1
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Verweij W, Griswold CK. Spatial structure and benefits to hosts allow plasmids with and without post-segregational killing systems to coexist. Biol Lett 2023; 19:20220376. [PMID: 36855853 PMCID: PMC9975649 DOI: 10.1098/rsbl.2022.0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
To persist, a plasmid relies on being passed on to a daughter cell, but this does not always occur. Plasmids with post-segregational killing (PSK) systems kill a daughter cell if the plasmid has not been passed on. By killing the host, it also kills competing plasmids in the same host, something competing plasmids without a similar system cannot do. Accordingly, plasmids with PSK systems can displace other plasmids. In nature, plasmids with and without PSK systems coexist and prior theory has suggested this is expected to be very rare or unstable, such that one or the other type of plasmid eventually takes over. Here, we show that if there is spatial structure and plasmids confer benefits to hosts, coexistence of plasmids occurs broadly. Often plasmids confer benefits (even ones with a PSK system) and bacteria are often spatially structured. So, our results may be generally applicable.
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Affiliation(s)
- Wilco Verweij
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Cortland K. Griswold
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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2
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Hernandez‐Beltran JCR, Miró Pina V, Siri‐Jégousse A, Palau S, Peña‐Miller R, González Casanova A. Segregational instability of multicopy plasmids: A population genetics approach. Ecol Evol 2022; 12:e9469. [PMID: 36479025 PMCID: PMC9720003 DOI: 10.1002/ece3.9469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 12/11/2022] Open
Abstract
Plasmids are extra-chromosomal genetic elements that encode a wide variety of phenotypes and can be maintained in bacterial populations through vertical and horizontal transmission, thus increasing bacterial adaptation to hostile environmental conditions like those imposed by antimicrobial substances. To circumvent the segregational instability resulting from randomly distributing plasmids between daughter cells upon division, nontransmissible plasmids tend to be carried in multiple copies per cell, with the added benefit of exhibiting increased gene dosage and resistance levels. But carrying multiple copies also results in a high metabolic burden to the bacterial host, therefore reducing the overall fitness of the population. This trade-off poses an existential question for plasmids: What is the optimal plasmid copy number? In this manuscript, we address this question by postulating and analyzing a population genetics model to evaluate the interaction between selective pressure, the number of plasmid copies carried by each cell, and the metabolic burden associated with plasmid bearing in the absence of selection for plasmid-encoded traits. Parameter values of the model were estimated experimentally using Escherichia coli K12 carrying a multicopy plasmid encoding for a fluorescent protein and bla TEM-1, a gene conferring resistance to β-lactam antibiotics. By numerically determining the optimal plasmid copy number for constant and fluctuating selection regimes, we show that plasmid copy number is a highly optimized evolutionary trait that depends on the rate of environmental fluctuation and balances the benefit between increased stability in the absence of selection with the burden associated with carrying multiple copies of the plasmid.
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Affiliation(s)
- J. Carlos R. Hernandez‐Beltran
- Systems Biology Program, Center for Genomic SciencesUniversidad Nacional Autónoma de MéxicoCuernavacaMexico,Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
| | - Verónica Miró Pina
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain,Universitat Pompeu Fabra (UPF)BarcelonaSpain,Departamento de Probabilidad y Estadística, Instituto de Investigación en Matemáticas Aplicadas y en SistemasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Arno Siri‐Jégousse
- Departamento de Probabilidad y Estadística, Instituto de Investigación en Matemáticas Aplicadas y en SistemasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Sandra Palau
- Departamento de Probabilidad y Estadística, Instituto de Investigación en Matemáticas Aplicadas y en SistemasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Rafael Peña‐Miller
- Systems Biology Program, Center for Genomic SciencesUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
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3
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Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. Nucleic Acids Res 2022; 50:3155-3168. [PMID: 35323968 PMCID: PMC8989519 DOI: 10.1093/nar/gkac163] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/30/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.
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Affiliation(s)
- Supriya Khedkar
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Georgy Smyshlyaev
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Ivica Letunic
- Biobyte solutions GmbH, Bothestr 142, 69117 Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Askarbek Orakov
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Sofia K Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Experimental and Clinical Research Center, Charité-Universitätsmedizin and Max-Delbrück Center, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Falk Hildebrand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Mechthild Luetge
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Orsolya Barabas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea
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4
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Hernández-Beltrán JCR, San Millán A, Fuentes-Hernández A, Peña-Miller R. Mathematical Models of Plasmid Population Dynamics. Front Microbiol 2021; 12:606396. [PMID: 34803935 PMCID: PMC8600371 DOI: 10.3389/fmicb.2021.606396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.
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Affiliation(s)
| | | | | | - Rafael Peña-Miller
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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5
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Wilkowska K, Mruk I, Furmanek-Blaszk B, Sektas M. Low-level expression of the Type II restriction-modification system confers potent bacteriophage resistance in Escherichia coli. DNA Res 2021; 27:5804985. [PMID: 32167561 PMCID: PMC7315355 DOI: 10.1093/dnares/dsaa003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/09/2020] [Indexed: 01/21/2023] Open
Abstract
Restriction–modification systems (R–M) are one of the antiviral defense tools used by bacteria, and those of the Type II family are composed of a restriction endonuclease (REase) and a DNA methyltransferase (MTase). Most entering DNA molecules are usually cleaved by the REase before they can be methylated by MTase, although the observed level of fragmented DNA may vary significantly. Using a model EcoRI R–M system, we report that the balance between DNA methylation and cleavage may be severely affected by transcriptional signals coming from outside the R–M operon. By modulating the activity of the promoter, we obtained a broad range of restriction phenotypes for the EcoRI R–M system that differed by up to 4 orders of magnitude in our biological assays. Surprisingly, we found that high expression levels of the R–M proteins were associated with reduced restriction of invading bacteriophage DNA. Our results suggested that the regulatory balance of cleavage and methylation was highly sensitive to fluctuations in transcriptional signals both up- and downstream of the R–M operon. Our data provided further insights into Type II R–M system maintenance and the potential conflict within the host bacterium.
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Affiliation(s)
- Karolina Wilkowska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Beata Furmanek-Blaszk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Marian Sektas
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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6
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Ramisetty BCM, Sudhakari PA. 'Bacterial Programmed Cell Death': cellular altruism or genetic selfism? FEMS Microbiol Lett 2020; 367:5895326. [PMID: 32821912 DOI: 10.1093/femsle/fnaa141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cell-dependent propagation of the 'self' is the driver of all species, organisms and even genes. Conceivably, elimination of these entities is caused by cellular death. Then, how can genes that cause the death of the same cell evolve? Programmed cell death (PCD) is the gene-dependent self-inflicted death. In multicellular organisms, PCD of a cell confers fitness to the surviving rest of the organism, which thereby allows the selection of genes responsible for PCD. However, PCD in free-living bacteria is intriguing; the death of the cell is the death of the organism. How can such PCD genes be selected in unicellular organisms? The bacterial PCD in a population is proposed to confer fitness to the surviving kin in the form of sporulation, nutrition, infection-containment and matrix materials. While the cell-centred view leading to propositions of 'altruism' is enticing, the gene-centred view of 'selfism' is neglected. In this opinion piece, we reconceptualize the PCD propositions as genetic selfism (death due to loss/mutation of selfish genes) rather than cellular altruism (death for the conferment of fitness to kin). Within the scope and the available evidence, we opine that some of the PCD-like observations in bacteria seem to be the manifestation of genetic selfism by Restriction-Modification systems and Toxin-Antitoxin systems.
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Affiliation(s)
- Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India 613401
| | - Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India 613401
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7
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Hernandez-Beltran JCR, Rodríguez-Beltrán J, Millán AS, Peña-Miller R, Fuentes-Hernández A. Quantifying plasmid dynamics using single-cell microfluidics and image bioinformatics. Plasmid 2020; 113:102517. [PMID: 32535165 DOI: 10.1016/j.plasmid.2020.102517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 01/22/2023]
Abstract
Multicopy plasmids play an important role in bacterial ecology and evolution by accelerating the rate of adaptation and providing a platform for rapid gene amplification and evolutionary rescue. Despite the relevance of plasmids in bacterial evolutionary dynamics, evaluating the population-level consequences of randomly segregating and replicating plasmids in individual cells remains a challenging problem, both in theory and experimentally. In recent years, technological advances in fluorescence microscopy and microfluidics have allowed studying temporal changes in gene expression by quantifying the fluorescent intensity of individual cells under controlled environmental conditions. In this paper, we will describe the manufacture, experimental setup, and data analysis pipeline of different microfluidic systems that can be used to study plasmid dynamics, both in single-cells and in populations. To illustrate the benefits and limitations of microfluidics to study multicopy plasmid dynamics, we will use an experimental model system consisting on Escherichia coli K12 carrying non-conjugative, multicopy plasmids (19 copies per cell, in average) encoding different fluorescent markers and β-lactam resistance genes. First, we will use an image-based flow cytometer to estimate changes in the allele distribution of a heterogeneous population under different selection regimes. Then we will use a mothermachine microfluidic device to obtain time-series of fluorescent intensity of individual cells to argue that plasmid segregation and replication dynamics are inherently stochastic processes. Finally, using a microchemostat, we track thousands of cells in time to reconstruct bacterial lineages and evaluate the allele frequency distributions that emerge in response to a range of selective pressures.
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Affiliation(s)
- J C R Hernandez-Beltran
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - J Rodríguez-Beltrán
- Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), Madrid, Spain
| | - A San Millán
- Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), Madrid, Spain
| | - R Peña-Miller
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico.
| | - A Fuentes-Hernández
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico.
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8
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Geesink P, Wegner CE, Probst AJ, Herrmann M, Dam HT, Kaster AK, Küsel K. Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater. Environ Microbiol 2019; 22:726-737. [PMID: 31742865 DOI: 10.1111/1462-2920.14865] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 11/27/2022]
Abstract
Subsurface ecosystems like groundwater harbour diverse microbial communities, including small-sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates (Cand. Roizmanbacterium ADI133) from oligotrophic groundwater using mini-metagenomics and monitored its spatio-temporal distribution using 16S rRNA gene analyses. A Roizmanbacteria-specific quantitative PCR assay allowed us to track its abundance over the course of 1 year within eight groundwater wells along a 5.4 km hillslope transect, where Roizmanbacteria reached maximum relative abundances of 2.3%. In-depth genomic analyses suggested that Cand. Roizmanbacterium ADI133 is a lactic acid fermenter, potentially able to utilize a range of complex carbon substrates, including cellulose. We hypothesize that it attaches to host cells using a trimeric autotransporter adhesin and inhibits their cell wall biosynthesis using a toxin-antitoxin system. Network analyses based on correlating Cand. Roizmanbacterium ADI133 abundances with amplicon sequencing-derived microbial community profiles suggested one potential host organism, classified as a member of the class Thermodesulfovibrionia (Nitrospirae). By providing lactate as an electron donor Cand. Roizmanbacterium ADI133 potentially mediates the transfer of carbon to other microorganisms and thereby is an important connector in the microbial community.
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Affiliation(s)
- Patricia Geesink
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Alexander J Probst
- Department for Chemistry, Biofilm Centre, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
| | - Martina Herrmann
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Hang T Dam
- Institute for Biological Interfaces (IGB 5), Karlsruhe Institute of Technology (KIT), Karlsruhe, Eggenstein-Leopoldshafen, Germany.,DSMZ, Braunschweig, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IGB 5), Karlsruhe Institute of Technology (KIT), Karlsruhe, Eggenstein-Leopoldshafen, Germany.,DSMZ, Braunschweig, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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9
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Koonin EV, Makarova KS, Wolf YI, Krupovic M. Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire. Nat Rev Genet 2019; 21:119-131. [PMID: 31611667 DOI: 10.1038/s41576-019-0172-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2019] [Indexed: 12/12/2022]
Abstract
All cellular life forms are afflicted by diverse genetic parasites, including viruses and other types of mobile genetic elements (MGEs), and have evolved multiple, diverse defence systems that protect them from MGE assault via different mechanisms. Here, we provide our perspectives on how recent evidence points to tight evolutionary connections between MGEs and defence systems that reach far beyond the proverbial arms race. Defence systems incur a fitness cost for the hosts; therefore, at least in prokaryotes, horizontal mobility of defence systems, mediated primarily by MGEs, is essential for their persistence. Moreover, defence systems themselves possess certain features of selfish elements. Common components of MGEs, such as site-specific nucleases, are 'guns for hire' that can also function as parts of defence mechanisms and are often shuttled between MGEs and defence systems. Thus, evolutionary and molecular factors converge to mould the multifaceted, inextricable connection between MGEs and anti-MGE defence systems.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France.
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10
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Morinière L, Lecomte S, Gueguen E, Bertolla F. In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes. Microb Genom 2019; 7. [PMID: 33760724 PMCID: PMC8627662 DOI: 10.1099/mgen.0.000546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The essential genome of a bacterium encompasses core genes associated with basic cellular processes and conditionally essential genes dependent upon environmental conditions or the genetic context. Comprehensive knowledge of those gene sets allows for a better understanding of fundamental bacterial biology and offers new perspectives for antimicrobial drug research against detrimental bacteria such as pathogens. We investigated the essential genome of Xanthomonas hortorum pv. vitians, a gammaproteobacterial plant pathogen of lettuce (Lactuca sativa L.) which belongs to the plant-pathogen reservoir genus Xanthomonas and is affiliated to the family Xanthomonadaceae. No practical means of disease control or prevention against this pathogen is currently available, and its molecular biology is virtually unknown. To reach a comprehensive overview of the essential genome of X. hortorum pv. vitians LM16734, we developed a mixed approach combining high-quality full genome sequencing, saturated transposon insertion sequencing (Tn-Seq) in optimal growth conditions, and coupled computational analyses such as comparative genomics, synteny assessment and phylogenomics. Among the 370 essential loci identified by Tn-Seq, a majority was bound to critical cell processes conserved across bacteria. The remaining genes were either related to specific ecological features of Xanthomonas or Xanthomonadaceae species, or acquired through horizontal gene transfer of mobile genetic elements and associated with ancestral parasitic gene behaviour and bacterial defence systems. Our study sheds new light on our usual concepts about gene essentiality and is pioneering in the molecular and genomic study of X. hortorum pv. vitians.
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Affiliation(s)
- Lucas Morinière
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Solène Lecomte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Erwan Gueguen
- Univ Lyon, Université Claude Bernard Lyon 1, INSA, CNRS, UMR Microbiologie, Adaptation, Pathogénie, F 69622 Villeurbanne, France
| | - Franck Bertolla
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
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11
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Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade. Sci Rep 2018; 8:2523. [PMID: 29410443 PMCID: PMC5802823 DOI: 10.1038/s41598-018-20847-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/25/2018] [Indexed: 01/14/2023] Open
Abstract
In this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit (ICU) in 2000 (9 strains referred to collectively as Ab_GEIH-2000) and 2010 (9 strains referred to collectively as Ab_GEIH-2010), during the GEIH-REIPI project (Umbrella BioProject PRJNA422585). We observed two main molecular differences between the Ab_GEIH-2010 and the Ab_GEIH-2000 collections, acquired over the course of the decade long sampling interval and involving the mobilome: i) a plasmid harbouring genes for blaOXA 24/40 ß-lactamase and abKA/abkB proteins of a toxin-antitoxin system; and ii) two temperate bacteriophages, Ab105-1ϕ (63 proteins) and Ab105-2ϕ (93 proteins), containing important viral defence proteins. Moreover, all Ab_GEIH-2010 strains contained a Quorum functional network of Quorum Sensing (QS) and Quorum Quenching (QQ) mechanisms, including a new QQ enzyme, AidA, which acts as a bacterial defence mechanism against the exogenous 3-oxo-C12-HSL. Interestingly, the infective capacity of the bacteriophages isolated in this study (Ab105-1ϕ and Ab105-2ϕ) was higher in the Ab_GEIH-2010 strains (carrying a functional Quorum network) than in the Ab_GEIH-2000 strains (carrying a deficient Quorum network), in which the bacteriophages showed little or no infectivity. This is the first study about the evolution of the Quorum network and the mobilome in clinical strains of Acinetobacter baumannii during a decade.
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12
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Libby E, Driscoll WW, Ratcliff WC. Programmed cell death can increase the efficacy of microbial bet -hedging. Sci Rep 2018; 8:1120. [PMID: 29348455 PMCID: PMC5773525 DOI: 10.1038/s41598-017-18687-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/13/2017] [Indexed: 11/09/2022] Open
Abstract
Programmed cell death (PCD) occurs in both unicellular and multicellular organisms. While PCD plays a key role in the development and maintenance of multicellular organisms, explaining why single-celled organisms would evolve to actively commit suicide has been far more challenging. Here, we explore the potential for PCD to act as an accessory to microbial bet-hedging strategies that utilize stochastic phenotype switching. We consider organisms that face unpredictable and recurring disasters, in which fitness depends on effective phenotypic diversification. We show that when reproductive opportunities are limited by carrying capacity, PCD drives population turnover, providing increased opportunities for phenotypic diversification through stochastic phenotype switching. The main cost of PCD, providing resources for growth to a PCD(−) competitor, is ameliorated by genetic assortment in spatially structured populations. Using agent -based simulations, we explore how basic demographic factors, namely bottlenecks and local dispersal, can generate sufficient spatial structure to favor the evolution of high PCD rates.
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Affiliation(s)
- Eric Libby
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - William W Driscoll
- Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, 55108, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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13
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Koonin EV. Viruses and mobile elements as drivers of evolutionary transitions. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0442. [PMID: 27431520 PMCID: PMC4958936 DOI: 10.1098/rstb.2015.0442] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2016] [Indexed: 12/22/2022] Open
Abstract
The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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14
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Skowron PM, Anton BP, Czajkowska E, Zebrowska J, Sulecka E, Krefft D, Jezewska-Frackowiak J, Zolnierkiewicz O, Witkowska M, Morgan RD, Wilson GG, Fomenkov A, Roberts RJ, Zylicz-Stachula A. The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities. Nucleic Acids Res 2017; 45:9005-9018. [PMID: 28911108 PMCID: PMC5587805 DOI: 10.1093/nar/gkx599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/04/2017] [Indexed: 11/12/2022] Open
Abstract
Two restriction-modification systems have been previously discovered in Thermus aquaticus YT-1. TaqI is a 263-amino acid (aa) Type IIP restriction enzyme that recognizes and cleaves within the symmetric sequence 5'-TCGA-3'. TaqII, in contrast, is a 1105-aa Type IIC restriction-and-modification enzyme, one of a family of Thermus homologs. TaqII was originally reported to recognize two different asymmetric sequences: 5'-GACCGA-3' and 5'-CACCCA-3'. We previously cloned the taqIIRM gene, purified the recombinant protein from Escherichia coli, and showed that TaqII recognizes the 5'-GACCGA-3' sequence only. Here, we report the discovery, isolation, and characterization of TaqIII, the third R-M system from T. aquaticus YT-1. TaqIII is a 1101-aa Type IIC/IIL enzyme and recognizes the 5'-CACCCA-3' sequence previously attributed to TaqII. The cleavage site is 11/9 nucleotides downstream of the A residue. The enzyme exhibits striking biochemical similarity to TaqII. The 93% identity between their aa sequences suggests that they have a common evolutionary origin. The genes are located on two separate plasmids, and are probably paralogs or pseudoparalogs. Putative positions and aa that specify DNA recognition were identified and recognition motifs for 6 uncharacterized Thermus-family enzymes were predicted.
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Affiliation(s)
- Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Brian P Anton
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Edyta Czajkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Joanna Zebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Ewa Sulecka
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Joanna Jezewska-Frackowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Olga Zolnierkiewicz
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Malgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | | | | | - Alexey Fomenkov
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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Jurėnas D, Garcia-Pino A, Van Melderen L. Novel toxins from type II toxin-antitoxin systems with acetyltransferase activity. Plasmid 2017; 93:30-35. [PMID: 28941941 DOI: 10.1016/j.plasmid.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 12/21/2022]
Abstract
Type II toxin-antitoxin (TA) systems are widespread in bacterial and archeal genomes. These modules are very dynamic and participate in bacterial genome evolution through horizontal gene transfer. TA systems are commonly composed of a labile antitoxin and a stable toxin. Toxins appear to preferentially inhibit the protein synthesis process. Toxins use a variety of molecular mechanisms and target nearly every step of translation to achieve their inhibitory function. This review focuses on a recently identified TA family that includes acetyltransferase toxins. The AtaT and TacT toxins are the best-characterized to date in this family. AtaT and TacT both inhibit translation by acetylating the amino acid charged on tRNAs. However, the specificities of these 2 toxins are different as AtaT inhibits translation initiation by acetylation of the initiator tRNA whereas TacT acetylates elongator tRNAs. The molecular mechanisms of these toxins are discussed, as well as the functions and possible evolutionary origins of this diverse toxin family.
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Affiliation(s)
- Dukas Jurėnas
- Department of Biochemistry and Molecular Biology, Vilnius University Joint Life Sciences Center, Vilnius, Lithuania; Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium.
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Abstract
Self-replicating genetic material presumably provided the architecture necessary for generating the last universal ancestor of all nucleic-acid-based life. As biological complexity increased in the billions of years that followed, the same genetic material also morphed into a wide spectrum of viruses and other parasitic genetic elements. The resulting struggle for existence drove the evolution of host defenses, giving rise to a perpetual arms race. This Perspective summarizes the antiviral mechanisms evident across the tree of life, discussing each in their evolutionary context to postulate how the coevolution of host and pathogen shaped the cellular antiviral defenses we know today.
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van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
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Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
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18
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Toxin-Antitoxin Systems in Clinical Pathogens. Toxins (Basel) 2016; 8:toxins8070227. [PMID: 27447671 PMCID: PMC4963858 DOI: 10.3390/toxins8070227] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/07/2016] [Indexed: 12/17/2022] Open
Abstract
Toxin-antitoxin (TA) systems are prevalent in bacteria and archaea. Although not essential for normal cell growth, TA systems are implicated in multiple cellular functions associated with survival under stress conditions. Clinical strains of bacteria are currently causing major human health problems as a result of their multidrug resistance, persistence and strong pathogenicity. Here, we present a review of the TA systems described to date and their biological role in human pathogens belonging to the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) and others of clinical relevance (Escherichia coli, Burkholderia spp., Streptococcus spp. and Mycobacterium tuberculosis). Better understanding of the mechanisms of action of TA systems will enable the development of new lines of treatment for infections caused by the above-mentioned pathogens.
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Cinelli T, Moscetti I, Marchi G. PsasM2I, a type II restriction-modification system in Pseudomonas savastanoi pv. savastanoi: differential distribution of carrier strains in the environment and the evolutionary history of homologous RM systems in the Pseudomonas syringae complex. MICROBIAL ECOLOGY 2014; 68:842-858. [PMID: 25008981 DOI: 10.1007/s00248-014-0451-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
A type II restriction-modification system was found in a native plasmid of Pseudomonas savastanoi pv. savastanoi MLLI2. Functional analysis of the methyltransferase showed that the enzyme acts by protecting the DNA sequence CTGCAG from cleavage. Restriction endonuclease expression in recombinant Escherichia coli cells resulted in mutations in the REase sequence or transposition of insertion sequence 1A in the coding sequence, preventing lethal gene expression. Population screening detected homologous RM systems in other P. savastanoi strains and in the Pseudomonas syringae complex. An epidemiological survey carried out by sampling olive and oleander knots in two Italian regions showed an uneven diffusion of carrier strains, whose presence could be related to a selective advantage in maintaining the RM system in particular environments or subpopulations. Moreover, carrier strains can coexist in the same orchards, plants, and knot tissues with non-carriers, revealing unexpected genetic variability on a very small spatial scale. Phylogenetic analysis of the RM system and housekeeping gene sequences in the P. syringae complex demonstrated the ancient acquisition of the RM systems. However, the evolutionary history of the gene complex also showed the involvement of horizontal gene transfer between related strains and recombination events.
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Affiliation(s)
- Tamara Cinelli
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), Sezione di Patologia Vegetale ed Entomologia, Università degli Studi di Firenze, Piazzale delle Cascine 28, 50144, Firenze, Italy,
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20
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Oliveira PH, Touchon M, Rocha EPC. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res 2014; 42:10618-31. [PMID: 25120263 PMCID: PMC4176335 DOI: 10.1093/nar/gku734] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/29/2014] [Accepted: 07/30/2014] [Indexed: 01/21/2023] Open
Abstract
The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.
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Affiliation(s)
- Pedro H Oliveira
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
| | - Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
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21
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Mosqueda N, Gato E, Roca I, López M, de Alegría CR, Fernández Cuenca F, Martínez-Martínez L, Pachón J, Cisneros JM, Rodríguez-Baño J, Pascual A, Vila J, Bou G, Tomás M. Characterization of plasmids carrying the blaOXA-24/40 carbapenemase gene and the genes encoding the AbkA/AbkB proteins of a toxin/antitoxin system. J Antimicrob Chemother 2014; 69:2629-33. [PMID: 24879663 DOI: 10.1093/jac/dku179] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Acinetobacter baumannii (CRAb) is a major source of nosocomial infections in Spain associated with the production of OXA-58-like or OXA-24/40-like β-lactamase enzymes. We analysed the plasmids carrying the bla(OXA-24/40)-like gene in CRAb isolates obtained a decade apart. METHODS The presence of β-lactamases was screened for by PCR (metallo-β-lactamases, carbapenem-hydrolysing class D β-lactamases, GES and KPC) in 101 CRAb isolates obtained in two multicentre studies (GEIH/REIPI-Ab-2000 and GEIH/REIPI-Ab-2010; n = 493 Acinetobacter spp). We analysed the distribution and characterization of the plasmids carrying the bla(OXA-24/40)-like gene and sequenced two plasmids, AbATCC223p (2000) and AbATCC329p (2010) from A. baumannii ATCC 17978 transformants. RESULTS Acquisition of the bla(OXA-24/40)-like gene was the main mechanism underlying resistance to carbapenems (48.7% in 2000 compared with 51.6% in 2010). This gene was mainly isolated in ST2 A. baumannii strains in both studies, although some novel STs (ST79 and ST80) appeared in 2010. The gene was located in plasmids (8-12 kbp) associated with the repAci2 or repAci2/repGR12 types. The sequences of AbATCC223p (8840 bp) and AbATCC329p (8842 bp) plasmids were similar, particularly regarding the presence of the genes encoding the AbkA/AbkB proteins associated with the toxin/antitoxin system. Moreover, the abkA/abkB gene sequences (>96% identity) were also located in plasmids harbouring the bla(OXA-58)-like gene. CONCLUSIONS The action of OXA-24/40 and OXA-58 β-lactamase-like enzymes represents the main mechanism underlying resistance to carbapenems in Spain in the last decade. AbkA/AbkB proteins in the toxin/antitoxin system may be involved in the successful dissemination of plasmids carrying the bla(OXA-24/40)-like gene, and probably also the bla(OXA-58)-like gene, thus contributing to the plasmid stability.
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Affiliation(s)
- Noraida Mosqueda
- Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Eva Gato
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
| | - Ignasi Roca
- Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - María López
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
| | - Carlos Ruíz de Alegría
- Microbiology Service, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Felipe Fernández Cuenca
- Clinical Unit for Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, and University of Seville, Seville, Spain
| | - Luis Martínez-Martínez
- Microbiology Service, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain Department of Molecular Biology, University of Cantabria, Santander, Spain
| | - Jerónimo Pachón
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine-IBiS, University Hospital Virgen del Rocío, Seville, Spain
| | - José Miguel Cisneros
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine-IBiS, University Hospital Virgen del Rocío, Seville, Spain
| | - Jesús Rodríguez-Baño
- Clinical Unit for Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, and University of Seville, Seville, Spain
| | - Alvaro Pascual
- Clinical Unit for Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, and University of Seville, Seville, Spain
| | - Jordi Vila
- Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Germán Bou
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
| | - María Tomás
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 2014; 42:3-19. [PMID: 24141096 PMCID: PMC3874209 DOI: 10.1093/nar/gkt990] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 11/16/2022] Open
Abstract
In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range. Unlike mutation, this change was reversible, and one cycle of growth in the previous host returned the virus to its original form. These simple observations heralded the discovery of the endonuclease and methyltransferase activities of what are now termed Type I, II, III and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave rise to recombinant DNA technology that has transformed molecular biology and medicine. This review traces the discovery of restriction enzymes and their continuing impact on molecular biology and medicine.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - David T. F. Dryden
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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Mruk I, Kobayashi I. To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. Nucleic Acids Res 2013; 42:70-86. [PMID: 23945938 PMCID: PMC3874152 DOI: 10.1093/nar/gkt711] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
One of the simplest classes of genes involved in programmed death is that containing the toxin–antitoxin (TA) systems of prokaryotes. These systems are composed of an intracellular toxin and an antitoxin that neutralizes its effect. These systems, now classified into five types, were initially discovered because some of them allow the stable maintenance of mobile genetic elements in a microbial population through postsegregational killing or the death of cells that have lost these systems. Here, we demonstrate parallels between some TA systems and restriction–modification systems (RM systems). RM systems are composed of a restriction enzyme (toxin) and a modification enzyme (antitoxin) and limit the genetic flux between lineages with different epigenetic identities, as defined by sequence-specific DNA methylation. The similarities between these systems include their postsegregational killing and their effects on global gene expression. Both require the finely regulated expression of a toxin and antitoxin. The antitoxin (modification enzyme) or linked protein may act as a transcriptional regulator. A regulatory antisense RNA recently identified in an RM system can be compared with those RNAs in TA systems. This review is intended to generalize the concept of TA systems in studies of stress responses, programmed death, genetic conflict and epigenetics.
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Affiliation(s)
- Iwona Mruk
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, Gdansk, 80-308, Poland, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
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Vasu K, Nagaraja V. Diverse functions of restriction-modification systems in addition to cellular defense. Microbiol Mol Biol Rev 2013; 77:53-72. [PMID: 23471617 PMCID: PMC3591985 DOI: 10.1128/mmbr.00044-12] [Citation(s) in RCA: 383] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.
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Affiliation(s)
- Kommireddy Vasu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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25
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Rheinberg A, Swierzy IJ, Nguyen TD, Horz HP, Conrads G. Cryptic Streptococcus mutans 5.6-kb plasmids encode a toxin-antitoxin system for plasmid stabilization. J Oral Microbiol 2013; 5:19729. [PMID: 23330057 PMCID: PMC3547324 DOI: 10.3402/jom.v5i0.19729] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In all Streptococcus mutans strains, 5-13% carry a 5.6-kb plasmid. Despite its frequency, little is known about its mediated functions with most of the information coming from a single study focussing on plasmid pUA140. OBJECTIVE Here, we describe the sequence and genetic organization of two S. mutans 5.6-kb plasmids, pDC09 and pNC101. RESULTS Based on PicoGreen dsDNA quantification and Real-Time quantitative PCR (RTQ-PCR), the plasmid copy number was found to range between 10 and 74, depending on the strain tested. In contrast to literature, we identified six instead of five open reading frames (ORFs). While the putative gene products of ORF1 (as a Rep-protein) and ORF2 (as a Mob-protein) could be confirmed as being identical to those from pUA140, the functions of ORF3 (unknown) and ORF 4 (possibly AtpE homologue) could not be further revealed. However, the product of ORF5 showed a fairly high identity (38-50%) and structural similarity (58-74%) to RelE of Streptococcus pneumoniae, Streptococcus equi, and Streptococcus downei. In addition, we identified a functionally corresponding ORF6 encoding a protein with 61-68% identity (81-86% similarity) to the S. equi and S. downei antitoxin of the RelB family. RelE and RelB together form a plasmid-encoded toxin-antitoxin (TA) system, RelBE(plas). Despite its rather limited sequence similarity with chromosomal TA systems in S. mutans (RelBE(chro), MazEF, HicBA), we found similar tertiary structures applying I-Tasser protein prediction analysis. CONCLUSION Type II-toxins, as the plasmid-encoded RelE, are RNA endonucleases. Depending on their mRNA cleavage activity, they might 1) kill every plasmid-free progeny, thereby stabilizing plasmid transfer at the expense of the host and/or 2) help S. mutans enter a dormant state and survive unfavourable environmental conditions. Whilst a function in plasmid stabilization has been confirmed, a function in persistence under nutritional stress, tested here by inducing amino acid starvation, could not be demonstrated so far.
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Affiliation(s)
- Anke Rheinberg
- Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry & Periodontology, RWTH Aachen University Hospital, Aachen, Germany
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Balado M, Lemos ML, Osorio CR. Integrating conjugative elements of the SXT/R391 family from fish-isolatedVibriosencode restriction-modification systems that confer resistance to bacteriophages. FEMS Microbiol Ecol 2012; 83:457-67. [DOI: 10.1111/1574-6941.12007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/03/2012] [Indexed: 01/21/2023] Open
Affiliation(s)
- Miguel Balado
- Departamento de Microbioloxía e Parasitoloxía; Instituto de Acuicultura; Universidade de Santiago de Compostela; Santiago de Compostela; Galicia; Spain
| | - Manuel L. Lemos
- Departamento de Microbioloxía e Parasitoloxía; Instituto de Acuicultura; Universidade de Santiago de Compostela; Santiago de Compostela; Galicia; Spain
| | - Carlos R. Osorio
- Departamento de Microbioloxía e Parasitoloxía; Instituto de Acuicultura; Universidade de Santiago de Compostela; Santiago de Compostela; Galicia; Spain
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Rankin DJ, Turner LA, Heinemann JA, Brown SP. The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict. Proc Biol Sci 2012; 279:3706-15. [PMID: 22787022 PMCID: PMC3415908 DOI: 10.1098/rspb.2012.0942] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/20/2012] [Indexed: 12/12/2022] Open
Abstract
Bacterial genomes commonly contain 'addiction' gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin-antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive 'rock-paper-scissors' dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes.
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Affiliation(s)
- Daniel J. Rankin
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Building Y27, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Leighton A. Turner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jack A. Heinemann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sam P. Brown
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
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28
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Furuta Y, Kobayashi I. Movement of DNA sequence recognition domains between non-orthologous proteins. Nucleic Acids Res 2012; 40:9218-32. [PMID: 22821560 PMCID: PMC3467074 DOI: 10.1093/nar/gks681] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a sequence-specific DNA methyltransferase and a restriction enzyme, contribute to maintenance/evolution of genomes/epigenomes. RM systems limit horizontal gene transfer but are themselves mobile. We compared Type III RM systems in Helicobacter pylori genomes and found that target recognition domain (TRD) sequences are mobile, moving between different orthologous groups that occupy unique chromosomal locations. Sequence comparisons suggested that a likely underlying mechanism is movement through homologous recombination of similar DNA sequences that encode amino acid sequence motifs that are conserved among Type III DNA methyltransferases. Consistent with this movement, incongruence was observed between the phylogenetic trees of TRD regions and other regions in proteins. Horizontal acquisition of diverse TRD sequences was suggested by detection of homologs in other Helicobacter species and distantly related bacterial species. One of these RM systems in H. pylori was inactivated by insertion of another RM system that likely transferred from an oral bacterium. TRD movement represents a novel route for diversification of DNA-interacting proteins.
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Affiliation(s)
- Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
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29
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Fukuyo M, Sasaki A, Kobayashi I. Success of a suicidal defense strategy against infection in a structured habitat. Sci Rep 2012; 2:238. [PMID: 22355751 PMCID: PMC3268160 DOI: 10.1038/srep00238] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 01/10/2012] [Indexed: 11/09/2022] Open
Abstract
Pathogen infection often leads to the expression of virulence and host death when the host-pathogen symbiosis seems more beneficial for the pathogen. Previously proposed explanations have focused on the pathogen's side. In this work, we tested a hypothesis focused on the host strategy. If a member of a host population dies immediately upon infection aborting pathogen reproduction, it can protect the host population from secondary infections. We tested this "Suicidal Defense Against Infection" (SDAI) hypothesis by developing an experimental infection system that involves a huge number of bacteria as hosts and their virus as pathogen, which is linked to modeling and simulation. Our experiments and simulations demonstrate that a population with SDAI strategy is successful in the presence of spatial structure but fails in its absence. The infection results in emergence of pathogen mutants not inducing the host suicide in addition to host mutants resistant to the pathogen.
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Affiliation(s)
- Masaki Fukuyo
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
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30
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Yatim N, Albert M. Dying to Replicate: The Orchestration of the Viral Life Cycle, Cell Death Pathways, and Immunity. Immunity 2011; 35:478-90. [DOI: 10.1016/j.immuni.2011.10.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 09/20/2011] [Accepted: 10/14/2011] [Indexed: 12/11/2022]
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31
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Baquero F. The 2010 Garrod Lecture: The dimensions of evolution in antibiotic resistance: ex unibus plurum et ex pluribus unum. J Antimicrob Chemother 2011; 66:1659-72. [DOI: 10.1093/jac/dkr214] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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32
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Domain movement within a gene: a novel evolutionary mechanism for protein diversification. PLoS One 2011; 6:e18819. [PMID: 21533192 PMCID: PMC3077401 DOI: 10.1371/journal.pone.0018819] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/10/2011] [Indexed: 12/30/2022] Open
Abstract
A protein function is carried out by a specific domain localized at a specific position. In the present study, we report that, within a gene, a specific amino acid sequence can move between a certain position and another position. This was discovered when the sequences of restriction-modification systems within the bacterial species Helicobacter pylori were compared. In the specificity subunit of Type I restriction-modification systems, DNA sequence recognition is mediated by target recognition domain 1 (TRD1) and TRD2. To our surprise, several sequences are shared by TRD1 and TRD2 of genes (alleles) at the same locus (chromosomal location); these domains appear to have moved between the two positions. The gene/protein organization can be represented as x-(TRD1)-y-x-(TRD2)-y, where x and y represent repeat sequences. Movement probably occurs by recombination at these flanking DNA repeats. In accordance with this hypothesis, recombination at these repeats also appears to decrease two TRDs into one TRD or increase these two TRDs to three TRDs (TRD1-TRD2-TRD2) and to allow TRD movement between genes even at different loci. Similar movement of domains between TRD1 and TRD2 was observed for the specificity subunit of a Type IIG restriction enzyme. Similar movement of domain between TRD1 and TRD2 was observed for Type I restriction-modification enzyme specificity genes in two more eubacterial species, Streptococcus pyogenes and Mycoplasma agalactiae. Lateral domain movements within a protein, which we have designated DOMO (domain movement), represent novel routes for the diversification of proteins.
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33
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Mruk I, Liu Y, Ge L, Kobayashi I. Antisense RNA associated with biological regulation of a restriction-modification system. Nucleic Acids Res 2011; 39:5622-32. [PMID: 21459843 PMCID: PMC3141266 DOI: 10.1093/nar/gkr166] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Restriction–modification systems consist of a modification enzyme that methylates a specific DNA sequence and a restriction endonuclease that cleaves DNA lacking this epigenetic signature. Their gene expression should be finely regulated because their potential to attack the host bacterial genome needs to be controlled. In the EcoRI system, where the restriction gene is located upstream of the modification gene in the same orientation, we previously identified intragenic reverse promoters affecting gene expression. In the present work, we identified a small (88 nt) antisense RNA (Rna0) transcribed from a reverse promoter (PREV0) at the 3′ end of the restriction gene. Its antisense transcription, as measured by transcriptional gene fusion, appeared to be terminated by the PM1,M2 promoter. PM1,M2 promoter-initiated transcription, in turn, appeared to be inhibited by PREV0. Mutational inactivation of PREV0 increased expression of the restriction gene. The biological significance of this antisense transcription is 2-fold. First, a mutation in PREV0 increased restriction of incoming DNA. Second, the presence of the antisense RNA gene (ecoRIA) in trans alleviated cell killing after loss of the EcoRI plasmid (post-segregational killing). Taken together, these results strongly suggested the involvement of an antisense RNA in the biological regulation of this restriction–modification system.
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Affiliation(s)
- Iwona Mruk
- Department of Microbiology, University of Gdansk, Kladki 24, Gdansk, 80-822, Poland
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34
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Abstract
Potential mobility of restriction-modification systems has been suggested by evolutionary/bioinformatic analysis of prokaryotic genomes. Here we demonstrate in vivo movement of a restriction-modification system within a genome under a laboratory condition. After blocking replication of a temperature-sensitive plasmid carrying a PaeR7I restriction-modification system in Escherichia coli cells, the plasmid was found integrated into the chromosome of the surviving cells. Sequence analysis revealed that, in the majority of products, the restriction-modification system was linked to chromosomal insertion sequences (ISs). Three types of products were: (I) apparent co-integration of the plasmid and the chromosome at a chromosomal IS1 or IS5 copy (24/28 analyzed); (II) de novo insertion of IS1 with the entire plasmid except for a 1–3 bp terminal deletion (2/28); and (III) reciprocal crossing-over between the plasmid and the chromosome involving 1–3 bp of sequence identity (2/28). An R-negative mutation apparently decreased the efficiency of successful integration by two orders of magnitude. Reconstruction experiments demonstrated that the restriction-dependence was mainly due to selection against cells without proper integration: their growth was inhibited by the restriction enzyme action. These results demonstrate collaboration of a mobile element and a restriction-modification system for successful joint migration. This collaboration may have promoted the spread and, therefore, the long-term persistence of these complexes and restriction-modification systems in a wide range of prokaryotes.
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35
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Rankin DJ, Rocha EPC, Brown SP. What traits are carried on mobile genetic elements, and why? Heredity (Edinb) 2011; 106:1-10. [PMID: 20332804 PMCID: PMC3183850 DOI: 10.1038/hdy.2010.24] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/28/2010] [Accepted: 02/02/2010] [Indexed: 01/22/2023] Open
Abstract
Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes.
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Affiliation(s)
- D J Rankin
- Department of Biochemistry, University of Zürich, Zürich, Switzerland.
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36
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Ishikawa K, Fukuda E, Kobayashi I. Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems. DNA Res 2010; 17:325-42. [PMID: 21059708 PMCID: PMC2993543 DOI: 10.1093/dnares/dsq027] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Epigenetic modification of genomic DNA by methylation is important for defining the epigenome and the transcriptome in eukaryotes as well as in prokaryotes. In prokaryotes, the DNA methyltransferase genes often vary, are mobile, and are paired with the gene for a restriction enzyme. Decrease in a certain epigenetic methylation may lead to chromosome cleavage by the partner restriction enzyme, leading to eventual cell death. Thus, the pairing of a DNA methyltransferase and a restriction enzyme forces an epigenetic state to be maintained within the genome. Although restriction enzymes were originally discovered for their ability to attack invading DNAs, it may be understood because such DNAs show deviation from this epigenetic status. DNAs with epigenetic methylation, by a methyltransferase linked or unlinked with a restriction enzyme, can also be the target of DNases, such as McrBC of Escherichia coli, which was discovered because of its methyl-specific restriction. McrBC responds to specific genome methylation systems by killing the host bacterial cell through chromosome cleavage. Evolutionary and genomic analysis of McrBC homologues revealed their mobility and wide distribution in prokaryotes similar to restriction–modification systems. These findings support the hypothesis that this family of methyl-specific DNases evolved as mobile elements competing with specific genome methylation systems through host killing. These restriction systems clearly demonstrate the presence of conflicts between epigenetic systems.
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Affiliation(s)
- Ken Ishikawa
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
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37
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Cooper TF, Paixão T, Heinemann JA. Within-host competition selects for plasmid-encoded toxin-antitoxin systems. Proc Biol Sci 2010; 277:3149-55. [PMID: 20504809 DOI: 10.1098/rspb.2010.0831] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Toxin-antitoxin (TA) systems are commonly found on bacterial plasmids. The antitoxin inhibits toxin activity unless the system is lost from the cell. Then the shorter lived antitoxin degrades and the cell becomes susceptible to the toxin. Selection for plasmid-encoded TA systems was initially thought to result from their reducing the number of plasmid-free cells arising during growth in monoculture. However, modelling and experiments have shown that this mechanism can only explain the success of plasmid TA systems under a restricted set of conditions. Previously, we have proposed and tested an alternative model explaining the success of plasmid TA systems as a consequence of competition occurring between plasmids during co-infection of bacterial hosts. Here, we test a further prediction of this model, that competition between plasmids will lead to the biased accumulation of TA systems on plasmids relative to chromosomes. Transposon-encoded TA systems were added to populations of plasmid-containing cells, such that TA systems could insert into either plasmids or chromosomes. These populations were enriched for transposon-containing cells and then incubated in environments that did, or did not, allow effective within-host plasmid competition to occur. Changes in the ratio of plasmid- to chromosome-encoded TA systems were monitored. In agreement with our model, we found that plasmid-encoded TA systems had a competitive advantage, but only when host cells were sensitive to the effect of TA systems. This result demonstrates that within-host competition between plasmids can select for TA systems.
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Affiliation(s)
- Tim F Cooper
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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38
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Prozorov AA, Danilenko VN. Toxin-antitoxin systems in bacteria: Apoptotic tools or metabolic regulators? Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710020013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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39
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Rickettsia felis infection in a common household insect pest, Liposcelis bostrychophila (Psocoptera: Liposcelidae). Appl Environ Microbiol 2010; 76:2280-5. [PMID: 20139311 DOI: 10.1128/aem.00026-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Many species of Rickettsia are well-known mammalian pathogens transmitted by blood-feeding arthropods. However, molecular surveys are continually uncovering novel Rickettsia species, often in unexpected hosts, including many arthropods that do not feed on blood. This study reports a systematic molecular characterization of a Rickettsia infecting the psocid Liposcelis bostrychophila (Psocoptera: Liposcelidae), a common and cosmopolitan household pest. Surprisingly, the psocid Rickettsia is shown to be Rickettsia felis, a human pathogen transmitted by fleas that causes serious morbidity and occasional mortality. The plasmid from the psocid R. felis was sequenced and was found to be virtually identical to the one in R. felis from fleas. As Liposcelis insects are often intimately associated with humans and other vertebrates, it is speculated that they acquired R. felis from fleas. Whether the R. felis in psocids causes disease in vertebrates is not known and warrants further study.
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40
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Furuta Y, Abe K, Kobayashi I. Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. Nucleic Acids Res 2010; 38:2428-43. [PMID: 20071371 PMCID: PMC2853133 DOI: 10.1093/nar/gkp1226] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The mobility of restriction–modification (RM) gene complexes and their association with genome rearrangements is a subject of active investigation. Here we conducted systematic genome comparisons and genome context analysis on fully sequenced prokaryotic genomes to detect RM-linked genome rearrangements. RM genes were frequently found to be linked to mobility-related genes such as integrase and transposase homologs. They were flanked by direct and inverted repeats at a significantly high frequency. Insertion by long target duplication was observed for I, II, III and IV restriction types. We found several RM genes flanked by long inverted repeats, some of which had apparently inserted into a genome with a short target duplication. In some cases, only a portion of an apparently complete RM system was flanked by inverted repeats. We also found a unit composed of RM genes and an integrase homolog that integrated into a tRNA gene. An allelic substitution of a Type III system with a linked Type I and IV system pair, and allelic diversity in the putative target recognition domain of Type IIG systems were observed. This study revealed the possible mobility of all types of RM systems, and the diversity in their mobility-related organization.
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Affiliation(s)
- Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
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41
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Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer. Proc Natl Acad Sci U S A 2009; 106:18861-6. [PMID: 19837694 DOI: 10.1073/pnas.0908404106] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Homing endonuclease genes are "selfish" mobile genetic elements whose endonuclease promotes the spread of its own gene by creating a break at a specific target site and using the host machinery to repair the break by copying and inserting the gene at this site. Horizontal transfer across the boundary of a species or population within which mating takes place has been thought to be necessary for their evolutionary persistence. This is based on the assumption that they will become fixed in a host population, where opportunities of homing will disappear, and become susceptible to degeneration. To test this hypothesis, we modeled behavior of a homing endonuclease gene that moves during meiosis through double-strand break repair. We mathematically explored conditions for persistence of the homing endonuclease gene and elucidated their parameter dependence as phase diagrams. We found that, if the cost of the pseudogene is lower than that of the homing endonuclease gene, the 2 forms can persist in a population through autonomous periodic oscillation. If the cost of the pseudogene is higher, 2 types of dynamics appear that enable evolutionary persistence: bistability dependent on initial frequency or fixation irrespective of initial frequency. The prediction of long persistence in the absence of horizontal transfer was confirmed by stochastic simulations in finite populations. The average time to extinction of the endonuclease gene was found to be thousands of meiotic generations or more based on realistic parameter values. These results provide a solid theoretical basis for an understanding of these and other extremely selfish elements.
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42
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Handa N, Ichige A, Kobayashi I. Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction-modification gene complex. MICROBIOLOGY-SGM 2009; 155:2320-2332. [PMID: 19389761 DOI: 10.1099/mic.0.026401-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Loss of a type II restriction-modification (RM) gene complex, such as EcoRI, from a bacterial cell leads to death of its descendent cells through attack by residual restriction enzymes on undermethylated target sites of newly synthesized chromosomes. Through such post-segregational host killing, these gene complexes impose their maintenance on their host cells. This finding led to the rediscovery of type II RM systems as selfish mobile elements. The host prokaryote cells were found to cope with such attacks through a variety of means. The RecBCD pathway of homologous recombination in Escherichia coli repairs the lethal lesions on the chromosome, whilst it destroys restricted non-self DNA. recBCD homologues, however, appear very limited in distribution among bacterial genomes, whereas homologues of the RecFOR proteins, responsible for another pathway, are widespread in eubacteria, just like the RM systems. In the present work, therefore, we examined the possible contribution of the RecFOR pathway to cell survival after loss of an RM gene complex. A recF mutation reduced survival in an otherwise rec-positive background and, more severely, in a recBC sbcBC background. We also found that its effect is prominent in the presence of specific non-null mutant forms of the RecBCD enzyme: the resistance to killing seen with recC1002, recC1004, recC2145 and recB2154 is severely reduced to the level of a null recBC allele when combined with a recF, recO or recR mutant allele. Such resistance was also dependent on RecJ and RecQ functions. UV resistance of these non-null recBCD mutants is also reduced by recF, recJ or recQ mutation. These results demonstrate that the RecFOR pathway of recombination can contribute greatly to resistance to RM-mediated host killing, depending on the genetic background.
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Affiliation(s)
- Naofumi Handa
- Laboratory of Social Genome Sciences, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Asao Ichige
- Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108-8639, Japan.,Laboratory of Social Genome Sciences, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Ichizo Kobayashi
- Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Japan.,Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108-8639, Japan.,Laboratory of Social Genome Sciences, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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43
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Abstract
Bacterial toxin–antitoxin (TA) systems are diverse and widespread in the prokaryotic kingdom. They are composed of closely linked genes encoding a stable toxin that can harm the host cell and its cognate labile antitoxin, which protects the host from the toxin's deleterious effect. TA systems are thought to invade bacterial genomes through horizontal gene transfer. Some TA systems might behave as selfish elements and favour their own maintenance at the expense of their host. As a consequence, they may contribute to the maintenance of plasmids or genomic islands, such as super-integrons, by post-segregational killing of the cell that loses these genes and so suffers the stable toxin's destructive effect. The function of the chromosomally encoded TA systems is less clear and still open to debate. This Review discusses current hypotheses regarding the biological roles of these evolutionarily successful small operons. We consider the various selective forces that could drive the maintenance of TA systems in bacterial genomes.
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Affiliation(s)
- Laurence Van Melderen
- Laboratoire de Génétique et Physiologie Bactérienne, IBMM, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
- * E-mail:
| | - Manuel Saavedra De Bast
- Laboratoire de Génétique et Physiologie Bactérienne, IBMM, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
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44
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Asakura Y, Kobayashi I. From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene complex. Nucleic Acids Res 2009; 37:3021-31. [PMID: 19304752 PMCID: PMC2685091 DOI: 10.1093/nar/gkp148] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetically programmed cell deaths play important roles in unicellular prokaryotes. In postsegregational killing, loss of a gene complex from a cell leads to its descendants' deaths. With type II restriction-modification gene complexes, such death is triggered by restriction endonuclease's attacks on under-methylated chromosomes. Here, we examined how the Escherichia coli transcriptome changes after loss of PaeR7I gene complex. At earlier time points, activation of SOS genes and sigma(E)-regulon was noticeable. With time, more SOS genes, stress-response genes (including sigma(S)-regulon, osmotic-, oxidative- and periplasmic-stress genes), biofilm-related genes, and many hitherto uncharacterized genes were induced, and genes for energy metabolism, motility and outer membrane biogenesis were repressed. As expected from the activation of sigma(E)-regulon, the death was accompanied by cell lysis and release of cellular proteins. Expression of several sigma(E)-regulon genes indeed led to cell lysis. We hypothesize that some signal was transduced, among multiple genes involved, from the damaged genome to the cell surface and led to its disintegration. These results are discussed in comparison with other forms of programmed deaths in bacteria and eukaryotes.
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Affiliation(s)
- Yoko Asakura
- Ajinomoto CO, INC, Kawasaki-shi, Kanagawa, Japan.
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45
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Humbert O, Salama NR. The Helicobacter pylori HpyAXII restriction-modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components. Nucleic Acids Res 2008; 36:6893-906. [PMID: 18978016 PMCID: PMC2588503 DOI: 10.1093/nar/gkn718] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 09/26/2008] [Accepted: 09/30/2008] [Indexed: 12/15/2022] Open
Abstract
The naturally competent organism Helicobacter pylori encodes a large number of restriction-modification (R-M) systems that consist of a restriction endonuclease and a DNA methyltransferase. R-M systems are not only believed to limit DNA exchange among bacteria but may also have other cellular functions. We report a previously uncharacterized H. pylori type II R-M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC sites, which are rare in the H. pylori chromosome but numerous in ribosomal RNA genes. As predicted, this type II R-M system showed attributes of a selfish element. Deletion of the methyltransferase M.HpyAXII is lethal when associated with an active endonuclease R.HpyAXII unless compensated by adaptive mutation or gene amplification. R.HpyAXII effectively restricted both unmethylated plasmid and chromosomal DNA during natural transformation and was predicted to belong to the novel 'half pipe' structural family of endonucleases. Analysis of a panel of clinical isolates revealed that R.HpyAXII was functional in a small number of H. pylori strains (18.9%, n = 37), whereas the activity of M.HpyAXII was highly conserved (92%, n = 50), suggesting that GTAC methylation confers a selective advantage to H. pylori. However, M.HpyAXII activity did not enhance H. pylori fitness during stomach colonization of a mouse infection model.
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Affiliation(s)
- Olivier Humbert
- Division of Human Biology, Fred Hutchinson Cancer Research Center and Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, USA
| | - Nina R. Salama
- Division of Human Biology, Fred Hutchinson Cancer Research Center and Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, USA
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Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases. Genome Biol 2008; 9:R163. [PMID: 19025584 PMCID: PMC2614495 DOI: 10.1186/gb-2008-9-11-r163] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 10/16/2008] [Accepted: 11/21/2008] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Alteration in epigenetic methylation can affect gene expression and other processes. In Prokaryota, DNA methyltransferase genes frequently move between genomes and present a potential threat. A methyl-specific deoxyribonuclease, McrBC, of Escherichia coli cuts invading methylated DNAs. Here we examined whether McrBC competes with genome methylation systems through host killing by chromosome cleavage. RESULTS McrBC inhibited the establishment of a plasmid carrying a PvuII methyltransferase gene but lacking its recognition sites, likely through the lethal cleavage of chromosomes that became methylated. Indeed, its phage-mediated transfer caused McrBC-dependent chromosome cleavage. Its induction led to cell death accompanied by chromosome methylation, cleavage and degradation. RecA/RecBCD functions affect chromosome processing and, together with the SOS response, reduce lethality. Our evolutionary/genomic analyses of McrBC homologs revealed: a wide distribution in Prokaryota; frequent distant horizontal transfer and linkage with mobility-related genes; and diversification in the DNA binding domain. In these features, McrBCs resemble type II restriction-modification systems, which behave as selfish mobile elements, maintaining their frequency by host killing. McrBCs are frequently found linked with a methyltransferase homolog, which suggests a functional association. CONCLUSIONS Our experiments indicate McrBC can respond to genome methylation systems by host killing. Combined with our evolutionary/genomic analyses, they support our hypothesis that McrBCs have evolved as mobile elements competing with specific genome methylation systems through host killing. To our knowledge, this represents the first report of a defense system against epigenetic systems through cell death.
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Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. BMC STRUCTURAL BIOLOGY 2008; 8:48. [PMID: 19014591 PMCID: PMC2630997 DOI: 10.1186/1472-6807-8-48] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2008] [Accepted: 11/14/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND Catalytic domains of Type II restriction endonucleases (REases) belong to a few unrelated three-dimensional folds. While the PD-(D/E)XK fold is most common among these enzymes, crystal structures have been also determined for single representatives of two other folds: PLD (R.BfiI) and half-pipe (R.PabI). Bioinformatics analyses supported by mutagenesis experiments suggested that some REases belong to the HNH fold (e.g. R.KpnI), and that a small group represented by R.Eco29kI belongs to the GIY-YIG fold. However, for a large fraction of REases with known sequences, the three-dimensional fold and the architecture of the active site remain unknown, mostly due to extreme sequence divergence that hampers detection of homology to enzymes with known folds. RESULTS R.Hpy188I is a Type II REase with unknown structure. PSI-BLAST searches of the non-redundant protein sequence database reveal only 1 homolog (R.HpyF17I, with nearly identical amino acid sequence and the same DNA sequence specificity). Standard application of state-of-the-art protein fold-recognition methods failed to predict the relationship of R.Hpy188I to proteins with known structure or to other protein families. In order to increase the amount of evolutionary information in the multiple sequence alignment, we have expanded our sequence database searches to include sequences from metagenomics projects. This search resulted in identification of 23 further members of R.Hpy188I family, both from metagenomics and the non-redundant database. Moreover, fold-recognition analysis of the extended R.Hpy188I family revealed its relationship to the GIY-YIG domain and allowed for computational modeling of the R.Hpy188I structure. Analysis of the R.Hpy188I model in the light of sequence conservation among its homologs revealed an unusual variant of the active site, in which the typical Tyr residue of the YIG half-motif had been substituted by a Lys residue. Moreover, some of its homologs have the otherwise invariant Arg residue in a non-homologous position in sequence that nonetheless allows for spatial conservation of the guanidino group potentially involved in phosphate binding. CONCLUSION The present study eliminates a significant "white spot" on the structural map of REases. It also provides important insight into sequence-structure-function relationships in the GIY-YIG nuclease superfamily. Our results reveal that in the case of proteins with no or few detectable homologs in the standard "non-redundant" database, it is useful to expand this database by adding the metagenomic sequences, which may provide evolutionary linkage to detect more remote homologs.
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Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 2008; 36:6688-719. [PMID: 18948295 PMCID: PMC2588523 DOI: 10.1093/nar/gkn668] [Citation(s) in RCA: 534] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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Ohno S, Handa N, Watanabe-Matsui M, Takahashi N, Kobayashi I. Maintenance forced by a restriction-modification system can be modulated by a region in its modification enzyme not essential for methyltransferase activity. J Bacteriol 2008; 190:2039-49. [PMID: 18192396 PMCID: PMC2258900 DOI: 10.1128/jb.01319-07] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 01/02/2008] [Indexed: 11/20/2022] Open
Abstract
Several type II restriction-modification gene complexes can force their maintenance on their host bacteria by killing cells that have lost them in a process called postsegregational killing or genetic addiction. It is likely to proceed by dilution of the modification enzyme molecule during rounds of cell division following the gene loss, which exposes unmethylated recognition sites on the newly replicated chromosomes to lethal attack by the remaining restriction enzyme molecules. This process is in apparent contrast to the process of the classical types of postsegregational killing systems, in which built-in metabolic instability of the antitoxin allows release of the toxin for lethal action after the gene loss. In the present study, we characterize a mutant form of the EcoRII gene complex that shows stronger capacity in such maintenance. This phenotype is conferred by an L80P amino acid substitution (T239C nucleotide substitution) mutation in the modification enzyme. This mutant enzyme showed decreased DNA methyltransferase activity at a higher temperature in vivo and in vitro than the nonmutated enzyme, although a deletion mutant lacking the N-terminal 83 amino acids did not lose activity at either of the temperatures tested. Under a condition of inhibited protein synthesis, the activity of the L80P mutant was completely lost at a high temperature. In parallel, the L80P mutant protein disappeared more rapidly than the wild-type protein. These results demonstrate that the capability of a restriction-modification system in forcing maintenance on its host can be modulated by a region of its antitoxin, the modification enzyme, as in the classical postsegregational killing systems.
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Affiliation(s)
- Satona Ohno
- Department of Medical Genome Sciences, Graduate School of Frontier Science and Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Krone SM, Lu R, Fox R, Suzuki H, Top EM. Modelling the spatial dynamics of plasmid transfer and persistence. MICROBIOLOGY-SGM 2007; 153:2803-2816. [PMID: 17660444 PMCID: PMC2613009 DOI: 10.1099/mic.0.2006/004531-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial plasmids are extra-chromosomal genetic elements that code for a wide variety of phenotypes in their bacterial hosts and are maintained in bacterial communities through both vertical and horizontal transfer. Current mathematical models of plasmid-bacteria dynamics, based almost exclusively on mass-action differential equations that describe these interactions in completely mixed environments, fail to adequately explain phenomena such as the long-term persistence of plasmids in natural and clinical bacterial communities. This failure is, at least in part, due to the absence of any spatial structure in these models, whereas most bacterial populations are spatially structured in microcolonies and biofilms. To help bridge the gap between theoretical predictions and observed patterns of plasmid spread and persistence, an individual-based lattice model (interacting particle system) that provides a predictive framework for understanding the dynamics of plasmid-bacteria interactions in spatially structured populations is presented here. To assess the accuracy and flexibility of the model, a series of experiments that monitored plasmid loss and horizontal transfer of the IncP-1beta plasmid pB10 : : rfp in Escherichia coli K12 and other bacterial populations grown on agar surfaces were performed. The model-based visual patterns of plasmid loss and spread, as well as quantitative predictions of the effects of different initial parental strain densities and incubation time on densities of transconjugants formed on a 2D grid, were in agreement with this and previously published empirical data. These results include features of spatially structured populations that are not predicted by mass-action differential equation models.
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Affiliation(s)
- Stephen M. Krone
- Department of Mathematics, Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-1103, USA
| | - Ruinan Lu
- Department of Mathematics, Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-1103, USA
| | - Randal Fox
- Department of Biological Sciences, Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051, USA
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, ID 83844-3052, USA
| | - Haruo Suzuki
- Department of Biological Sciences, Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051, USA
| | - Eva M. Top
- Department of Biological Sciences, Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051, USA
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