to reveal a mosaic of similarities. The ProX proteins of B. subtilis and E. coli are implicated in glycine betaine transport in response to hyperosmotic stress. However, disruption of orfTH4 did not cause any obvious phenotypic changes in growth or development on media of varying osmotic strengths.
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Affiliation(s)
- H Tan
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
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28
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Guthrie EP, Flaxman CS, White J, Hodgson DA, Bibb MJ, Chater KF. A response-regulator-like activator of antibiotic synthesis from Streptomyces coelicolor A3(2) with an amino-terminal domain that lacks a phosphorylation pocket. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 3):727-738. [PMID: 9534242 DOI: 10.1099/00221287-144-3-727] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In Streptomyces coelicolor A3(2), bldA mutants that lack the tRNA for the rare leucine codon UUA fail to make the red undecylprodigiosin antibiotic complex. To find out why, red-pigmented while bald (Pwb) derivatives of a bldA mutant were isolated. Using a cloning strategy that allowed for (and demonstrated) dominance of the mutations, they were localized to the red gene cluster. By using insert-mediated integration of a phi C31 phage-based vector, one of the Pwb mutations was more precisely located between red structural genes to a segment of approximately 1 kb about 4 kb from the known pathway-specific regulatory gene redD. The segment contained most of an ORF (redZ) encoding a protein (RedZ) with end-to-end similarity to response regulators of diverse function from a variety of bacteria. Remarkably, in RedZ hydrophobic residues replace nearly all of the charged residues that usually make up the phosphorylation pocket present in typical response regulators, including the aspartic acid residue that is normally phosphorylated by a cognate sensory protein kinase. A single TTA codon in redZ provided a potential explanation for the bldA-dependence of undecylprodigiosin synthesis. This codon was unchanged in three Pwb mutants, but further analysis of one of the mutants revealed a potential up-promoter mutation. It seems possible that a combination of low-level natural translation of the UUA codon by a charged non-cognate tRNA, coupled with increased transcription of redZ in the Pwb mutant allows the accumulation of a threshold level of the RedD protein.
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MESH Headings
- Amino Acid Sequence
- Anti-Bacterial Agents/biosynthesis
- Bacterial Proteins
- Base Sequence
- Codon
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Genetic Vectors
- Models, Genetic
- Molecular Sequence Data
- Mutagenesis, Insertional
- Phosphorylation
- Phylogeny
- Prodigiosin/analogs & derivatives
- Prodigiosin/biosynthesis
- Promoter Regions, Genetic
- RNA, Bacterial
- RNA, Transfer, Leu/genetics
- Sequence Analysis, DNA
- Streptomyces/genetics
- Streptomyces/growth & development
- Streptomyces/metabolism
- Trans-Activators/chemistry
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription, Genetic
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Affiliation(s)
- Ellen P Guthrie
- John Innes Centre, Norwich Research Park,Colney, Norwich NR4 7UH,UK
| | - Christine S Flaxman
- Department of Biological Sciences, University of Warwick,Coventry CV4 7AL,UK
| | - Janet White
- John Innes Centre, Norwich Research Park,Colney, Norwich NR4 7UH,UK
| | - David A Hodgson
- Department of Biological Sciences, University of Warwick,Coventry CV4 7AL,UK
| | - Mervyn J Bibb
- John Innes Centre, Norwich Research Park,Colney, Norwich NR4 7UH,UK
| | - Keith F Chater
- John Innes Centre, Norwich Research Park,Colney, Norwich NR4 7UH,UK
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29
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Martin MC, Schneider D, Bruton CJ, Chater KF, Hardisson C. A glgC gene essential only for the first of two spatially distinct phases of glycogen synthesis in Streptomyces coelicolor A3(2). J Bacteriol 1997; 179:7784-9. [PMID: 9401038 PMCID: PMC179742 DOI: 10.1128/jb.179.24.7784-7789.1997] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
By using a PCR approach based on conserved regions of ADP-glucose pyrophosphorylases, a glgC gene was cloned from Streptomyces coelicolor A3(2). The deduced glgC gene product showed end-to-end relatedness to other bacterial ADP-glucose pyrophosphorylases. The glgC gene is about 1,000 kb from the leftmost chromosome end and is not closely linked to either of the two glgB genes of S. coelicolor, which encode glycogen branching enzymes active in different locations in differentiated colonies. Disruption of glgC eliminated only the first of two temporal peaks of ADP-glucose pyrophosphorylase activity and glycogen accumulation and prevented cytologically observable glycogen accumulation in the substrate mycelium of colonies (phase I), while glycogen deposition in young spore chains (phase II) remained readily detectable. The cloned glgC gene therefore encodes an ADP-glucose pyrophosphorylase essential only for phase I (and it is therefore named glgCI). A second, phase II-specific, glgC gene should also exist in S. coelicolor, though it was not detected by hybridization analysis.
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Affiliation(s)
- M C Martin
- Area de Microbiología, Facultad de Medicina and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, Spain
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30
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de León P, Marco S, Isiegas C, Marina A, Carrascosa JL, Mellado RP. Streptomyces lividans groES, groEL1 and groEL2 genes. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 11):3563-3571. [PMID: 9387235 DOI: 10.1099/00221287-143-11-3563] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Streptomyces lividans groES/EL1 operon and groEL2 gene were cloned and their respective DNA sequences determined. The sequenced DNA comprised the genes and their respective regulatory regions in both cases. Transcription of both groES/EL1 and groEL2 seemed to be subjected to temporal control at 30 degrees C. At 45 degrees C the amount of the groEL2 transcript increased considerably in comparison to that of groES/EL1. Among the proteins synthesized under heat shock by S. lividans, a fraction enriched in GroEL2 showed the presence of a ring-shaped structure that resembles that of other chaperonins and was active in a rhodanase folding assay.
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Affiliation(s)
- Patricia de León
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Sergio Marco
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Carolina Isiegas
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Anabel Marina
- Centra de Biología Molecular Severo Ochoa, Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - José L Carrascosa
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Rafael P Mellado
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
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Flett F, Mersinias V, Smith CP. High efficiency intergeneric conjugal transfer of plasmid DNA from Escherichia coli to methyl DNA-restricting streptomycetes. FEMS Microbiol Lett 1997; 155:223-9. [PMID: 9351205 DOI: 10.1111/j.1574-6968.1997.tb13882.x] [Citation(s) in RCA: 362] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Many streptomycetes, including S. coelicolor A3(2), possess a potent methyl-specific restriction which can present an effective barrier to the introduction of heterologous DNA. We have compared the efficiency of intergeneric conjugal transfer of different types of plasmids to S. coelicolor and S. lividans 66 using two E. coli donors: the standard, methylation proficient strain S17-1, and the methylation deficient donor, ET12567(pUB307). We demonstrate that the methylation deficient donor can yield > 10(4)-fold more S. coelicolor exconjugants than the standard donor. In the case of pSET152 derivatives, which integrate into the host chromosome by site-specific recombination, up to 10% of streptomycete spores in the conjugation mixture inherit the plasmid. The conjugation procedure is efficient enough to obtain exconjugants with 'suicide' delivery plasmids and therefore provides a simple route for conducting gene disruptions in methyl DNA-restricting streptomycetes, and possibly other bacteria.
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Affiliation(s)
- F Flett
- Department of Biochemistry and Applied Molecular Biology, UMIST, Manchester, UK
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32
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Binnie C, Cossar JD, Stewart DI. Heterologous biopharmaceutical protein expression in Streptomyces. Trends Biotechnol 1997; 15:315-20. [PMID: 9263479 DOI: 10.1016/s0167-7799(97)01062-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The commercial production of human proteins in recombinant microorganisms for therapeutic use is well established. Systems have been developed to exploit the natural ability of certain bacteria to secrete properly folded, bioactive proteins into the extracellular medium. The streptomycetes are a relatively well-characterized group of nonpathogenic filamentous bacteria that have the capacity to secrete large amounts of protein. In particular, Streptomyces lividans has the ability to secrete human proteins at a commercially viable level, thanks to relatively well-established plasmid-based expression system, a high-biomass fermentation process and a low level of endogenous protease activity.
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Affiliation(s)
- C Binnie
- Cangene Corporation, Mississauga, Ontario, Canada.
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33
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Alves AM, Euverink GJ, Bibb MJ, Dijkhuizen L. Identification of ATP-dependent phosphofructokinase as a regulatory step in the glycolytic pathway of the actinomycete Streptomyces coelicolor A3(2). Appl Environ Microbiol 1997; 63:956-61. [PMID: 9055413 PMCID: PMC168387 DOI: 10.1128/aem.63.3.956-961.1997] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The ATP-dependent phosphofructokinase (ATP-PFK) of Streptomyces coelicolor A3(2) was purified to homogeneity (1,600-fold) and characterized (110 kDa, with a single type of subunit of 40 kDa); it is allosterically inhibited by phosphoenolpyruvate. Cloning of the pfk gene of S. coelicolor A3(2) and analysis of the deduced amino acid sequence (343 amino acids; 36,667 Da) revealed high similarities to the PPi-PFK enzyme from Amycolatopsis methanolica (tetramer, nonallosteric; 70%) and to the allosteric ATP-PFK enzymes from other bacteria, e.g., Escherichia coli (tetramer; 37%) and Bacillus stearothermophilus (tetramer, 41%). Further structural and functional analysis of the two actinomycete PFK enzymes should elucidate the features of these proteins that determine substrate specificity (ATP versus PPi) and allosteric (in)sensitivity.
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Affiliation(s)
- A M Alves
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
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34
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Yeung MK, Kozelsky CS. Transfection of Actinomyces spp. by genomic DNA of bacteriophages from human dental plaque. Plasmid 1997; 37:141-53. [PMID: 9169205 DOI: 10.1006/plas.1997.1285] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bacteriophages that produced turbid or clear zones of lysis in strains of Actinomyces were isolated from 22 of 124 samples of fresh human dental plaque. All human and nonhuman strains of Actinomyces viscosus or Actinomyces naeslundii tested in this study were sensitive to infection by one or more of these phages. In contrast, none of the Actinomyces odontolyticus, Actinomyces israelii, or Actinomyces bovis strains tested were susceptible. Results of restriction endonuclease analyses indicated that the genomes of these phages consisted of double-stranded DNA molecules ranging in size between 16 and 60 kbp. Sequence homology under hybridization conditions of high stringency was observed among a few of the isolated phages. A lysogenized isolate of A. viscosus MG-1 was obtained following infection with a temperate phage, designated phi 225. Results of Southern blot analyses indicated that phi 225 replicated as a plasmid in the lysogenized strain. Genomic DNA from several lytic phages was used to establish conditions for transfection by electroporation of strains of Actinomyces spp. Efficiencies of DNA transfer ranged from 10(2) to 10(5) plaque-forming units per microgram of DNA were obtained under optimal transfection conditions. The results of these studies demonstrate that transfer of genetic information in Actinomyces spp. can be achieved by transfection.
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Affiliation(s)
- M K Yeung
- Department of Pediatric Dentistry, University of Texas Health Science Center at San Antonio 78284-7888, USA.
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35
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Oh SH, Chater KF. Denaturation of circular or linear DNA facilitates targeted integrative transformation of Streptomyces coelicolor A3(2): possible relevance to other organisms. J Bacteriol 1997; 179:122-7. [PMID: 8981988 PMCID: PMC178669 DOI: 10.1128/jb.179.1.122-127.1997] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Using Streptomyces coelicolor A3(2) protoplasts, the number of transformants obtained by homologous recombination of incoming double-stranded circular DNA with the recipient chromosome was greatly stimulated by simple denaturation of the donor DNA. This procedure was very effective with inserts over a ca. 100-fold size range, the largest tested being ca. 40-kb inserts in cosmids. These observations led to transformation experiments with linearized cloned DNA and randomly sheared genomic DNA. In both cases, DNA denaturation led to significant levels of transformation. Most of the transformants had resulted from the predicted homologous recombination events. A number of genetic manipulations will be made easier or possible by these procedures.
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Affiliation(s)
- S H Oh
- Department of Genetics, John Innes Centre, Colney, Norwich, United Kingdom
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36
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Wang P, Denoya CD, Morgenstern MR, Skinner DD, Wallace KK, Digate R, Patton S, Banavali N, Schuler G, Speedie MK, Reynolds KA. Cloning and characterization of the gene encoding 1-cyclohexenylcarbonyl coenzyme A reductase from Streptomyces collinus. J Bacteriol 1996; 178:6873-81. [PMID: 8955309 PMCID: PMC178588 DOI: 10.1128/jb.178.23.6873-6881.1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We report the cloning of the gene encoding the 1-cyclohexenylcarbonyl coenzyme A reductase (ChcA) of Streptomyces collinus, an enzyme putatively involved in the final reduction step in the formation of the cyclohexyl moiety of ansatrienin from shikimic acid. The cloned gene, with a proposed designation of chcA, encodes an 843-bp open reading frame which predicts a primary translation product of 280 amino acids and a calculated molecular mass of 29.7 kDa. Highly significant sequence similiarity extending along almost the entire length of the protein was observed with members of the short-chain alcohol dehydrogenase superfamily. The S. collinus chcA gene was overexpressed in Escherichia coli by using a bacteriophage T7 transient expression system, and a protein with a specific ChcA activity was detected. The E. coli-produced ChcA protein was purified and shown to have similar steady-state kinetics and electrophoretic mobility on sodium dodecyl sulfate-polyacrylamide gels as the enoyl-coenzyme A reductase protein prepared from S. collinus. The enzyme demonstrated the ability to catalyze, in vitro, three of the reductive steps involved in the formation of cyclohexanecarboxylic acid. An S. collinus chcA mutant, constructed by deletion of a genomic region comprising the 5' end of chcA, lost the ChcA activity and the ability to synthesize either cyclohexanecarboxylic acid or ansatrienin. These results suggest that chcA encodes the ChcA that is involved in catalyzing multiple reductive steps in the pathway that provides the cyclohexanecarboxylic acid from shikimic acid.
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Affiliation(s)
- P Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, 21201, USA
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37
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Denoya CD, Fedechko RW, Hafner EW, McArthur HA, Morgenstern MR, Skinner DD, Stutzman-Engwall K, Wax RG, Wernau WC. A second branched-chain alpha-keto acid dehydrogenase gene cluster (bkdFGH) from Streptomyces avermitilis: its relationship to avermectin biosynthesis and the construction of a bkdF mutant suitable for the production of novel antiparasitic avermectins. J Bacteriol 1995; 177:3504-11. [PMID: 7768860 PMCID: PMC177055 DOI: 10.1128/jb.177.12.3504-3511.1995] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A second cluster of genes encoding the E1 alpha, E1 beta, and E2 subunits of branched-chain alpha-keto acid dehydrogenase (BCDH), bkdFGH, has been cloned and characterized from Streptomyces avermitilis, the soil microorganism which produces anthelmintic avermectins. Open reading frame 1 (ORF1) (bkdF, encoding E1 alpha), would encode a polypeptide of 44,394 Da (406 amino acids). The putative start codon of the incompletely sequenced ORF2 (bkdG, encoding E1 beta) is located 83 bp downstream from the end of ORF1. The deduced amino acid sequence of bkdF resembled the corresponding E1 alpha subunit of several prokaryotic and eukaryotic BCDH complexes. An S. avermitilis bkd mutant constructed by deletion of a genomic region comprising the 5' end of bkdF is also described. The mutant exhibited a typical Bkd- phenotype: it lacked E1 BCDH activity and had lost the ability to grow on solid minimal medium containing isoleucine, leucine, and valine as sole carbon sources. Since BCDH provides an alpha-branched-chain fatty acid starter unit, either S(+)-alpha-methylbutyryl coenzyme A or isobutyryl coenzyme A, which is essential to initiate the synthesis of the avermectin polyketide backbone in S. avermitilis, the disrupted mutant cannot make the natural avermectins in a medium lacking both S(+)-alpha-methylbutyrate and isobutyrate. Supplementation with either one of these compounds restores production of the corresponding natural avermectins, while supplementation of the medium with alternative fatty acids results in the formation of novel avermectins. These results verify that the BCDH-catalyzed reaction of branched-chain amino acid catabolism constitutes a crucial step to provide fatty acid precursors for antibiotic biosynthesis in S. avermitilis.
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Affiliation(s)
- C D Denoya
- Central Research Division, Pfzer Inc., Groton, Connecticut 06340, USA
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38
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Copy number determination of different derivatives of the streptomycete mini-plasmid pSLG33. Folia Microbiol (Praha) 1995. [DOI: 10.1007/bf02814198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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39
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Affiliation(s)
- W R Strohl
- Department of Microbiology, Ohio State University, Columbus 43210-1292, USA
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40
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Hopwood DA, Chater KF, Bibb MJ. Genetics of antibiotic production in Streptomyces coelicolor A3(2), a model streptomycete. BIOTECHNOLOGY (READING, MASS.) 1995; 28:65-102. [PMID: 8688641 DOI: 10.1016/b978-0-7506-9095-9.50009-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- D A Hopwood
- Department of Genetics, John Innes Centre, Colney, Norwich, UK
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41
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Abstract
The gram-negative broad-host-range vector pJRD215 was transferred by electroporation into strains of Actinomyces viscosus or Actinomyces naeslundii at efficiencies which ranged from 10(2) to 10(7) transformants per microgram of plasmid DNA. The Actinomyces transformants expressed pJRD215-encoded resistance to kanamycin and streptomycin. Moreover, the transforming plasmid DNA had not undergone any deletions or rearrangements, nor had it integrated into the genomes of these strains.
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Affiliation(s)
- M K Yeung
- Department of Pediatric Dentistry, University of Texas Health Science Center at San Antonio 78284-7888
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42
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Zhou X, Deng Z, Hopwood DA, Kieser T. Streptomyces lividans 66 contains a gene for phage resistance which is similar to the phage lambda ea59 endonuclease gene. Mol Microbiol 1994; 12:789-97. [PMID: 8052130 DOI: 10.1111/j.1365-2958.1994.tb01065.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The DNA of wild-type Streptomyces lividans 66 is degraded during electrophoresis in buffers containing traces of ferrous iron. S. lividans ZX1, a mutant selected for resistance to DNA degradation, simultaneously became sensitive to phi HAU3, a wide-host-range temperate bacteriophage. A DNA fragment conferring phi HAU3 resistance was cloned; it contains a phage resistance gene whose deduced amino acid sequence is similar to the phage lambda Ea59 endonuclease. The S. lividans phi HAU3 resistance does not seem to be a classical restriction-modification system, because no host-modified phages able to propagate on the wild-type strain could be isolated. The cloned fragment did not make the host DNA prone to degradation during electrophoresis, indicating that the two phenotypes are controlled by different genes which were deleted together from the chromosome of ZX1.
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Affiliation(s)
- X Zhou
- Department of Soil Sciences and Agrochemistry, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
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43
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Qin Z, Peng K, Zhou X, Liang R, Zhou Q, Chen H, Hopwood DA, Kieser T, Deng Z. Development of a gene cloning system for Streptomyces hygroscopicus subsp. yingchengensis, a producer of three useful antifungal compounds, by elimination of three barriers to DNA transfer. J Bacteriol 1994; 176:2090-5. [PMID: 8144475 PMCID: PMC205315 DOI: 10.1128/jb.176.7.2090-2095.1994] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Streptomyces hygroscopicus 10-22 could not be transformed with any of the commonly used Streptomyces plasmid vectors and was resistant to plaque formation by the Streptomyces phages phi C31 and R4. Repeated selection resulted in the isolation of derivatives of S. hygroscopicus 10-22 that could be transformed with pIJ101- and pJV1-derived cloning vectors and of restriction-deficient derivatives that could accept DNA propagated in Streptomyces lividans 66. These new strains, which include three that still produce the original antibiotics, can be used as hosts for gene cloning. Insertion of nonreplicating vectors by homologous recombination and transposition of Tn4560 were demonstrated in S. hygroscopicus 10-22.
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Affiliation(s)
- Z Qin
- Department of Soil Sciences and Agrochemistry, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
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44
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Abstract
Polyketide synthases (PKSs) are multifunctional enzymes that catalyze the biosynthesis of a huge variety of carbon chains differing in their length and patterns of functionality and cyclization. Many polyketides are valuable therapeutic agents. A Streptomyces host-vector system has been developed for efficient construction and expression of recombinant PKSs. Using this expression system, several novel compounds have been synthesized in vivo in significant quantities. Characterization of these metabolites has provided new insights into key features of actinomycete aromatic PKS specificity. Thus, carbon chain length is dictated, at least in part, by a protein that appears to be distinctive to this family of PKSs, whereas the acyl carrier proteins of different PKSs can be interchanged without affecting product structure. A given ketoreductase can recognize and reduce polyketide chains of different length; this ketoreduction always occurs at the C-9 position. The regiospecificity of the first cyclization of the nascent polyketide chain is either determined by the ketoreductase, or the chain-extending enzymes themselves. However, the regiospecificity of the second cyclization is determined by a distinct cyclase, which can discriminate between substrates of different chain lengths.
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Affiliation(s)
- R McDaniel
- Department of Chemical Engineering, Stanford University, CA 94305-5025
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45
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Abstract
Streptomycetes are Gram-positive soil bacteria with a well differentiated morphology. They are considered interesting candidates for the production of heterologous proteins for several reasons, including their efficient secretion mechanism by which the secreted proteins are localized into the culture supernatant. In view of this potential, this review article describes different aspects of gene expression and regulation in Streptomyces, and summarizes and discusses results obtained using Streptomyces lividans as host for secretion of heterologous proteins of prokaryotic and eukaryotic origin.
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Affiliation(s)
- J Anné
- Rega Institute, Katholieke Universiteit Leuven, Belgium
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46
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Donadio S, McAlpine JB, Sheldon PJ, Jackson M, Katz L. An erythromycin analog produced by reprogramming of polyketide synthesis. Proc Natl Acad Sci U S A 1993; 90:7119-23. [PMID: 8346223 PMCID: PMC47087 DOI: 10.1073/pnas.90.15.7119] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The polyketide-derived macrolactone of the antibiotic erythromycin is made through successive condensation and processing of seven three-carbon units. The fourth cycle involves complete processing of the newly formed beta-keto group (beta-keto reduction, dehydration, and enoyl reduction) to yield the methylene that will appear at C-7 of the lactone ring. Synthesis of this molecule in Saccharopolyspora erythraea is determined by the three large eryA genes, organized in six modules, each governing one condensation cycle. Two amino acid substitutions were introduced in the putative NAD(P)H binding motif in the proposed enoyl reductase domain encoded by eryAII. The metabolite produced by the resulting strain was identified as delta 6,7-anhydroerythromycin C resulting from failure of enoyl reduction during the fourth cycle of synthesis of the macrolactone. This result demonstrates the involvement of at least the enoyl reductase from the fourth module in the fourth cycle and indicates that a virtually complete macrolide can be produced through reprogramming of polyketide synthesis.
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Affiliation(s)
- S Donadio
- Pharmaceutical Products Division, Abbott Laboratories, Abbott Park, IL 60064
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47
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Stassi D, Donadio S, Staver MJ, Katz L. Identification of a Saccharopolyspora erythraea gene required for the final hydroxylation step in erythromycin biosynthesis. J Bacteriol 1993; 175:182-9. [PMID: 8416893 PMCID: PMC196112 DOI: 10.1128/jb.175.1.182-189.1993] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In analyzing the region of the Saccharopolyspora erythraea chromosome responsible for the biosynthesis of the macrolide antibiotic erythromycin, we identified a gene, designated eryK, located about 50 kb downstream of the erythromycin resistance gene, ermE. eryK encodes a 44-kDa protein which, on the basis of comparative analysis, belongs to the P450 monooxygenase family. An S. erythraea strain disrupted in eryK no longer produced erythromycin A but accumulated the B and D forms of the antibiotic, indicating that eryK is responsible for the C-12 hydroxylation of the macrolactone ring, one of the last steps in erythromycin biosynthesis.
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Affiliation(s)
- D Stassi
- Corporate Molecular Biology, Abbott Laboratories, Abbott Park, Illinois 60064
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48
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49
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Forsman M, Granström M. Mutagenic analysis of the promoter of the Streptomyces fradiae beta-lactamase-encoding gene. Gene X 1992; 121:87-94. [PMID: 1385267 DOI: 10.1016/0378-1119(92)90165-l] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The Streptomyces fradiae beta-lactamase promoter (PblaF) was sequenced and characterized by promoter probing, primer extension, and exonuclease III-mediated deletions. The transcription start point (tsp) was the same in both S. lividans and S. fradiae. Oligodeoxyribonucleotide-directed random mutations and site-specific mutations were introduced in the promoter region. The effects of these mutations on transcription were assayed by an RNA colony hybridization method. This analysis identified cis-acting sequence determinants located similarly to the -10 and -35 regions of a typical Escherichia coli promoter. Also, a change in the distance between these regions from 19 to 17 bp drastically reduced promoter activity. PblaF was shown not to be recognized by sigma-whiG or by sigma-hrdA, hrdC, or hrdD. Sequence alignment of PblaF to sigma factor-classified Streptomyces promoters revealed little homology. Thus, PblaF is probably recognized by an as yet unidentified sigma factor.
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Affiliation(s)
- M Forsman
- Department of Microbiology, National Defence Research Establishment, Umeå, Sweden
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50
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Khosla C, Ebert-Khosla S, Hopwood DA. Targeted gene replacements in a Streptomyces polyketide synthase gene cluster: role for the acyl carrier protein. Mol Microbiol 1992; 6:3237-49. [PMID: 1453961 DOI: 10.1111/j.1365-2958.1992.tb01778.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A methodology was developed to construct any desired chromosomal mutation in the gene cluster that encodes the actinorhodin polyketide synthase (PKS) of Streptomyces coelicolor A3(2). A positive selection marker (resistance gene) is first introduced by double crossing-over into the chromosomal site of interest by use of an unstable delivery plasmid. This marker is subsequently replaced by the desired mutant allele via a second high-frequency double recombination event. The technology has been used to: (i) explore the significance of translational coupling between two adjacent PKS genes; (ii) prove that the acyl carrier protein (ACP) encoded by a gene in the cluster is necessary for the function of the actinorhodin PKS; (iii) provide genetic evidence supporting the hypothesis that serine 42 is the site of phosphopantetheinylation in the ACP of the actinorhodin PKS; and (iv) demonstrate that this ACP can be replaced by a Saccharopolyspora fatty acid synthase ACP to generate an active hybrid PKS.
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Affiliation(s)
- C Khosla
- Department of Genetics, John Innes Institute, John Innes Centre, Norwich, UK
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