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Kogay R, Zhaxybayeva O. Co-evolution of gene transfer agents and their alphaproteobacterial hosts. J Bacteriol 2024; 206:e0039823. [PMID: 38240570 PMCID: PMC10883770 DOI: 10.1128/jb.00398-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 02/23/2024] Open
Abstract
Gene transfer agents (GTAs) are enigmatic elements that resemble small viruses and are known to be produced during nutritional stress by some bacteria and archaea. The production of GTAs is regulated by quorum sensing, under which a small fraction of the population acts as GTA producers, while the rest becomes GTA recipients. In contrast to canonical viruses, GTAs cannot propagate themselves because they package pieces of the producing cell's genome. In alphaproteobacteria, GTAs are mostly vertically inherited and reside in their hosts' genomes for hundreds of millions of years. While GTAs' ability to transfer genetic material within a population and their long-term preservation suggest an increased fitness of GTA-producing microbes, the associated benefits and type of selection that maintains GTAs are poorly understood. By comparing rates of evolutionary change in GTA genes to the rates in gene families abundantly present across 293 alphaproteobacterial genomes, we detected 59 gene families that likely co-evolve with GTA genes. These gene families are predominantly involved in stress response, DNA repair, and biofilm formation. We hypothesize that biofilm formation enables the physical proximity of GTA-producing cells, limiting GTA-derived benefits only to a group of closely related cells. We further conjecture that the population structure of biofilm-forming sub-populations ensures that the trait of GTA production is maintained despite the inevitable rise of "cheating" genotypes. Because release of GTA particles kills the producing cell, maintenance of GTAs is an exciting example of social evolution in a microbial population.IMPORTANCEGene transfer agents (GTAs) are viruses domesticated by some archaea and bacteria as vehicles for carrying pieces of the host genome. Produced under certain environmental conditions, GTA particles can deliver DNA to neighboring, closely related cells. The function of GTAs remains uncertain. While making GTAs is suicidal for a cell, GTA-encoding genes are widespread in genomes of alphaproteobacteria. Such GTA persistence implies functional benefits but raises questions about how selection maintains this lethal trait. By showing that GTA genes co-evolve with genes involved in stress response, DNA repair, and biofilm formation, we provide support for the hypothesis that GTAs facilitate DNA exchange during the stress conditions and present a model for how GTAs persist in biofilm-forming bacterial populations despite being lethal.
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Affiliation(s)
- Roman Kogay
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
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2
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Genomic repertoire of Mameliella alba Ep20 associated with Symbiodinium from the endemic coral Mussismilia braziliensis. Symbiosis 2019. [DOI: 10.1007/s13199-019-00655-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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3
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Grüll MP, Mulligan ME, Lang AS. Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents. FEMS Microbiol Lett 2019; 365:5067299. [PMID: 30085064 DOI: 10.1093/femsle/fny192] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/04/2018] [Indexed: 12/18/2022] Open
Abstract
Bacteria are known to release different types of particles that serve various purposes such as the processing of metabolites, communication, and the transfer of genetic material. One of the most interesting aspects of the production of such particles is the biogenesis and trafficking of complex particles that can carry DNA, RNA, proteins or toxins into the surrounding environment to aid in bacterial survival or lead to gene transfer. Two important bacterial extracellular complexes are membrane vesicles and gene transfer agents. In this review, we will discuss the production, contents and functions of these two types of particles as related to their abilities to facilitate horizontal gene transfer.
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Affiliation(s)
| | - M E Mulligan
- Biochemistry, Memorial University of Newfoundland, St John's, NL, Canada
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4
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Tamarit D, Neuvonen MM, Engel P, Guy L, Andersson SGE. Origin and Evolution of the Bartonella Gene Transfer Agent. Mol Biol Evol 2019; 35:451-464. [PMID: 29161442 DOI: 10.1093/molbev/msx299] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces that drive the emergence of GTAs are still poorly understood. Two GTAs have been identified in the Alphaproteobacteria: the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range that includes vector-borne intracellular bacteria of the genus Bartonella. The RcGTA packages chromosomal DNA randomly, whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplified from a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bacteriophage genes identified in the genomes of Bartonella species and close relatives. Unlike the BaGTA, the prophage genes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and substitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integration and recombination events in the prophages. Furthermore, the organization of segments flanking the BaGTA differs from that of the prophages by a few rearrangement events, which have abolished the normal coordination between phage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose a model for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.
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Affiliation(s)
- Daniel Tamarit
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Minna-Maria Neuvonen
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Lionel Guy
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Siv G E Andersson
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
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5
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Bakenhus I, Voget S, Poehlein A, Brinkhoff T, Daniel R, Simon M. Genome sequence of Planktotalea frisia type strain (SH6-1 T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. Stand Genomic Sci 2018; 13:7. [PMID: 29682168 PMCID: PMC5896138 DOI: 10.1186/s40793-018-0311-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/21/2018] [Indexed: 12/15/2022] Open
Abstract
Planktotalea frisia SH6-1T Hahnke et al. (Int J Syst Evol Microbiol 62:1619-24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Here we describe the draft genome sequence and annotation of the type strain SH6-1T. The genome comprises 4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome sequence provides evidence for at least three extrachromosomal elements, encodes genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV secretion system. This indicates not only adaptation to a free-living lifestyle of P. frisia but points also to interactions with prokaryotic or eukaryotic organisms.
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Affiliation(s)
- Insa Bakenhus
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Sonja Voget
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Thorsten Brinkhoff
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
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6
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Lang AS, Westbye AB, Beatty JT. The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange. Annu Rev Virol 2017; 4:87-104. [DOI: 10.1146/annurev-virology-101416-041624] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, A1B 3X9, Canada
| | - Alexander B. Westbye
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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7
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Westbye AB, Beatty JT, Lang AS. Guaranteeing a captive audience: coordinated regulation of gene transfer agent (GTA) production and recipient capability by cellular regulators. Curr Opin Microbiol 2017; 38:122-129. [DOI: 10.1016/j.mib.2017.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/24/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
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8
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von Wintersdorff CJH, Penders J, van Niekerk JM, Mills ND, Majumder S, van Alphen LB, Savelkoul PHM, Wolffs PFG. Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Front Microbiol 2016; 7:173. [PMID: 26925045 PMCID: PMC4759269 DOI: 10.3389/fmicb.2016.00173] [Citation(s) in RCA: 706] [Impact Index Per Article: 88.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antibiotic resistance among pathogenic bacteria has been a rising problem for public health in recent decades. It is becoming increasingly recognized that not only antibiotic resistance genes (ARGs) encountered in clinical pathogens are of relevance, but rather, all pathogenic, commensal as well as environmental bacteria—and also mobile genetic elements and bacteriophages—form a reservoir of ARGs (the resistome) from which pathogenic bacteria can acquire resistance via horizontal gene transfer (HGT). HGT has caused antibiotic resistance to spread from commensal and environmental species to pathogenic ones, as has been shown for some clinically important ARGs. Of the three canonical mechanisms of HGT, conjugation is thought to have the greatest influence on the dissemination of ARGs. While transformation and transduction are deemed less important, recent discoveries suggest their role may be larger than previously thought. Understanding the extent of the resistome and how its mobilization to pathogenic bacteria takes place is essential for efforts to control the dissemination of these genes. Here, we will discuss the concept of the resistome, provide examples of HGT of clinically relevant ARGs and present an overview of the current knowledge of the contributions the various HGT mechanisms make to the spread of antibiotic resistance.
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Affiliation(s)
- Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+ Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands
| | - Julius M van Niekerk
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Nathan D Mills
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Snehali Majumder
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Lieke B van Alphen
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology and Infection Control, VU University Medical CenterAmsterdam, Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands
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9
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Song J, Xia F, Jiang H, Li X, Hu L, Gong P, Lei L, Feng X, Sun C, Gu J, Han W. Identification and characterization of HolGH15: the holin of Staphylococcus aureus bacteriophage GH15. J Gen Virol 2016; 97:1272-1281. [PMID: 26873847 DOI: 10.1099/jgv.0.000428] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Holins are phage-encoded hydrophobic membrane proteins that spontaneously and non-specifically accumulate and form lesions in the cytoplasmic membrane. The ORF72 gene (also designated HolGH15) derived from the genome of the Staphylococcus aureus phage GH15 was predicted to encode a membrane protein. An analysis indicated that the protein encoded by HolGH15 potentially consisted of two hydrophobic transmembrane helices. This protein exhibited the structural characteristics of class II holins and belonged to the phage_holin_1 superfamily. Expression of HolGH15 in Escherichia coli BL21 cells resulted in growth retardation of the host cells, which was triggered prematurely by the addition of 2,4-dinitrophenol. The expression of HolGH15 caused morphological alterations in engineered E. coli cells, including loss of the cell wall and cytoplasmic membrane integrity and release of intracellular components, which were visualized by transmission electron microscopy. HolGH15 exerted efficient antibacterial activity at 37 °C and pH 5.2. Mutation analysis indicated that the two transmembrane domains of HolGH15 were indispensable for the activity of the full-length protein. HolGH15 showed a broad antibacterial range: it not only inhibited Staphylococcus aureus, but also demonstrated antibacterial activity against other species, including Listeria monocytogenes, Bacillus subtilis, Pseudomonas aeruginosa, Klebsiella pneumoniae and E. coli. At the minimal inhibitory concentration, HolGH15 evoked the release of cellular contents and resulted in the shrinkage and death of Staphylococcus aureus and Listeria monocytogenes cells. To the best of our knowledge, this study is the first report of a Staphylococcus aureus phage holin that exerts antibacterial activity against heterogeneous pathogens.
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Affiliation(s)
- Jun Song
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Feifei Xia
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Haiyan Jiang
- The First Affiliated Hospital to Changchun University of Chinese Medicine,Changchun 130021, PRChina
| | - Xinwei Li
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Liyuan Hu
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Pengjuan Gong
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Liancheng Lei
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Xin Feng
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Changjiang Sun
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Jingmin Gu
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina
| | - Wenyu Han
- College of Veterinary Medicine,Jilin University, Changchun 130062, PRChina.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses,Yangzhou 225009, PRChina
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10
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Westbye AB, Kuchinski K, Yip CK, Beatty JT. The Gene Transfer Agent RcGTA Contains Head Spikes Needed for Binding to the Rhodobacter capsulatus Polysaccharide Cell Capsule. J Mol Biol 2015; 428:477-91. [PMID: 26711507 DOI: 10.1016/j.jmb.2015.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/25/2015] [Accepted: 12/06/2015] [Indexed: 11/15/2022]
Abstract
Viruses and bacteriophages recognize cell surface proteins using receptor-binding proteins. In most tailed bacteriophages, receptor-binding proteins are located on the bacteriophage tail. The gene transfer agent of Rhodobacter capsulatus, RcGTA, morphologically resembles a tailed bacteriophage and binds to a capsular polysaccharide covering R. capsulatus cells. Here, we report that the RcGTA capsid (head) is decorated by spikes that are needed for binding to the capsule. The triangular spikes measured ~12nm and appeared to be attached at the capsid vertices. Head spike production required the putative carbohydrate-binding protein ghsB (rcc01080) previously thought to encode a side tail fiber protein. We found that ghsB is likely co-transcribed with ghsA (rcc01079) and that ghsA/ghsB is regulated by the CckA-ChpT-CtrA phosphorelay homologues and a quorum-sensing system. GhsA and GhsB were found to be CckA-dependent RcGTA maturation factors, as GhsA- and GhsB-deficient particles were found to have altered native-gel electrophoresis migration. Additionally, we provide electron microscopy images showing that RcGTA contains side tail fibers and a baseplate-like structure near the tip of the tail, which are independent of ghsB.
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Affiliation(s)
- Alexander B Westbye
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Kevin Kuchinski
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - J Thomas Beatty
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.
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11
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Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA. J Bacteriol 2015; 197:2653-63. [PMID: 26031909 DOI: 10.1128/jb.00332-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/27/2015] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED Gene transfer agents (GTAs) morphologically resemble small, double-stranded DNA (dsDNA) bacteriophages; however, their only known role is to package and transfer random pieces of the producing cell genome to recipient cells. The best understood GTA is that of Rhodobacter capsulatus, termed RcGTA. We discovered that homologues of three genes involved in natural transformation in other bacteria, comEC, comF, and comM, are essential for RcGTA-mediated gene acquisition. This paper gives genetic and biochemical evidence that RcGTA-borne DNA entry into cells requires the ComEC and ComF putative DNA transport proteins and genetic evidence that putative cytoplasmic ComM protein of unknown function is required for recipient capability. Furthermore, the master regulator of RcGTA production in <1% of a cell population, CtrA, which is also required for gene acquisition in recipient cells, is expressed in the vast majority of the population. Our results indicate that RcGTA-mediated gene transfer combines key aspects of two bacterial horizontal gene transfer mechanisms, where donor DNA is packaged in transducing phage-like particles and recipient cells take up DNA using natural transformation-related machinery. Both of these differentiated subsets of a culture population, donors and recipients, are dependent on the same response regulator, CtrA. IMPORTANCE Horizontal gene transfer (HGT) is a major driver of bacterial evolution and adaptation to environmental stresses. Traits such as antibiotic resistance or metabolic properties can be transferred between bacteria via HGT; thus, HGT can have a tremendous effect on the fitness of a bacterial population. The three classically described HGT mechanisms are conjugation, transformation, and phage-mediated transduction. More recently, the HGT factor GTA was described, where random pieces of producing cell genome are packaged into phage-like particles that deliver DNA to recipient cells. In this report, we show that transport of DNA borne by the R. capsulatus RcGTA into recipient cells requires key genes previously thought to be specific to natural transformation pathways. These findings indicate that RcGTA combines central aspects of phage-mediated transduction and natural transformation in an efficient, regulated mode of HGT.
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12
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Holins in bacteria, eukaryotes, and archaea: multifunctional xenologues with potential biotechnological and biomedical applications. J Bacteriol 2014; 197:7-17. [PMID: 25157079 DOI: 10.1128/jb.02046-14] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Holins form pores in the cytoplasmic membranes of bacteria for the primary purpose of releasing endolysins that hydrolyze the cell wall and induce cell death. Holins are encoded within bacteriophage genomes, where they promote cell lysis for virion release, and within bacterial genomes, where they serve a diversity of potential or established functions. These include (i) release of gene transfer agents, (ii) facilitation of programs of differentiation such as those that allow sporulation and spore germination, (iii) contribution to biofilm formation, (iv) promotion of responses to stress conditions, and (v) release of toxins and other proteins. There are currently 58 recognized families of holins and putative holins with members exhibiting between 1 and 4 transmembrane α-helical spanners, but many more families have yet to be discovered. Programmed cell death in animals involves holin-like proteins such as Bax and Bak that may have evolved from bacterial holins. Holin homologues have also been identified in archaea, suggesting that these proteins are ubiquitous throughout the three domains of life. Phage-mediated cell lysis of dual-membrane Gram-negative bacteria also depends on outer membrane-disrupting "spanins" that function independently of, but in conjunction with, holins and endolysins. In this minireview, we provide an overview of their modes of action and the first comprehensive summary of the many currently recognized and postulated functions and uses of these cell lysis systems. It is anticipated that future studies will result in the elucidation of many more such functions and the development of additional applications.
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Breider S, Teshima H, Petersen J, Chertkov O, Dalingault H, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Tindall BJ, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. Stand Genomic Sci 2014; 9:687-703. [PMID: 25197454 PMCID: PMC4148953 DOI: 10.4056/sigs.3828824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leisingera nanhaiensis DSM 24252T is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252T possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
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Affiliation(s)
- Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Brian J Tindall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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Extracellular tRNAs of the Marine Photosynthetic BacteriumRhodovulum sulfidophilumAre Not Aminoacylated. Biosci Biotechnol Biochem 2014; 73:425-7. [DOI: 10.1271/bbb.80465] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 2013; 9:142-59. [PMID: 24501652 PMCID: PMC3910554 DOI: 10.4056/sigs.4287962] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
TF-218T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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16
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Bondarev V, Richter M, Romano S, Piel J, Schwedt A, Schulz-Vogt HN. The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ Microbiol 2013; 15:2095-113. [PMID: 23601235 PMCID: PMC3806328 DOI: 10.1111/1462-2920.12123] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/08/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
Abstract
The majority of strains belonging to the genus Pseudovibrio have been isolated from marine invertebrates such as tunicates, corals and particularly sponges, but the physiology of these bacteria is poorly understood. In this study, we analyse for the first time the genomes of two Pseudovibrio strains – FO-BEG1 and JE062. The strain FO-BEG1 is a required symbiont of a cultivated Beggiatoa strain, a sulfide-oxidizing, autotrophic bacterium, which was initially isolated from a coral. Strain JE062 was isolated from a sponge. The presented data show that both strains are generalistic bacteria capable of importing and oxidizing a wide range of organic and inorganic compounds to meet their carbon, nitrogen, phosphorous and energy requirements under both, oxic and anoxic conditions. Several physiological traits encoded in the analysed genomes were verified in laboratory experiments with both isolates. Besides the versatile metabolic abilities of both Pseudovibrio strains, our study reveals a number of open reading frames and gene clusters in the genomes that seem to be involved in symbiont–host interactions. Both Pseudovibrio strains have the genomic potential to attach to host cells, interact with the eukaryotic cell machinery, produce secondary metabolites and supply the host with cofactors.
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Affiliation(s)
- Vladimir Bondarev
- Max Planck Institute for Marine Microbiology, Ecophysiology Group, Celsiusstr. 1, 28359 Bremen, Germany
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17
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Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang H, Wollherr A, Kjelleberg S, Daniel R, Simon M, Thomas T, Brinkhoff T. Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME JOURNAL 2012; 6:2229-44. [PMID: 22717884 DOI: 10.1038/ismej.2012.62] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.
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Affiliation(s)
- Sebastian Thole
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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18
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Lang AS, Zhaxybayeva O, Beatty JT. Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 2012; 10:472-82. [PMID: 22683880 DOI: 10.1038/nrmicro2802] [Citation(s) in RCA: 245] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cell's genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.
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Affiliation(s)
- Andrew S Lang
- Department of Biology, Memorial University, St. John's, Newfoundland and Labrador A1B 3X9, Canada.
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19
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Engelhardt T, Sahlberg M, Cypionka H, Engelen B. Induction of prophages from deep-subseafloor bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:459-465. [PMID: 23761308 DOI: 10.1111/j.1758-2229.2010.00232.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The deep-subseafloor biosphere harbours a major part of the total microbial biomass on Earth. However, how life and death in this environment are regulated is not yet understood. While organisms from higher trophic levels appear to be absent, viruses might be a factor for microbial mortality. In this study, we found an increasing ratio between viral and total cell counts with depth in deep-subseafloor sediments recovered during Leg 201 of the Ocean Drilling Program. A phylogenetically diverse culture collection from corresponding sediment layers was tested for the presence of inducible prophages. A treatment by mitomycin C as inducing agent indicated the presence of prophages in 46% of the bacterial isolates. Different morphotypes of myoviruses and siphoviruses were detected by transmission electron microscopy. Pulsed-field gel electrophoresis applied to viral DNA extracts showed their genetic diversity. Three host strains even harboured more than one prophage. Thus, our results prove the existence of functional viruses in the deep-subseafloor biosphere. Bacteriophages might take over the role of the main predators, as anoxia and oligotrophy favour the importance of viruses as mortality factors. Furthermore, the fact that the viral shunt recycles organic compounds might be of special relevance to this severely nutrient-depleted habitat.
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Affiliation(s)
- Tim Engelhardt
- Carl-von-Ossietzky Universität Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Straße 9-11, D-26129 Oldenburg, Germany
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20
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Tadmor AD, Ottesen EA, Leadbetter JR, Phillips R. Probing individual environmental bacteria for viruses by using microfluidic digital PCR. Science 2011; 333:58-62. [PMID: 21719670 PMCID: PMC3261838 DOI: 10.1126/science.1200758] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viruses may very well be the most abundant biological entities on the planet. Yet neither metagenomic studies nor classical phage isolation techniques have shed much light on the identity of the hosts of most viruses. We used a microfluidic digital polymerase chain reaction (PCR) approach to physically link single bacterial cells harvested from a natural environment with a viral marker gene. When we implemented this technique on the microbial community residing in the termite hindgut, we found genus-wide infection patterns displaying remarkable intragenus selectivity. Viral marker allelic diversity revealed restricted mixing of alleles between hosts, indicating limited lateral gene transfer of these alleles despite host proximity. Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments.
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Affiliation(s)
- Arbel D. Tadmor
- Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elizabeth A. Ottesen
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jared R. Leadbetter
- Ronald and Maxine Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Departments of Applied Physics and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
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21
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Leung MM, Florizone SM, Taylor TA, Lang AS, Beatty JT. The gene transfer agent of Rhodobacter capsulatus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 675:253-64. [PMID: 20532745 DOI: 10.1007/978-1-4419-1528-3_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
When Rhodobacter capsulatus cultures enter the stationary phase of growth, particles of the gene transfer agent (RcGTA) are released from cells. The morphology of RcGTA resembles that of a small, tailed bacteriophage, with a protein capsid surrounding a ~4 kb linear, double-stranded fragment of DNA. However, the DNA present consists of random segments of the R. capsulatus genome, which may be transferred to another strain of R. capsulatus. The recipient in RcGTA-mediated gene transduction may acquire new alleles and thus express a new phenotype. The genes encoding the structural proteins of the RcGTA are clustered on the R. capsulatus chromosome, whereas genes that encode proteins that regulate the production of RcGTA are scattered around the chromosome. These regulatory proteins include a homoserine lactone synthase (GtaI) that produces a quorum-sensing signal, a two-component sensor-kinase protein (CckA), and a two-component response regulator protein (CtrA). We review the proposed evolutionary origin of RcGTA, as well as environmental and cellular factors involved in the induction of this unusual process of genetic exchange.
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Affiliation(s)
- Molly M Leung
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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22
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Chen F, Spano A, Goodman BE, Blasier KR, Sabat A, Jeffery E, Norris A, Shabanowitz J, Hunt DF, Lebedev N. Proteomic analysis and identification of the structural and regulatory proteins of the Rhodobacter capsulatus gene transfer agent. J Proteome Res 2009; 8:967-73. [PMID: 19105630 DOI: 10.1021/pr8006045] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gene transfer agent of Rhodobacter capsulatus (GTA) is a unique phage-like particle that exchanges genetic information between members of this same species of bacterium. Besides being an excellent tool for genetic mapping, the GTA has a number of advantages for biotechnological and nanoengineering purposes. To facilitate the GTA purification and identify the proteins involved in GTA expression, assembly and regulation, in the present work we construct and transform into R. capsulatus Y262 a gene coding for a C-terminally His-tagged capsid protein. The constructed protein was expressed in the cells, assembled into chimeric GTA particles inside the cells and excreted from the cells into surrounding medium. Transmission electron micrographs of phosphotungstate-stained, NiNTA-purified chimeric GTA confirm that its structure is similar to normal GTA particles, with many particles composed both of a head and a tail. The mass spectrometric proteomic analysis of polypeptides present in the GTA recovered outside the cells shows that GTA is composed of at least 9 proteins represented in the GTA gene cluster including proteins coded for by Orf's 3, 5, 6-9, 11, 13, and 15.
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Affiliation(s)
- Frank Chen
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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23
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Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay. ISME JOURNAL 2008; 3:364-73. [DOI: 10.1038/ismej.2008.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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25
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Paul JH. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME JOURNAL 2008; 2:579-89. [PMID: 18521076 DOI: 10.1038/ismej.2008.35] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteriophages are realized to be numerous and important components of oceanic food webs principally because of their lytic capabilities. The subtle changes that temperate phages impart to their hosts in the oceans are far less understood. Occurrences of lysogeny in the oceans correlate well with conditions unfavorable for rapid host growth. In coliphage lambda, phage encoded repressors have been shown to modulate host metabolic gene expression and phenotype, resulting in economizing host energy expenditure. Comparison of lysogenized marine bacteria to the uninfected hosts indicated that prophage acquisition is correlated with host metabolic gene suppression. Screening 113 marine bacterial genomes for prophages yielded 64 prophage-like elements, 21 of which strongly resembled gene transfer agents (GTAs). The remaining 39 putative prophages had a relatively high incidence of transcriptional regulatory and repressor-like proteins (approximately 2/40 kb prophage sequence) compared to lytic marine phages (approximately 0.25/40 kb phage sequence). Here, it has been hypothesized that marine prophages directly contribute to host survival in unfavorable environments by suppression of unneeded metabolic activities. It has been further suggested that such metabolic downshifts are the result of phage-encoded repressors and transcriptional regulators acting directly on host genes. Finally, the widespread occurrence of GTAs may be an efficient mechanism for horizontal gene transfer in the oceans.
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Affiliation(s)
- John H Paul
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA.
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26
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Occurrence and expression of gene transfer agent genes in marine bacterioplankton. Appl Environ Microbiol 2008; 74:2933-9. [PMID: 18359833 DOI: 10.1128/aem.02129-07] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles ( approximately 50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.
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27
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Stanton TB. Prophage-like gene transfer agents-novel mechanisms of gene exchange for Methanococcus, Desulfovibrio, Brachyspira, and Rhodobacter species. Anaerobe 2007; 13:43-9. [PMID: 17513139 DOI: 10.1016/j.anaerobe.2007.03.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 03/04/2007] [Indexed: 11/29/2022]
Abstract
Gene transfer agents (GTAs) are novel mechanisms for bacterial gene transfer. They resemble small, tailed bacteriophages in ultrastructure and act like generalized transducing prophages. In contrast to functional prophages, GTAs package random fragments of bacterial genomes and incomplete copies of their own genomes. The packaged DNA content is characteristic of the GTA and ranges in size from 4.4 to 13.6kb. GTAs have been reported in species of Brachyspira, Methanococcus, Desulfovibrio, and Rhodobacter. The best studied GTAs are VSH-1 of the anaerobic, pathogenic spirochete Brachyspira hyodysenteriae and RcGTA of the nonsulfur, purple, photosynthetic bacterium Rhodobacter capsulatus. VSH-1 and RcGTA have likely contributed to the ecology and evolution of these bacteria. The existence of GTAs in phylogenetically diverse bacteria suggests GTAs may be more common in nature than is now appreciated.
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Affiliation(s)
- Thad B Stanton
- Enteric Diseases and Food Safety Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, 2300 Dayton Road, Ames, IA 50010, USA.
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28
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In vitro assembly of a prohead-like structure of the Rhodobacter capsulatus gene transfer agent. Virology 2007; 364:95-102. [PMID: 17408713 DOI: 10.1016/j.virol.2007.02.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Revised: 12/26/2006] [Accepted: 02/23/2007] [Indexed: 12/14/2022]
Abstract
The gene transfer agent (GTA) is a phage-like particle capable of exchanging double-stranded DNA fragments between cells of the photosynthetic bacterium Rhodobacter capsulatus. Here we show that the major capsid protein of GTA, expressed in E. coli, can be assembled into prohead-like structures in the presence of calcium ions in vitro. Transmission electron microscopy (TEM) of uranyl acetate staining material and thin sections of glutaraldehyde-fixed material demonstrates that these associates have spherical structures with diameters in the range of 27-35 nm. The analysis of scanning TEM images revealed particles of mass approximately 4.3 MDa, representing 101+/-11 copies of the monomeric subunit. The establishment of this simple and rapid method to form prohead-like particles permits the GTA system to be used for genome manipulation within the photosynthetic bacterium, for specific targeted drug delivery, and for the construction of biologically based distributed autonomous sensors for environmental monitoring.
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29
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Lang AS, Beatty JT. Importance of widespread gene transfer agent genes in α-proteobacteria. Trends Microbiol 2007; 15:54-62. [PMID: 17184993 DOI: 10.1016/j.tim.2006.12.001] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 11/13/2006] [Accepted: 12/06/2006] [Indexed: 10/23/2022]
Abstract
The gene transfer agent produced by Rhodobacter capsulatus (RcGTA) is a model for several virus-like elements that seem to function solely for mediating gene exchange. Several genes that encode RcGTA are clearly related to bacteriophage genes but the cellular regulatory mechanisms that control RcGTA production indicate that RcGTA is more than just a defective prophage. Genome sequencing projects show that seemingly functional RcGTA-like structural gene clusters are present in many other species of alpha-proteobacteria, which might also produce RcGTA-like particles. Here, we use the genomic sequence data that are currently available to identify candidate GTA-producing species and propose an evolutionary scheme for RcGTA-like elements in the alpha-proteobacteria.
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Affiliation(s)
- Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
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30
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Matson EG, Thompson MG, Humphrey SB, Zuerner RL, Stanton TB. Identification of genes of VSH-1, a prophage-like gene transfer agent of Brachyspira hyodysenteriae. J Bacteriol 2005; 187:5885-92. [PMID: 16109929 PMCID: PMC1196157 DOI: 10.1128/jb.187.17.5885-5892.2005] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
VSH-1 is a mitomycin C-inducible prophage of the anaerobic spirochete Brachyspira hyodysenteriae. Purified VSH-1 virions are noninfectious, contain random 7.5-kb fragments of the bacterial genome, and mediate generalized transduction of B. hyodysenteriae cells. In order to identify and sequence genes of this novel gene transfer agent (GTA), proteins associated either with VSH-1 capsids or with tails were purified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The N-terminal amino acid sequences of 11 proteins were determined. Degenerate PCR primers were designed from the amino acid sequences and used to amplify several VSH-1 genes from B. hyodysenteriae strain B204 DNA. A lambda clone library of B. hyodysenteriae B204 DNA was subsequently screened by Southern hybridization methods and used to identify and sequence overlapping DNA inserts containing additional VSH-1 genes. VSH-1 genes spanned 16.3 kb of the B. hyodysenteriae chromosome and were flanked by bacterial genes. VSH-1 identified genes and unidentified, intervening open reading frames were consecutively organized in head (seven genes), tail (seven genes), and lysis (four genes) clusters in the same transcriptional direction. Putative lysis genes encoding endolysin (Lys) and holin proteins were identified from sequence and structural similarities of their translated protein products with GenBank bacteriophage proteins. Recombinant Lys protein hydrolyzed peptidoglycan purified from B. hyodysenteriae cells. The identified VSH-1 genes exceed the DNA capacity of VSH-1 virions and do not encode traditional bacteriophage early functions involved in DNA replication. These genome properties explain the noninfectious nature of VSH-1 virions and further confirm its resemblance to known prophage-like, GTAs of other bacterial species, such as the GTA from Rhodobacter capsulatus. The identification of VSH-1 genes will enable analysis of the regulation of this GTA and should facilitate investigations of VSH-1-like prophages from other Brachyspira species.
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Affiliation(s)
- Eric G Matson
- Enteric Diseases and Food Safety Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, 2300 Dayton Road, Ames, IA 50010, USA
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31
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Jeblick J, Kusch J. Sequence, Transcription Activity, and Evolutionary Origin of the R-BodyCoding Plasmid pKAP298 from the Intracellular Parasitic BacteriumCaedibacter taeniospiralis. J Mol Evol 2005; 60:164-73. [PMID: 15785846 DOI: 10.1007/s00239-004-0002-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2004] [Accepted: 09/09/2004] [Indexed: 10/25/2022]
Abstract
We isolated the intracellular parasitic bacterium Caedibacter taeniospiralis from cultures of the freshwater ciliate Paramecium tetraurelia strain 298. Plasmid pKAP298 as well as the total RNA were isolated from the bacteria. pKAP298 was totally sequenced (49.1 kb; NCBI accession number AY422720). From southern blots of pKAP-fragments and Digoxigenin-labeled cDNA of the Caedibacter-RNA, we generated transcription maps of pKAP298. The observed transcription activity indicated functions of the plasmid besides the synthesis of the R-body, a complex protein inclusion associated with toxic effects of Caedibacter cells on host paramecia. We identified 63 potential protein coding regions on pKAP298, and a novel transposon as well as known transposons were characterized. A group II intron was identified. Homologies with putative phage genes were detected on pKAP298 that direct to the evolution of pKAP298 from a bacteriophage. This original phage most probably belonged to the Caudovirales. Hints on a toxin coding region of pKAP298 are given: a protein with homology to the Soj-/ParA-family also has homologies to a membrane associated ATPase, which is involved in eukaryotic ATPase dependent ion carriers and may be associated with toxic effects on paramecia ingesting this protein.
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Affiliation(s)
- Jörn Jeblick
- Department of Biology/Ecology, University of Kaiserslautern, Erwin-Schroedinger-Strasse 13/14, 67663 Kaiserslautern, Germany
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32
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Casjens SR, Gilcrease EB, Winn-Stapley DA, Schicklmaier P, Schmieger H, Pedulla ML, Ford ME, Houtz JM, Hatfull GF, Hendrix RW. The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J Bacteriol 2005; 187:1091-104. [PMID: 15659686 PMCID: PMC545730 DOI: 10.1128/jb.187.3.1091-1104.2005] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 11/03/2004] [Indexed: 11/20/2022] Open
Abstract
The generalized transducing double-stranded DNA bacteriophage ES18 has an icosahedral head and a long noncontractile tail, and it infects both rough and smooth Salmonella enterica strains. We report here the complete 46,900-bp genome nucleotide sequence and provide an analysis of the sequence. Its 79 genes and their organization clearly show that ES18 is a member of the lambda-like (lambdoid) phage group; however, it contains a novel set of genes that program assembly of the virion head. Most of its integration-excision, immunity, Nin region, and lysis genes are nearly identical to those of the short-tailed Salmonella phage P22, while other early genes are nearly identical to Escherichia coli phages lambda and HK97, S. enterica phage ST64T, or a Shigella flexneri prophage. Some of the ES18 late genes are novel, while others are most closely related to phages HK97, lambda, or N15. Thus, the ES18 genome is mosaically related to other lambdoid phages, as is typical for all group members. Analysis of virion DNA showed that it is circularly permuted and about 10% terminally redundant and that initiation of DNA packaging series occurs across an approximately 1-kbp region rather than at a precise location on the genome. This supports a model in which ES18 terminase can move substantial distances along the DNA between recognition and cleavage of DNA destined to be packaged. Bioinformatic analysis of large terminase subunits shows that the different functional classes of phage-encoded terminases can usually be predicted from their amino acid sequence.
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Affiliation(s)
- Sherwood R Casjens
- Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132, USA.
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Weinbauer MG. Ecology of prokaryotic viruses. FEMS Microbiol Rev 2004; 28:127-81. [PMID: 15109783 DOI: 10.1016/j.femsre.2003.08.001] [Citation(s) in RCA: 898] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2002] [Revised: 07/22/2003] [Accepted: 08/05/2003] [Indexed: 11/24/2022] Open
Abstract
The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.
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Affiliation(s)
- Markus G Weinbauer
- Department of Biological Oceanography, Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands.
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Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres JLTY, Peres C, Harrison FH, Gibson J, Harwood CS. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 2003; 22:55-61. [PMID: 14704707 DOI: 10.1038/nbt923] [Citation(s) in RCA: 480] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2003] [Accepted: 11/03/2003] [Indexed: 01/26/2023]
Abstract
Rhodopseudomonas palustris is among the most metabolically versatile bacteria known. It uses light, inorganic compounds, or organic compounds, for energy. It acquires carbon from many types of green plant-derived compounds or by carbon dioxide fixation, and it fixes nitrogen. Here we describe the genome sequence of R. palustris, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes and a plasmid of 8,427 bp. The sequence reveals genes that confer a remarkably large number of options within a given type of metabolism, including three nitrogenases, five benzene ring cleavage pathways and four light harvesting 2 systems. R. palustris encodes 63 signal transduction histidine kinases and 79 response regulator receiver domains. Almost 15% of the genome is devoted to transport. This genome sequence is a starting point to use R. palustris as a model to explore how organisms integrate metabolic modules in response to environmental perturbations.
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Affiliation(s)
- Frank W Larimer
- Genome Analysis and Systems Modeling, Oak Ridge National Laboratory, One Bethel Valley Rd., Oak Ridge, Tennessee 37831, USA
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Abstract
Bacterial genome nucleotide sequences are being completed at a rapid and increasing rate. Integrated virus genomes (prophages) are common in such genomes. Fifty-one of the 82 such genomes published to date carry prophages, and these contain 230 recognizable putative prophages. Prophages can constitute as much as 10-20% of a bacterium's genome and are major contributors to differences between individuals within species. Many of these prophages appear to be defective and are in a state of mutational decay. Prophages, including defective ones, can contribute important biological properties to their bacterial hosts. Therefore, if we are to comprehend bacterial genomes fully, it is essential that we are able to recognize accurately and understand their prophages from nucleotide sequence analysis. Analysis of the evolution of prophages can shed light on the evolution of both bacteriophages and their hosts. Comparison of the Rac prophages in the sequenced genomes of three Escherichia coli strains and the Pnm prophages in two Neisseria meningitidis strains suggests that some prophages can lie in residence for very long times, perhaps millions of years, and that recombination events have occurred between related prophages that reside at different locations in a bacterium's genome. In addition, many genes in defective prophages remain functional, so a significant portion of the temperate bacteriophage gene pool resides in prophages.
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Affiliation(s)
- Sherwood Casjens
- Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132-2501, USA.
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Martin W, Russell MJ. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans R Soc Lond B Biol Sci 2003; 358:59-83; discussion 83-5. [PMID: 12594918 PMCID: PMC1693102 DOI: 10.1098/rstb.2002.1183] [Citation(s) in RCA: 401] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
All life is organized as cells. Physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA-world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes.
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Affiliation(s)
- William Martin
- Institut für Botanik III, Heinrich-Heine Universitaet Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
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Schaefer AL, Taylor TA, Beatty JT, Greenberg EP. Long-chain acyl-homoserine lactone quorum-sensing regulation of Rhodobacter capsulatus gene transfer agent production. J Bacteriol 2002; 184:6515-21. [PMID: 12426339 PMCID: PMC135431 DOI: 10.1128/jb.184.23.6515-6521.2002] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many proteobacteria use acyl-homoserine lactones as quorum-sensing signals. Traditionally, biological detection systems have been used to identify bacteria that produce acyl-homoserine lactones, although the specificities of these detection systems can limit discovery. We used a sensitive approach that did not require a bioassay to detect production of long-acyl-chain homoserine lactone production by Rhodobacter capsulatus and Paracoccus denitrificans. These long-chain acyl-homoserine lactones are not readily detected by standard bioassays. The most abundant acyl-homoserine lactone was N-hexadecanoyl-homoserine lactone. The long-chain acyl-homoserine lactones were concentrated in cells but were also found in the culture fluid. An R. capsulatus gene responsible for long-chain acyl-homoserine lactone synthesis was identified. A mutation in this gene, which we named gtaI, resulted in decreased production of the R. capsulatus gene transfer agent, and gene transfer agent production was restored by exogenous addition of N-hexadecanoyl-homoserine lactone. Thus, long-chain acyl-homoserine lactones serve as quorum-sensing signals to enhance genetic exchange in R. capsulatus.
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Affiliation(s)
- Amy L Schaefer
- Department of Microbiology and W. M. Keck Foundation Microbial Communities & Cell Signaling Laboratory, University of Iowa, Iowa City, Iowa 52242, USA
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Abstract
The bacterium Rhodobacter capsulatus is capable of an unusual form of genetic exchange, mediated by a transducing bacteriophage-like particle called the gene transfer agent (GTA). GTA production by R. capsulatus is controlled at the level of transcription by a cellular two-component signal transduction system that includes a putative histidine kinase (CckA) and response regulator (CtrA). We found that, in addition to regulating genetic exchange by R. capsulatus, this signal transduction system controls motility. As with the regulation of GTA production, the control of motility by CckA and CtrA occurs through modulation of gene transcription. Disruptions of the cckA and ctrA genes resulted in a loss of class II, class III, and class IV flagellar gene transcripts, suggesting that cckA and ctrA function in motility as class I flagellar genes. We also found that, analogous to the GTA genes, transcription of R. capsulatus flagellar genes appears to be growth phase dependent: class II flagellar gene transcripts are maximal in the mid-log phase of the culture growth cycle, whereas class III gene transcripts are maximal in the late-log phase of growth. We speculate that coordinate regulation of motility and GTA-mediated genetic exchange in R. capsulatus exists because these two processes are complementary mechanisms for cells to cope with unfavorable conditions in natural environments.
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Affiliation(s)
- Andrew S Lang
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Abstract
Prokaryotic mobile elements have traditionally been classified as bacteriophages, plasmids, and transposons. We propose here a global classification of these and other bacterial and archaeal mobile elements based on their modular structure. This would allow for setting up interconnected databases where mobile elements could be stored as combinations of functional modules. Such a database would be very helpful. It would, for instance, allow for analyzing the phylogeny of individual blocks within an element, to understand how modules get associated and properly express the functions they carry in various bacterial hosts. Modules of practical importance, as for instance those that encode toxins or other virulence factors, could be identified and compared, and probes devised to test bacterial populations for the presence of such modules.
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Affiliation(s)
- Ariane Toussaint
- Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, 50 av. FD Roosevelt, Brussels, B1050, Belgium
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40
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Abstract
Do bacteria have genes for genetic exchange? The idea that the bacterial processes that cause genetic exchange exist because of natural selection for this process is shared by almost all microbiologists and population geneticists. However, this assumption has been perpetuated by generations of biology, microbiology and genetics textbooks without ever being critically examined.
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Affiliation(s)
- R J Redfield
- Rosemary J. Redfield is at the Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.
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