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Zambri MP, Williams MA, Elliot MA. How Streptomyces thrive: Advancing our understanding of classical development and uncovering new behaviors. Adv Microb Physiol 2022; 80:203-236. [PMID: 35489792 DOI: 10.1016/bs.ampbs.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Streptomyces are soil- and marine-dwelling microbes that need to survive dramatic fluctuations in nutrient levels and environmental conditions. Here, we explore the advances made in understanding how Streptomyces bacteria can thrive in their natural environments. We examine their classical developmental cycle, and the intricate regulatory cascades that govern it. We discuss alternative growth strategies and behaviors, like the rapid expansion and colonization properties associated with exploratory growth, the release of membrane vesicles and S-cells from hyphal tips, and the acquisition of exogenous DNA along the lateral walls. We further investigate Streptomyces interactions with other organisms through the release of volatile compounds that impact nutrient levels, microbial growth, and insect behavior. Finally, we explore the increasingly diverse strategies employed by Streptomyces species in escaping and thwarting phage infections.
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Affiliation(s)
- Matthew P Zambri
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Michelle A Williams
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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Holman NDM, Wilkinson AJ, Smith MCM. Alanine-scanning mutagenesis of protein mannosyl-transferase from Streptomyces coelicolor reveals strong activity-stability correlation. MICROBIOLOGY-SGM 2021; 167. [PMID: 34676818 PMCID: PMC8698208 DOI: 10.1099/mic.0.001103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In Actinobacteria, protein O-mannosyl transferase (Pmt)-mediated protein O-glycosylation has an important role in cell envelope physiology. In S. coelicolor, defective Pmt leads to increased susceptibility to cell wall-targeting antibiotics, including vancomycin and β-lactams, and resistance to phage ϕC31. The aim of this study was to gain a deeper understanding of the structure and function of S. coelicolor Pmt. Sequence alignments and structural bioinformatics were used to identify target sites for an alanine-scanning mutagenesis study. Mutant alleles were introduced into pmt-deficient S. coelicolor strains using an integrative plasmid and scored for their ability to complement phage resistance and antibiotic hypersusceptibility phenotypes. Twenty-three highly conserved Pmt residues were each substituted for alanine. Six mutant alleles failed to complement the pmt▬ strains in either assay. Mapping the six corresponding residues onto a homology model of the three-dimensional structure of Pmt, indicated that five are positioned close to the predicted catalytic DE motif. Further mutagenesis to produce more conservative substitutions at these six residues produced Pmts that invariably failed to complement the DT1025 pmt▬ strain, indicating that strict residue conservation was necessary to preserve function. Cell fractionation and Western blotting of strains with the non-complementing pmt alleles revealed undetectable levels of the enzyme in either the membrane fractions or whole cell lysates. Meanwhile for all of the strains that complemented the antibiotic hypersusceptibility and phage resistance phenotypes, Pmt was readily detected in the membrane fraction. These data indicate a tight correlation between the activity of Pmt and its stability or ability to localize to the membrane.
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Affiliation(s)
| | - Anthony J Wilkinson
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
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Isaev AB, Musharova OS, Severinov KV. Microbial Arsenal of Antiviral Defenses - Part I. BIOCHEMISTRY (MOSCOW) 2021; 86:319-337. [PMID: 33838632 DOI: 10.1134/s0006297921030081] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). Constant threat of phage infection is a major force that shapes evolution of the microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering have been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection, with a focus on novel systems discovered in recent years. First chapter covers defense associated with cell surface, role of small molecules, and innate immunity systems relying on DNA modification.
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Affiliation(s)
- Artem B Isaev
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.
| | - Olga S Musharova
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. .,Institute of Molecular Genetics, Moscow, 119334, Russia
| | - Konstantin V Severinov
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. .,Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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4
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Read N, Howlett R, Smith MCM. An operon encoding enzymes for synthesis of a putative extracellular carbohydrate attenuates acquired vancomycin resistance in Streptomyces coelicolor. MICROBIOLOGY-SGM 2019; 165:208-223. [PMID: 30632959 DOI: 10.1099/mic.0.000763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Actinomycete bacteria use polyprenol phosphate mannose as a lipid-linked sugar donor for extra-cytoplasmic glycosyl transferases that transfer mannose to cell envelope polymers, including glycoproteins and glycolipids. Strains of Streptomyces coelicolor with mutations in the gene ppm1, encoding polyprenol phosphate mannose synthase, and in pmt, encoding a protein O-mannosyltransferase, are resistant to phage ϕC31 and have greatly increased susceptibility to some antibiotics, including vancomycin. In this work, second-site suppressors of the vancomycin susceptibility were isolated. The suppressor strains fell into two groups. Group 1 strains had increased resistance to vancomycin, teicoplanin and β-lactams, and had mutations in the two-component sensor regulator system encoded by vanSR, leading to upegulation of the vanSRJKHAX cluster. Group 2 strains only had increased resistance to vancomycin and these mostly had mutations in sco2592 or sco2593, genes that are derepressed in the presence of phosphate and are likely to be required for the synthesis of a phosphate-containing extracellular polymer. In some suppressor strains the increased resistance was only observed in media with limited phosphate (mimicking the phenotype of wild-type S. coelicolor), but two strains, DT3017_R21 (ppm1-vanR-) and DT3017_R15 (ppm1- sco2593-), retained resistance on media with high phosphate content. These results support the view that vancomycin resistance in S. coelicolor is a trade-off between mechanisms that confer resistance and at least one that interferes with resistance mediated through the sco2594-sco2593-sco2592 operon.
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Keenan T, Mills R, Pocock E, Budhadev D, Parmeggiani F, Flitsch S, Fascione M. The characterisation of a galactokinase from Streptomyces coelicolor. Carbohydr Res 2019; 472:132-137. [DOI: 10.1016/j.carres.2018.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 01/08/2023]
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Howlett R, Anttonen K, Read N, Smith MCM. Disruption of the GDP-mannose synthesis pathway in Streptomyces coelicolor results in antibiotic hyper-susceptible phenotypes. MICROBIOLOGY-SGM 2018; 164:614-624. [PMID: 29493491 PMCID: PMC5982138 DOI: 10.1099/mic.0.000636] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Actinomycete bacteria use polyprenol phosphate mannose as a lipid linked sugar donor for extra-cytoplasmic glycosyl transferases that transfer mannose to cell envelope polymers, including glycoproteins and glycolipids. We showed recently that strains of Streptomyces coelicolor with mutations in the gene ppm1 encoding polyprenol phosphate mannose synthase were both resistant to phage φC31 and have greatly increased susceptibility to antibiotics that mostly act on cell wall biogenesis. Here we show that mutations in the genes encoding enzymes that act upstream of Ppm1 in the polyprenol phosphate mannose synthesis pathway can also confer phage resistance and antibiotic hyper-susceptibility. GDP-mannose is a substrate for Ppm1 and is synthesised by GDP-mannose pyrophosphorylase (GMP; ManC) which uses GTP and mannose-1-phosphate as substrates. Phosphomannomutase (PMM; ManB) converts mannose-6-phosphate to mannose-1-phosphate. S. coelicolor strains with knocked down GMP activity or with a mutation in sco3028 encoding PMM acquire phenotypes that resemble those of the ppm1- mutants i.e. φC31 resistant and susceptible to antibiotics. Differences in the phenotypes of the strains were observed, however. While the ppm1- strains have a small colony phenotype, the sco3028 :: Tn5062 mutants had an extremely small colony phenotype indicative of an even greater growth defect. Moreover we were unable to generate a strain in which GMP activity encoded by sco3039 and sco4238 is completely knocked out, indicating that GMP is also an important enzyme for growth. Possibly GDP-mannose is at a metabolic branch point that supplies alternative nucleotide sugar donors.
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Affiliation(s)
| | - Katri Anttonen
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Margaret C M Smith
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK.,Department of Biology, University of York, York, UK
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Burroughs AM, Aravind L. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res 2016; 44:8525-8555. [PMID: 27536007 PMCID: PMC5062991 DOI: 10.1093/nar/gkw722] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/08/2016] [Indexed: 12/16/2022] Open
Abstract
RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Fayed B, Ashford DA, Hashem AM, Amin MA, El Gazayerly ON, Gregory MA, Smith MCM. Multiplexed integrating plasmids for engineering of the erythromycin gene cluster for expression in Streptomyces spp. and combinatorial biosynthesis. Appl Environ Microbiol 2015; 81:8402-13. [PMID: 26431970 PMCID: PMC4644662 DOI: 10.1128/aem.02403-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/25/2015] [Indexed: 01/11/2023] Open
Abstract
Bacteria in the genus Streptomyces and its close relatives are prolific producers of secondary metabolites with antibiotic activity. Genome sequencing of these bacteria has revealed a rich source of potentially new antibiotic pathways, whose products have never been observed. Moreover, these new pathways can provide novel genes that could be used in combinatorial biosynthesis approaches to generate unnatural analogues of existing antibiotics. We explore here the use of multiple orthologous integrating plasmid systems, based on the int/attP loci from phages TG1, SV1, and ϕBT1, to express the polyketide synthase (PKS) for erythromycin in a heterologous Streptomyces host. Streptomyces strains containing the three polyketide synthase genes eryAI, eryAII, and eryAIII expressed from three different integrated plasmids produced the aglycone intermediate, 6-deoxyerythronolide B (6-dEB). A further pair of integrating plasmids, both derived from the ϕC31 int/attP locus, were constructed carrying a gene cassette for glycosylation of the aglycone intermediates, with or without the tailoring gene, eryF, required for the synthesis of erythronolide B (EB). Liquid chromatography-mass spectrometry of the metabolites indicated the production of angolosaminyl-6-dEB and angolosaminyl-EB. The advantages of using multiplexed integrating plasmids for engineering expression and for combinatorial biosynthesis were demonstrated.
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Affiliation(s)
- Bahgat Fayed
- Department of Biology, University of York, York, United Kingdom Chemistry of Natural and Microbial Products Department, National Research Centre, Cairo, Egypt
| | - David A Ashford
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Amal M Hashem
- Chemistry of Natural and Microbial Products Department, National Research Centre, Cairo, Egypt
| | - Magdy A Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Omaima N El Gazayerly
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Matthew A Gregory
- Isomerase Therapeutics, Science Village, Chesterford Research Park, Cambridge, United Kingdom
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Hoskisson PA, Sumby P, Smith MCM. The phage growth limitation system in Streptomyces coelicolor A(3)2 is a toxin/antitoxin system, comprising enzymes with DNA methyltransferase, protein kinase and ATPase activity. Virology 2015; 477:100-109. [PMID: 25592393 PMCID: PMC4365076 DOI: 10.1016/j.virol.2014.12.036] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/20/2014] [Accepted: 12/22/2014] [Indexed: 11/19/2022]
Abstract
The phage growth limitation system of Streptomyces coelicolor A3(2) is an unusual bacteriophage defence mechanism. Progeny ϕC31 phage from an initial infection are thought to be modified such that subsequent infections are attenuated in a Pgl(+) host but normal in a Pgl(-) strain. Earlier work identified four genes required for phage resistance by Pgl. Here we demonstrate that Pgl is an elaborate and novel phage restriction system that, in part, comprises a toxin/antitoxin system where PglX, a DNA methyltransferase is toxic in the absence of a functional PglZ. In addition, the ATPase activity of PglY and a protein kinase activity in PglW are shown to be essential for phage resistance by Pgl. We conclude that on infection of a Pgl(+) cell by bacteriophage ϕC31, PglW transduces a signal, probably via phosphorylation, to other Pgl proteins resulting in the activation of the DNA methyltransferase, PglX and this leads to phage restriction.
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Affiliation(s)
- Paul A Hoskisson
- Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Science, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Paul Sumby
- Department of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Margaret C M Smith
- Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Science, Foresterhill, Aberdeen AB25 2ZD, UK.
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Fayed B, Younger E, Taylor G, Smith MCM. A novel Streptomyces spp. integration vector derived from the S. venezuelae phage, SV1. BMC Biotechnol 2014; 14:51. [PMID: 24885867 PMCID: PMC4068962 DOI: 10.1186/1472-6750-14-51] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Integrating vectors based on the int/attP loci of temperate phages are convenient and used widely, particularly for cloning genes in Streptomyces spp. RESULTS We have constructed and tested a novel integrating vector based on g27, encoding integrase, and attP site from the phage, SV1. This plasmid, pBF3 integrates efficiently in S. coelicolor and S. lividans but surprisingly fails to generate stable integrants in S. venezuelae, the natural host for phage SV1. CONCLUSION pBF3 promises to be a useful addition to the range of integrating vectors currently available for Streptomyces molecular genetics.
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Smith MCM, Hendrix RW, Dedrick R, Mitchell K, Ko CC, Russell D, Bell E, Gregory M, Bibb MJ, Pethick F, Jacobs-Sera D, Herron P, Buttner MJ, Hatfull GF. Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp. J Bacteriol 2013; 195:4924-35. [PMID: 23995638 PMCID: PMC3807479 DOI: 10.1128/jb.00618-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/14/2013] [Indexed: 11/20/2022] Open
Abstract
The genome sequences of eight Streptomyces phages are presented, four of which were isolated for this study. Phages R4, TG1, Hau3, and SV1 were isolated previously and have been exploited as tools for understanding and genetically manipulating Streptomyces spp. We also extracted five apparently intact prophages from recent Streptomyces spp. genome projects and, together with six phage genomes in the database, we analyzed all 19 Streptomyces phage genomes with a view to understanding their relationships to each other and to other actinophages, particularly the mycobacteriophages. Fifteen of the Streptomyces phages group into four clusters of related genomes. Although the R4-like phages do not share nucleotide sequence similarity with other phages, they clearly have common ancestry with cluster A mycobacteriophages, sharing many protein homologues, common gene syntenies, and similar repressor-stoperator regulatory systems. The R4-like phage Hau3 and the prophage StrepC.1 (from Streptomyces sp. strain C) appear to have hijacked a unique adaptation of the streptomycetes, i.e., use of the rare UUA codon, to control translation of the essential phage protein, the terminase. The Streptomyces venezuelae generalized transducing phage SV1 was used to predict the presence of other generalized transducing phages for different Streptomyces species.
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Affiliation(s)
| | - Roger W. Hendrix
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rebekah Dedrick
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kaitlin Mitchell
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ching-Chung Ko
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel Russell
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emma Bell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - Maureen J. Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Florence Pethick
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Paul Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Graham F. Hatfull
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Córdova-Dávalos LE, Espitia C, González-Cerón G, Arreguín-Espinosa R, Soberón-Chávez G, Servín-González L. LipoproteinN-acyl transferase (Lnt1) is dispensable for proteinO-mannosylation byStreptomyces coelicolor. FEMS Microbiol Lett 2013; 350:72-82. [DOI: 10.1111/1574-6968.12298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/09/2013] [Accepted: 10/07/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Laura Elena Córdova-Dávalos
- Departamento de Biología Molecular y Biotecnología; Instituto de Investigaciones Biomédicas; Universidad Nacional Autónoma de México; Ciudad Universitaria; Ciudad de Mexico DF México
| | - Clara Espitia
- Departamento de Inmunología; Instituto de Investigaciones Biomédicas; Universidad Nacional Autónoma de México; Ciudad Universitaria; Ciudad de Mexico DF México
| | - Gabriela González-Cerón
- Departamento de Biología Molecular y Biotecnología; Instituto de Investigaciones Biomédicas; Universidad Nacional Autónoma de México; Ciudad Universitaria; Ciudad de Mexico DF México
| | - Roberto Arreguín-Espinosa
- Departamento de Química de Biomacromoléculas; Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria; Ciudad de Mexico DF México
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología; Instituto de Investigaciones Biomédicas; Universidad Nacional Autónoma de México; Ciudad Universitaria; Ciudad de Mexico DF México
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología; Instituto de Investigaciones Biomédicas; Universidad Nacional Autónoma de México; Ciudad Universitaria; Ciudad de Mexico DF México
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Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct 2013; 8:15. [PMID: 23768067 PMCID: PMC3710099 DOI: 10.1186/1745-6150-8-15] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022] Open
Abstract
Background The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess RNase activity. Results The HEPN superfamily is comprised of all α-helical domains that were first identified as being associated with DNA polymerase β-type nucleotidyltransferases in prokaryotes and animal Sacsin proteins. Using sensitive sequence and structure comparison methods, we vastly extend the HEPN superfamily by identifying numerous novel families and by detecting diverged HEPN domains in several known protein families. The new HEPN families include the RNase LS and LsoA catalytic domains, KEN domains (e.g. RNaseL and Ire1) and the RNase domains of RloC and PrrC. The majority of HEPN domains contain conserved motifs that constitute a metal-independent endoRNase active site. Some HEPN domains lacking this motif probably function as non-catalytic RNA-binding domains, such as in the case of the mannitol repressor MtlR. Our analysis shows that HEPN domains function as toxins that are shared by numerous systems implicated in intra-genomic, inter-genomic and intra-organismal conflicts across the three domains of cellular life. In prokaryotes HEPN domains are essential components of numerous toxin-antitoxin (TA) and abortive infection (Abi) systems and in addition are tightly associated with many restriction-modification (R-M) and CRISPR-Cas systems, and occasionally with other defense systems such as Pgl and Ter. We present evidence of multiple modes of action of HEPN domains in these systems, which include direct attack on viral RNAs (e.g. LsoA and RNase LS) in conjunction with other RNase domains (e.g. a novel RNase H fold domain, NamA), suicidal or dormancy-inducing attack on self RNAs (RM systems and possibly CRISPR-Cas systems), and suicidal attack coupled with direct interaction with phage components (Abi systems). These findings are compatible with the hypothesis on coupling of pathogen-targeting (immunity) and self-directed (programmed cell death and dormancy induction) responses in the evolution of robust antiviral strategies. We propose that altruistic cell suicide mediated by HEPN domains and other functionally similar RNases was essential for the evolution of kin and group selection and cell cooperation. HEPN domains were repeatedly acquired by eukaryotes and incorporated into several core functions such as endonucleolytic processing of the 5.8S-25S/28S rRNA precursor (Las1), a novel ER membrane-associated RNA degradation system (C6orf70), sensing of unprocessed transcripts at the nuclear periphery (Swt1). Multiple lines of evidence suggest that, similar to prokaryotes, HEPN proteins were recruited to antiviral, antitransposon, apoptotic systems or RNA-level response to unfolded proteins (Sacsin and KEN domains) in several groups of eukaryotes. Conclusions Extensive sequence and structure comparisons reveal unexpectedly broad presence of the HEPN domain in an enormous variety of defense and stress response systems across the tree of life. In addition, HEPN domains have been recruited to perform essential functions, in particular in eukaryotic rRNA processing. These findings are expected to stimulate experiments that could shed light on diverse cellular processes across the three domains of life. Reviewers This article was reviewed by Martijn Huynen, Igor Zhulin and Nick Grishin
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Affiliation(s)
- Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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The origin of the bacterial immune response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 738:1-13. [PMID: 22399370 DOI: 10.1007/978-1-4614-1680-7_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bacteriophages are probably the oldest viruses, having appeared early during bacterial evolution. Therefore, bacteria and bacteriophages have a long history of co-evolution in which bacteria have developed multiple resistance mechanisms against bacteriophages. These mechanisms, that are very diverse and are in constant evolution, allow the survival of the bacteria. Bacteriophages have adapted to bacterial defense systems, devised strategies to evade these anti-phage mechanisms and restored their infective capacity. In this chapter, we review the bacterial strategies that hinder the phage infection as well as the counter-defense mechanisms developed.
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Wehmeier S, Varghese AS, Gurcha SS, Tissot B, Panico M, Hitchen P, Morris HR, Besra GS, Dell A, Smith MCM. Glycosylation of the phosphate binding protein, PstS, in Streptomyces coelicolor by a pathway that resembles protein O-mannosylation in eukaryotes. Mol Microbiol 2008; 71:421-33. [PMID: 19017269 DOI: 10.1111/j.1365-2958.2008.06536.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously mutations in a putative protein O-mannosyltransferase (SCO3154, Pmt) and a polyprenol phosphate mannose synthase (SCO1423, Ppm1) were found to cause resistance to phage, phiC31, in the antibiotic producing bacteria Streptomyces coelicolor A3(2). It was proposed that these two enzymes were part of a protein O-glycosylation pathway that was necessary for synthesis of the phage receptor. Here we provide the evidence that Pmt and Ppm1 are indeed both required for protein O-glycosylation. The phosphate binding protein PstS was found to be glycosylated with a trihexose in the S. coelicolor parent strain, J1929, but not in the pmt(-) derivative, DT1025. Ppm1 was necessary for the transfer of mannose to endogenous polyprenol phosphate in membrane preparations of S. coelicolor. A mutation in ppm1 that conferred an E218V substitution in Ppm1 abolished mannose transfer and glycosylation of PstS. Mass spectrometry analysis of extracted lipids showed the presence of a glycosylated polyprenol phosphate (PP) containing nine repeated isoprenyl units (C(45)-PP). S. coelicolor membranes were also able to catalyse the transfer of mannose to peptides derived from PstS, indicating that these could be targets for Pmt in vivo.
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Affiliation(s)
- S Wehmeier
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
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16
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Hoskisson PA, Smith MCM. Hypervariation and phase variation in the bacteriophage 'resistome'. Curr Opin Microbiol 2007; 10:396-400. [PMID: 17719266 DOI: 10.1016/j.mib.2007.04.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Accepted: 04/17/2007] [Indexed: 11/20/2022]
Abstract
Most bacteria encode proteins for defence against infection by bacteriophages. The mechanisms that bring about phage defence are extremely diverse, suggesting frequent independent evolution of novel processes. Phage defence determinants are often plasmid or phage-encoded and many that are chromosomal show evidence of lateral transfer. Recent studies on restriction-modification (R-M) systems show that these genes are amongst the most rapidly evolving. Some bacteria have contingency genes that encode alternative target specificity determinants for Type I or Type III R-M systems, thus expanding the range of phages against which the host population is immune. The most counter-intuitive observation, however, is the prevalence of phase variation in many restriction systems, but recent arguments suggest that switching off expression of R-M systems can aid phage defence.
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Affiliation(s)
- Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biological Science, University of Strathclyde, Royal College Building, George Street, Glasgow, United Kingdom
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17
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Khodakaramian G, Lissenden S, Gust B, Moir L, Hoskisson PA, Chater KF, Smith MCM. Expression of Cre recombinase during transient phage infection permits efficient marker removal in Streptomyces. Nucleic Acids Res 2006; 34:e20. [PMID: 16473843 PMCID: PMC1363781 DOI: 10.1093/nar/gnj019] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report a system for the efficient removal of a marker flanked by two loxP sites in Streptomyces coelicolor, using a derivative of the temperate phage phiC31 that expresses Cre recombinase during a transient infection. As the test case for this recombinant phage (called Cre-phage), we present the construction of an in-frame deletion of a gene, pglW, required for phage growth limitation or Pgl in S.coelicolor. Cre-phage was also used for marker deletion in other strains of S.coelicolor.
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Affiliation(s)
| | | | - Bertolt Gust
- John Innes Centre, Norwich Research ParkColney Lane, Norwich NR4 7UH, UK
| | - Laura Moir
- Institute of Medical Sciences, University of AberdeenForesterhill, Aberdeen AB25 2ZD, UK
| | - Paul A. Hoskisson
- Institute of Medical Sciences, University of AberdeenForesterhill, Aberdeen AB25 2ZD, UK
| | - Keith F. Chater
- John Innes Centre, Norwich Research ParkColney Lane, Norwich NR4 7UH, UK
| | - Margaret C. M. Smith
- Institute of Medical Sciences, University of AberdeenForesterhill, Aberdeen AB25 2ZD, UK
- To whom correspondence should be addressed. Tel: +44 1224 555739; Fax: + 44 1224 555844;
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18
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Rodríguez-García A, Combes P, Pérez-Redondo R, Smith MCA, Smith MCM. Natural and synthetic tetracycline-inducible promoters for use in the antibiotic-producing bacteria Streptomyces. Nucleic Acids Res 2005; 33:e87. [PMID: 15917435 PMCID: PMC1140374 DOI: 10.1093/nar/gni086] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteria in the genus Streptomyces are major producers of antibiotics and other pharmacologically active compounds. Genetic and physiological manipulations of these bacteria are important for new drug discovery and production development. An essential part of any 'genetic toolkit' is the availability of regulatable promoters. We have adapted the tetracycline (Tc) repressor/operator (TetR/tetO) regulatable system from transposon Tn10 for use in Streptomyces. The synthetic Tc controllable promoter (tcp), tcp830, was active in a wide range of Streptomyces species, and varying levels of induction were observed after the addition of 1-100 ng/ml of anhydrotetracycline (aTc). Streptomyces coelicolor contained an innate Tc-controllable promoter regulated by a TetR homologue (SCO0253). Both natural and synthetic promoters were active and inducible throughout growth. Using the luxAB genes expressing luciferase as a reporter system, we showed that induction factors of up to 270 could be obtained for tcp830. The effect of inducers on the growth of S.coelicolor was determined; addition of aTc at concentrations where induction is optimal, i.e. 0.1-1 microg/ml, ranged from no effect on growth rate to a small increase in the lag period compared with cultures with no inducer.
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Affiliation(s)
| | | | | | | | - Margaret C. M. Smith
- To whom correspondence should be addressed at Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK. Tel: +44 01224 555739; Fax: +44 01224 555844;
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19
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Abstract
During lysogenic growth many temperate bacteriophage genomes are integrated into the host's chromosome and efficient integration and excision are therefore an essential part of the phage life cycle. The Streptomyces phage phiC31 encodes an integrase related to the resolvase/invertases and is evolutionarily and mechanistically distinct from the integrase of phage lambda. We show that during phiC31 integration the polarity of the recombination sites, attB and attP, is dependent on the sequences of the two base pairs (bp) where crossover occurs. A loss or switch in polarity of the recombination sites can occur by mutation of this dinucleotide, leading to incorrectly joined products. The properties of the mutant sites implies that phiC31 integrase interacts symmetrically with the substrates, which during synapsis can align apparently freely in either of two alternative forms that lead to correct or incorrect joining of products. Analysis of the topologies of the reaction products provided evidence that integrase can synapse and activate strand exchange even when recombinant products cannot form due to mismatches at the crossover site. The topologies of the recombination products are complex and indicative of multiple pathways to product formation. The efficiency of integration of a phiC31 derivative, KC859, into an attB site with switched polarity was assayed in vivo and shown to be no different from integration into a wild-type attB. Thus neither the host nor KC859 express a factor that influences the alignment of the recombination sites at synapsis.
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Affiliation(s)
- Matthew C A Smith
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
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20
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Gregory MA, Till R, Smith MCM. Integration site for Streptomyces phage phiBT1 and development of site-specific integrating vectors. J Bacteriol 2003; 185:5320-3. [PMID: 12923110 PMCID: PMC180994 DOI: 10.1128/jb.185.17.5320-5323.2003] [Citation(s) in RCA: 225] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite extensive similarities between the genomes of the Streptomyces temperate phages phiC31 and phiBT1, the attP-int loci are poorly conserved. Here we demonstrate that phiBT1 integrates into a different attachment site than phiC31. phiBT1 attB lies within SCO4848 encoding a 79-amino-acid putative integral membrane protein. Integration vectors based on phiBT1 integrase were shown to have a broad host range and are fully compatible with those based on the phiC31 attP-int locus.
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Affiliation(s)
- Matthew A Gregory
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, United Kingdom
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21
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Sumby P, Smith MCM. Phase variation in the phage growth limitation system of Streptomyces coelicolor A3(2). J Bacteriol 2003; 185:4558-63. [PMID: 12867465 PMCID: PMC165769 DOI: 10.1128/jb.185.15.4558-4563.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phase-variable phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2) is an unusual bacteriophage resistance mechanism that confers protection against the temperate phage phiC31 and homoimmune relatives. Pgl is subject to phase variation, and data presented here show that this is at least partially due to expansion and contraction of a polyguanine tract present within the putative adenine-specific DNA methyltransferase gene, pglX. Furthermore, the pglX paralogue SC6G9.02, here renamed pglS, was shown to be able to interfere with the Pgl phenotype, suggesting that PglS could provide an alternative activity to that conferred by PglX.
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Affiliation(s)
- Paul Sumby
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, United Kingdom
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22
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Cowlishaw DA, Smith MCM. A gene encoding a homologue of dolichol phosphate-beta-D-mannose synthase is required for infection of Streptomyces coelicolor A3(2) by phage (phi)C31. J Bacteriol 2002; 184:6081-3. [PMID: 12374845 PMCID: PMC135388 DOI: 10.1128/jb.184.21.6081-6083.2002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have shown previously that a gene encoding a homologue to the eukaryotic dolichol-phosphate-D-mannose, protein O-D-mannosyltransferase, was required for (phi)C31 infection of Streptomyces coelicolor. Here we show that a gene encoding the homologue to dolichol-phosphate-mannose synthase is also essential for phage sensitivity. These data confirm the role of glycosylation in the phage receptor for (phi)C31 in S. coelicolor.
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Affiliation(s)
- Deborah A Cowlishaw
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, United Kingdom
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23
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Combes P, Till R, Bee S, Smith MCM. The streptomyces genome contains multiple pseudo-attB sites for the (phi)C31-encoded site-specific recombination system. J Bacteriol 2002; 184:5746-52. [PMID: 12270833 PMCID: PMC139614 DOI: 10.1128/jb.184.20.5746-5752.2002] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2002] [Accepted: 07/22/2002] [Indexed: 11/20/2022] Open
Abstract
The integrase from the Streptomyces phage (phi)C31 is a member of the serine recombinase family of site-specific recombinases and is fundamentally different from that of lambda or its relatives. Moreover, (phi)C31 int/attP is used widely as an essential component of integration vectors (such as pSET152) employed in the genetic analysis of Streptomyces species. phiC31 or integrating plasmids containing int/attP have been shown previously to integrate at a locus, attB, in the chromosome. The DNA sequences of the attB sites of various Streptomyces species revealed nonconserved positions. In particular, the crossover site was narrowed to the sequence 5'TT present in both attP and attB. Strains of Streptomyces coelicolor and S. lividans were constructed with a deletion of the attB site ((Delta)attB), and pSET152 was introduced into these strains by conjugation. Thus, secondary or pseudo-attB sites were identified by Southern blotting and after rescue of plasmids containing DNA flanking the insertion sites from the chromosome. The sequences of the integration sites had similarity to those of attB. Analysis of the insertions of pSET152 into both attB(+) and (Delta)attB strains indicated that this plasmid can integrate at several loci via independent recombination events within a transconjugant.
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Affiliation(s)
- Patricia Combes
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, United Kingdom
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24
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Abstract
Whenever the state of a biological system is not determined solely by present conditions but depends on its past history, we can say that the system has memory. Bacteria and bacteriophage use a variety of memory mechanisms, some of which seem to convey adaptive value. A genetic type of heritable memory is the programmed inversion of specific DNA sequences, which causes switching between alternative patterns of gene expression. Heritable memory can also be based on epigenetic circuits, in which a system with two possible steady states is locked in one or the other state by a positive feedback loop. Epigenetic states have been observed in a variety of cellular processes, and are maintained by diverse mechanisms. Some of these involve alternative DNA methylation patterns that are stably transmitted to daughter molecules and can affect DNA-protein interactions (e.g., gene transcription). Other mechanisms exploit autocatalytic loops whereby proteins establish the proper conditions for their continued synthesis. Template polymers other than nucleic acids (e.g., components of the cell wall) may also propagate epigenetic states. Non-heritable memory is exemplified by parasitic organisms that bear a signature of their previous host, such as host-controlled modification of phage DNA or porin hitchhiking in predatory bacteria. The heterogeneous nature of the examples known may be indicative of widespread occurrence of memory mechanisms in bacteria and phage. However, the actual extent, variety and potential selective value of prokaryotic memory devices remain open questions, still to be addressed experimentally.
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Affiliation(s)
- Josep Casadesús
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
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25
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Sumby P, Smith MCM. Genetics of the phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2). Mol Microbiol 2002; 44:489-500. [PMID: 11972785 DOI: 10.1046/j.1365-2958.2002.02896.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The phage growth limitation (Pgl) system, encoded by Streptomyces coelicolor A3(2), confers protection against the temperate bacteriophage phiC31 and its homoimmune relatives. The Pgl phenotype is characterized by the ability of Pgl+ hosts to support a phage burst on initial infection but subsequent cycles are severely attenuated. Previously, two adjacent genes pglY and pglZ were shown to be required for Pgl. It had been shown by Southern blotting that Streptomyces lividans, a close relative of S. coelicolor and naturally Pgl-, does not contain homologues of pglYZ and that introduction of pglYZ into S. lividans is not sufficient to confer a Pgl+ phenotype. Moreover, the mechanism of the Pgl+<--> Pgl- phase variation associated with this phenotype is also not understood. Here we describe two novel genes, pglW and pglX, that were shown to be part of this system by complementation of Pgl- mutants and by insertional mutagenesis. pglW encodes a 169 kDa protein that includes putative motifs for both serine/threonine protein kinase activity and DNA binding. pglX encodes a 136 kDa protein with putative adenine-specific DNA methyltransferase activity. pglW and pglX have overlapping stop-start codons suggesting transcriptional and translational coupling. S1 mapping of transcripts initiating up-stream of pglW indicated that, like pglYZ, pglWX is expressed in uninfected cultures. A homologue of pglX with 76% amino acid identity was identified in S. coelicolor, and insertional mutagenesis indicated that this gene was not required for the Pgl+ phenotype. Southern blots indicated that S. lividans does not contain homologues of pglW or pglX. A plasmid encoding pglWXYZ was able to confer the Pgl+ phenotype to S. lividans implying that these four genes constitute the whole system.
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Affiliation(s)
- Paul Sumby
- Institute of Genetics, University of Nottingham, Queens Medical Centre, UK
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26
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Cowlishaw DA, Smith MC. Glycosylation of a Streptomyces coelicolor A3(2) cell envelope protein is required for infection by bacteriophage phi C31. Mol Microbiol 2001; 41:601-10. [PMID: 11532128 DOI: 10.1046/j.1365-2958.2001.02510.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mutants of Streptomyces coelicolor A3(2) J1929 (Delta pglY) were isolated that were resistant to the Streptomyces temperate phage phi C31. These strains could be transfected with phi C31 DNA, but could not act as infective centres after exposure to phage. Thus, it was concluded that infection was blocked at the adsorption/DNA injection step. The mutants fell into three classes. Class I mutants were complemented by a gene, SCE87.05, isolated from the cosmid library of S. coelicolor A3(2). The product of SCE87.05 had good overall homology to a Mycobacterium tuberculosis hypothetical protein and regions with similarity to dolichol phosphate-D-mannose:protein O-D-mannosyltransferases. Concanavalin A (ConA) inhibited phi C31 infection of S. coelicolor J1929, and this could be partially reversed by the addition of the sugar, alpha-D-methyl-pyranoside. Moreover, glycosylated proteins from J1929, but not from the class I mutant DT1017, were detected using ConA as a probe in Western blots. Class I and II mutants were sensitive to phi C31hc, a previously isolated phage exhibiting an extended host range phenotype, conferred by h. A phage with the same phenotype, phi DT4002, was isolated independently, and a missense mutation was found in a putative tail gene. It is proposed that the phi C31 receptor is a cell wall glycoprotein, and that the phi C31h mutation compensates for the lack of glycosylation of the receptor.
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Affiliation(s)
- D A Cowlishaw
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
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27
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Billington SJ, Huggins AS, Johanesen PA, Crellin PK, Cheung JK, Katz ME, Wright CL, Haring V, Rood JI. Complete nucleotide sequence of the 27-kilobase virulence related locus (vrl) of Dichelobacter nodosus: evidence for extrachromosomal origin. Infect Immun 1999; 67:1277-86. [PMID: 10024571 PMCID: PMC96457 DOI: 10.1128/iai.67.3.1277-1286.1999] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vrl locus is preferentially associated with virulent isolates of the ovine footrot pathogen, Dichelobacter nodosus. The complete nucleotide sequence of this 27.1-kb region has now been determined. The data reveal that the locus has a G+C content much higher than the rest of the D. nodosus chromosome and contains 22 open reading frames (ORFs) encoding products including a putative adenine-specific methylase, two potential DEAH ATP-dependent helicases, and two products with sequence similarity to a bacteriophage resistance system. These ORFs are all in the same orientation, and most are either overlapping or separated by only a few nucleotides, suggesting that they comprise an operon and are translationally coupled. Expression vector studies have led to the identification of proteins that correspond to many of these ORFs. These data, in combination with evidence of insertion of vrl into the 3' end of an ssrA gene, are consistent with the hypothesis that the vrl locus was derived from the insertion of a bacteriophage or plasmid into the D. nodosus genome.
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Affiliation(s)
- S J Billington
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
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28
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Chakraburtty R, Bibb M. The ppGpp synthetase gene (relA) of Streptomyces coelicolor A3(2) plays a conditional role in antibiotic production and morphological differentiation. J Bacteriol 1997; 179:5854-61. [PMID: 9294445 PMCID: PMC179477 DOI: 10.1128/jb.179.18.5854-5861.1997] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Deletion of most of the coding region of the ppGpp synthetase gene (relA) of Streptomyces coelicolor A3(2) resulted in loss of ppGpp synthesis, both upon entry into stationary phase under conditions of nitrogen limitation and following amino acid starvation during exponential growth, but had no effect on growth rate. The relA mutant, which showed continued rRNA synthesis upon amino acid depletion (the relaxed response), failed to produce the antibiotics undecylprodigiosin (Red) and actinorhodin (Act) under conditions of nitrogen limitation. The latter appears to reflect diminished transcription of pathway-specific regulatory genes for Red and Act production, redD and actII-ORF4, respectively. In addition to the changes in secondary metabolism, the relA mutant showed a marked delay in the onset and extent of morphological differentiation, resulting in a conspicuously altered colony morphology.
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Affiliation(s)
- R Chakraburtty
- Department of Genetics, John Innes Centre, Norwich Research Park, Colney, United Kingdom
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29
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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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