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Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus. J Bacteriol 2017; 199:JB.00629-16. [PMID: 28138100 DOI: 10.1128/jb.00629-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/25/2017] [Indexed: 01/04/2023] Open
Abstract
ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013 A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.
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Coluzzi C, Guédon G, Devignes MD, Ambroset C, Loux V, Lacroix T, Payot S, Leblond-Bourget N. A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins. Front Microbiol 2017; 8:443. [PMID: 28373865 PMCID: PMC5357655 DOI: 10.3389/fmicb.2017.00443] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022] Open
Abstract
Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of Streptococcus reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.
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Affiliation(s)
- Charles Coluzzi
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Marie-Dominique Devignes
- UMR7503 Laboratoire Lorrain de Recherche en Informatique et ses Applications, Centre National de la Recherche Scientifique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Chloé Ambroset
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Valentin Loux
- UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Thomas Lacroix
- UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sophie Payot
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Nathalie Leblond-Bourget
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
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153
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The transjugation machinery of Thermus thermophilus: Identification of TdtA, an ATPase involved in DNA donation. PLoS Genet 2017; 13:e1006669. [PMID: 28282376 PMCID: PMC5365140 DOI: 10.1371/journal.pgen.1006669] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 03/24/2017] [Accepted: 03/04/2017] [Indexed: 11/19/2022] Open
Abstract
In addition to natural competence, some Thermus thermophilus strains show a high rate of DNA transfer via direct cell-to-cell contact. The process is bidirectional and follows a two-step model where the donor cell actively pushes out DNA and the recipient cell employs the natural competence system to take up the DNA, in a hybrid transformation-dependent conjugation process (transjugation). While the DNA uptake machinery is well known as in other bacterial species that undergo transformation, the pushing step of transjugation remains to be characterized. Here we have searched for hypothetical DNA translocases putatively involved in the pushing step of transjugation. Among candidates encoded by T. thermophilus HB27, the TdtA protein was found to be required for DNA pushing but not for DNA pulling during transjugation, without affecting other cellular processes. Purified TdtA shows ATPase activity and oligomerizes as hexamers with a central opening that can accommodate double-stranded DNA. The tdtA gene was found to belong to a mobile 14 kbp-long DNA element inserted within the 3′ end of a tRNA gene, flanked by 47 bp direct repeats. The insertion also encoded a homolog of bacteriophage site-specific recombinases and actively self-excised from the chromosome at high frequency to form an apparently non-replicative circular form. The insertion also encoded a type II restriction endonuclease and a NurA-like nuclease, whose activities were required for efficient transjugation. All these data support that TdtA belongs to a new type of Integrative and Conjugative Element which promotes the generalized and efficient transfer of genetic traits that could facilitate its co-selection among bacterial populations. Transjugation is a new type of horizontal gene transfer process in which a donor cell pushes out genomic DNA upon cell contact and a recipient cell pulls this DNA inside by natural transformation. Here we describe TdtA, a DNA translocase of the pushing system of T. thermophilus, which is encoded within ICEth1, a new class of Integrative and Conjugative Element whose presence leads to generalized cell-to-cell transfer of any gene marker, circumventing the Argonaute surveillance system that controls access of extracellular DNA acquired by transformation.
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Orlek A, Phan H, Sheppard AE, Doumith M, Ellington M, Peto T, Crook D, Walker AS, Woodford N, Anjum MF, Stoesser N. Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids. Plasmid 2017; 91:42-52. [PMID: 28286183 PMCID: PMC5466382 DOI: 10.1016/j.plasmid.2017.03.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/08/2017] [Indexed: 01/17/2023]
Abstract
Plasmid typing can provide insights into the epidemiology and transmission of plasmid-mediated antibiotic resistance. The principal plasmid typing schemes are replicon typing and MOB typing, which utilize variation in replication loci and relaxase proteins respectively. Previous studies investigating the proportion of plasmids assigned a type by these schemes (‘typeability’) have yielded conflicting results; moreover, thousands of plasmid sequences have been added to NCBI in recent years, without consistent annotation to indicate which sequences represent complete plasmids. Here, a curated dataset of complete Enterobacteriaceae plasmids from NCBI was compiled, and used to assess the typeability and concordance of in silico replicon and MOB typing schemes. Concordance was assessed at hierarchical replicon type resolutions, from replicon family-level to plasmid multilocus sequence type (pMLST)-level, where available. We found that 85% and 65% of the curated plasmids could be replicon and MOB typed, respectively. Overall, plasmid size and the number of resistance genes were significant independent predictors of replicon and MOB typing success. We found some degree of non-concordance between replicon families and MOB types, which was only partly resolved when partitioning plasmids into finer-resolution groups (replicon and pMLST types). In some cases, non-concordance was attributed to ambiguous boundaries between MOBP and MOBQ types; in other cases, backbone mosaicism was considered a more plausible explanation. β-lactamase resistance genes tended not to show fidelity to a particular plasmid type, though some previously reported associations were supported. Overall, replicon and MOB typing schemes are likely to continue playing an important role in plasmid analysis, but their performance is constrained by the diverse and dynamic nature of plasmid genomes. 92% of clinically-relevant plasmids could be replicon typed, compared with reports of 100% typeability in 2014. Replicon and MOB typing were partly concordant; partitioning plasmids into finer-resolution groups increased concordance. Overlap between MOBP and MOBQ relaxase families complicates assignment of MOBP and MOBQ types. Generally, resistance genes showed low fidelity towards particular plasmid backbones. PacBio sequencing has driven increased availability of complete plasmid sequences, but retrieved datasets require curation.
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Affiliation(s)
- Alex Orlek
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.
| | - Hang Phan
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Anna E Sheppard
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Matthew Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK; Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Tim Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Neil Woodford
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK; Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Muna F Anjum
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK; Department of Bacteriology, Animal and Plant Health Agency, Addlestone, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Conjugative type IV secretion in Gram-positive pathogens: TraG, a lytic transglycosylase and endopeptidase, interacts with translocation channel protein TraM. Plasmid 2017; 91:9-18. [PMID: 28219792 DOI: 10.1016/j.plasmid.2017.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/30/2017] [Accepted: 02/02/2017] [Indexed: 11/24/2022]
Abstract
Conjugative transfer plays a major role in the transmission of antibiotic resistance in bacteria. pIP501 is a Gram-positive conjugative model plasmid with the broadest transfer host-range known so far and is frequently found in Enterococcus faecalis and Enterococcus faecium clinical isolates. The pIP501 type IV secretion system is encoded by 15 transfer genes. In this work, we focus on the VirB1-like protein TraG, a modular peptidoglycan metabolizing enzyme, and the VirB8-homolog TraM, a potential member of the translocation channel. By providing full-length traG in trans, but not with a truncated variant, we achieved full recovery of wild type transfer efficiency in the traG-knockout mutant E. faecalis pIP501ΔtraG. With peptidoglycan digestion experiments and tandem mass spectrometry we could assign lytic transglycosylase and endopeptidase activity to TraG, with the CHAP domain alone displaying endopeptidase activity. We identified a novel interaction between TraG and TraM in a bacterial-2-hybrid assay. In addition we found that both proteins localize in focal spots at the E. faecalis cell membrane using immunostaining and fluorescence microscopy. Extracellular protease digestion to evaluate protein cell surface exposure revealed that correct membrane localization of TraM requires the transmembrane helix of TraG. Thus, we suggest an essential role for TraG in the assembly of the pIP501 type IV secretion system.
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156
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Orlek A, Stoesser N, Anjum MF, Doumith M, Ellington MJ, Peto T, Crook D, Woodford N, Walker AS, Phan H, Sheppard AE. Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology. Front Microbiol 2017; 8:182. [PMID: 28232822 PMCID: PMC5299020 DOI: 10.3389/fmicb.2017.00182] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/25/2017] [Indexed: 11/20/2022] Open
Abstract
Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made.
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Affiliation(s)
- Alex Orlek
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
| | - Muna F. Anjum
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Department of Bacteriology, Animal and Plant Health AgencyAddlestone, UK
| | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - Matthew J. Ellington
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - Tim Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Hang Phan
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
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157
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Marbouty M, Baudry L, Cournac A, Koszul R. Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay. SCIENCE ADVANCES 2017; 3:e1602105. [PMID: 28232956 PMCID: PMC5315449 DOI: 10.1126/sciadv.1602105] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/09/2017] [Indexed: 05/05/2023]
Abstract
The biochemical activities of microbial communities, or microbiomes, are essential parts of environmental and animal ecosystems. The dynamics, balance, and effects of these communities are strongly influenced by phages present in the population. Being able to characterize bacterium-phage relationships is therefore essential to investigate these ecosystems to the full extent of their complexity. However, this task is currently limited by (i) the ability to characterize complete bacterial and viral genomes from a complex mix of species and (ii) the difficulty to assign phage sequences to their bacterial hosts. We show that both limitations can be circumvented using meta3C, an experimental and computational approach that exploits the physical contacts between DNA molecules to infer their proximity. In a single experiment, dozens of bacterial and phage genomes present in a complex mouse gut microbiota were assembled and scaffolded de novo. The phage genomes were then assigned to their putative bacterial hosts according to the physical contacts between the different DNA molecules, opening new perspectives for a comprehensive picture of the genomic structure of the gut flora. Therefore, this work holds far-reaching implications for human health studies aiming to bridge the virome to the microbiome.
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Affiliation(s)
- Martial Marbouty
- Institut Pasteur, Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France
- CNRS, UMR 3525, 75015 Paris, France
| | - Lyam Baudry
- Institut Pasteur, Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France
- CNRS, UMR 3525, 75015 Paris, France
| | - Axel Cournac
- Institut Pasteur, Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France
- CNRS, UMR 3525, 75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France
- CNRS, UMR 3525, 75015 Paris, France
- Corresponding author.
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158
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Colombi E, Straub C, Künzel S, Templeton MD, McCann HC, Rainey PB. Evolution of copper resistance in the kiwifruit pathogenPseudomonas syringaepv.actinidiaethrough acquisition of integrative conjugative elements and plasmids. Environ Microbiol 2017; 19:819-832. [DOI: 10.1111/1462-2920.13662] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/02/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Elena Colombi
- New Zealand Institute for Advanced Study, Massey University; Auckland New Zealand
| | - Christina Straub
- New Zealand Institute for Advanced Study, Massey University; Auckland New Zealand
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology; Plön Germany
| | - Matthew D. Templeton
- Plant and Food Research; Auckland New Zealand
- School of Biological Sciences; University of Auckland; Auckland New Zealand
| | - Honour C. McCann
- New Zealand Institute for Advanced Study, Massey University; Auckland New Zealand
- South China Botanical Institute; Chinese Academy of Sciences; Guangzhou China
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University; Auckland New Zealand
- Max Planck Institute for Evolutionary Biology; Plön Germany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris-Tech), PSL Research University; Paris France
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159
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López-Pérez M, Ramon-Marco N, Rodriguez-Valera F. Networking in microbes: conjugative elements and plasmids in the genus Alteromonas. BMC Genomics 2017; 18:36. [PMID: 28056800 PMCID: PMC5217437 DOI: 10.1186/s12864-016-3461-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/22/2016] [Indexed: 12/15/2022] Open
Abstract
Background To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time. Results We have found nine different plasmids of sizes ranging from 85 to 600 Kb, most of them were found in a single strain. Networks of gene similarity could be established among six of the plasmids that were also connected with another cluster of plasmids found in Shewanella strains. The cargo genes found in these plasmids included cassettes found before in chromosome flexible genomic islands of Alteromonas strains. We describe also the plasmids pAMCP48-600 and pAMCP49-600, the largest found in Alteromonas thus far (ca. 600 Kb) and containing all the hallmarks to be classified as chromids. We found in them some housekeeping genes and a cluster that code for an exocellular polysaccharide. They could represent the transport vectors for the previously described replacement flexible genomic islands. Integrative and conjugative elements (ICEs) were more common than plasmids and showed similar patterns of variation with cargo genes coding for components of additive flexible genomic islands. A nearly identical ICE was found in A. mediterranea MED64 and Vibrio cholera AHV1003 isolated from a human pathogen, indicating the potential exchange of these genes across phylogenetic distances exceeding the family threshold. Conclusion We have seen evidence of how CEs can be vectors to transfer gene cassettes acquired in the chromosomal flexible genomic islands, both of the additive and replacement kind. These CEs showed evidence of how genetic material is exchanged among members of the same species but also (albeit less frequently) across genus and family barriers. These gradients of exchange frequency are probably one of the main drivers of species origin and maintenance in prokaryotes and also provide these taxa with large genetic diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3461-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mario López-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Apartado 18, San Juan, 03550, Alicante, Spain
| | - Nieves Ramon-Marco
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Apartado 18, San Juan, 03550, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Apartado 18, San Juan, 03550, Alicante, Spain.
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160
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Abstract
All plasmids that spread by conjugative transfer encode a relaxase. That includes plasmids that encode the type IV secretion machinery necessary to mediate cell to cell transfer, as well as mobilizable plasmids that exploit the existence of other plasmids' type IV secretion machinery to enable their own lateral spread. Relaxases perform key functions in plasmid transfer by first binding to their cognate plasmid as part of a multiprotein complex called the relaxosome, which is then specifically recognized by a receptor protein at the opening of the secretion channel. Relaxases catalyze a site- and DNA-strand-specific cleavage reaction on the plasmid then pilot the single strand of plasmid DNA through the membrane-spanning type IV secretion channel as a nucleoprotein complex. In the recipient cell, relaxases help terminate the transfer process efficiently and stabilize the incoming plasmid DNA. Here, we review the well-studied MOBF family of relaxases to describe the biochemistry of these versatile enzymes and integrate current knowledge into a mechanistic model of plasmid transfer in Gram-negative bacteria.
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161
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A New Member of the Growing Family of Contact-Dependent Growth Inhibition Systems in Xenorhabdus doucetiae. PLoS One 2016; 11:e0167443. [PMID: 27907104 PMCID: PMC5131962 DOI: 10.1371/journal.pone.0167443] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/14/2016] [Indexed: 12/29/2022] Open
Abstract
Xenorhabdus is a bacterial symbiont of entomopathogenic Steinernema nematodes and is pathogenic for insects. Its life cycle involves a stage inside the insect cadaver, in which it competes for environmental resources with microorganisms from soil and the insect gut. Xenorhabdus is, thus, a useful model for identifying new interbacterial competition systems. For the first time, in an entomopathogenic bacterium, Xenorhabdus doucetiae strain FRM16, we identified a cdi-like locus. The cdi loci encode contact-dependent inhibition (CDI) systems composed of proteins from the two-partner secretion (TPS) family. CdiB is the outer membrane protein and CdiA is the toxic exoprotein. An immunity protein, CdiI, protects bacteria against inhibition. We describe here the growth inhibition effect of the toxic C-terminus of CdiA from X. doucetiae FRM16, CdiA-CTFRM16, following its production in closely and distantly related enterobacterial species. CdiA-CTFRM16 displayed Mg2+-dependent DNase activity, in vitro. CdiA-CTFRM16-mediated growth inhibition was specifically neutralized by CdiIFRM16. Moreover, the cdi FRM16 locus encodes an ortholog of toxin-activating proteins C that we named CdiCFRM16. In addition to E. coli, the cdiBCAI-type locus was found to be widespread in environmental bacteria interacting with insects, plants, rhizospheres and soils. Phylogenetic tree comparisons for CdiB, CdiA and CdiC suggested that the genes encoding these proteins had co-evolved. By contrast, the considerable variability of CdiI protein sequences suggests that the cdiI gene is an independent evolutionary unit. These findings further characterize the sparsely described cdiBCAI-type locus.
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162
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Martínez JL, Coque TM, Lanza VF, de la Cruz F, Baquero F. Genomic and metagenomic technologies to explore the antibiotic resistance mobilome. Ann N Y Acad Sci 2016; 1388:26-41. [PMID: 27861983 DOI: 10.1111/nyas.13282] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health-integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so-called resistance mobilome. High-throughput sequencing techniques allow an unprecedented opportunity to describe the genetic composition of a given microbiome without the need to subculture the organisms present inside. However, bioinformatic methods for analyzing this bulk of data, mainly with respect to binning each resistance gene with the organism hosting it, are still in their infancy. Here, we discuss how current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes. In addition, we describe the drawbacks of current methodologies for analyzing the resistance mobilome, mainly in cases of complex microbiotas, and discuss the possibility of implementing novel tools to improve our current metagenomic toolbox.
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Affiliation(s)
- José L Martínez
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
| | - Teresa M Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
| | - Val F Lanza
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Cantabria, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
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163
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Gillings MR, Paulsen IT, Tetu SG. Genomics and the evolution of antibiotic resistance. Ann N Y Acad Sci 2016; 1388:92-107. [DOI: 10.1111/nyas.13268] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
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164
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Assembly and transfer of tripartite integrative and conjugative genetic elements. Proc Natl Acad Sci U S A 2016; 113:12268-12273. [PMID: 27733511 DOI: 10.1073/pnas.1613358113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are ubiquitous mobile genetic elements present as "genomic islands" within bacterial chromosomes. Symbiosis islands are ICEs that convert nonsymbiotic mesorhizobia into symbionts of legumes. Here we report the discovery of symbiosis ICEs that exist as three separate chromosomal regions when integrated in their hosts, but through recombination assemble as a single circular ICE for conjugative transfer. Whole-genome comparisons revealed exconjugants derived from nonsymbiotic mesorhizobia received three separate chromosomal regions from the donor Mesorhizobium ciceri WSM1271. The three regions were each bordered by two nonhomologous integrase attachment (att) sites, which together comprised three homologous pairs of attL and attR sites. Sequential recombination between each attL and attR pair produced corresponding attP and attB sites and joined the three fragments to produce a single circular ICE, ICEMcSym1271 A plasmid carrying the three attP sites was used to recreate the process of tripartite ICE integration and to confirm the role of integrase genes intS, intM, and intG in this process. Nine additional tripartite ICEs were identified in diverse mesorhizobia and transfer was demonstrated for three of them. The transfer of tripartite ICEs to nonsymbiotic mesorhizobia explains the evolution of competitive but suboptimal N2-fixing strains found in Western Australian soils. The unheralded existence of tripartite ICEs raises the possibility that multipartite elements reside in other organisms, but have been overlooked because of their unusual biology. These discoveries reveal mechanisms by which integrases dramatically manipulate bacterial genomes to allow cotransfer of disparate chromosomal regions.
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165
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Huang J, Ma J, Shang K, Hu X, Liang Y, Li D, Wu Z, Dai L, Chen L, Wang L. Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in Streptococcus suis: A Probable Mobile Genetic Elements Reservoir for Other Streptococci. Front Cell Infect Microbiol 2016; 6:118. [PMID: 27774436 PMCID: PMC5053989 DOI: 10.3389/fcimb.2016.00118] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/21/2016] [Indexed: 02/04/2023] Open
Abstract
Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S. suis. Integrative conjugative elements (ICEs), prophages and tandem MGEs were located at different insertion sites, while 86% of the AMR-associated MGEs were inserted at rplL and rum loci. Comprehensive analysis of insertions at rplL and rum loci among four pathogenic Streptococcus species (Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and S. suis) revealed the existence of different groups of MGEs, including Tn5252, ICESp1108, and TnGBS2 groups ICEs, Φm46.1 group prophage, ICE_ICE and ICE_prophage tandem MGEs. Comparative ICE genomics of ICESa2603 family revealed that module exchange and acquisition/deletion were the main mechanisms in MGEs' expansion and evolution. Furthermore, the observation of tandem MGEs reflected a novel mechanism for MGE diversity. Moreover, an in vitro competition assay showed no visible fitness cost was observed between different MGE-carrying isolates and a conjugation assay revealed the transferability of ICESa2603 family of ICEs. Our statistics further indicated that the prevalence and diversity of MGEs in S. suis is much greater than in other three species which prompted our hypothesis that S. suis is probably a MGEs reservoir for other streptococci. In conclusion, our results showed that acquisition of MGEs confers S. suis not only its capability as a multidrug resistance pathogen, but also represents a paradigm to study the modular evolution and matryoshkas of MGEs.
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Affiliation(s)
- Jinhu Huang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Jiale Ma
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Kexin Shang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Yuan Liang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Daiwei Li
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State UniversityAmes, IA, USA; Department of Pharmacy, The Second Hospital of Dalian Medical UniversityDalian, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Lei Dai
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Li Chen
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Liping Wang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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166
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Gillings MR. Lateral gene transfer, bacterial genome evolution, and the Anthropocene. Ann N Y Acad Sci 2016; 1389:20-36. [DOI: 10.1111/nyas.13213] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/20/2016] [Accepted: 07/28/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Michael R. Gillings
- Genes to Geoscience Research Centre, Department of Biological Sciences Macquarie University Sydney New South Wales Australia
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167
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Zamarro MT, Martín-Moldes Z, Díaz E. The ICE XTD of Azoarcus sp. CIB, an integrative and conjugative element with aerobic and anaerobic catabolic properties. Environ Microbiol 2016; 18:5018-5031. [PMID: 27450529 DOI: 10.1111/1462-2920.13465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 11/28/2022]
Abstract
Integrative and conjugative elements (ICE) play a major role in aerobic degradation of aromatic compounds, but they have not yet been shown to be involved in anaerobic degradation. We have characterized here the ICEXTD element which endows to the beta-proteobacterium Azoarcus sp. CIB with the ability to utilize aromatic hydrocarbons. The core region of ICEXTD , which shows a remarkable synteny with that of ICEclc-like elements, allows its own intracellular and intercellular mobility. ICEXTD integrates at the tRNAGly of the host chromosome, but it can also excise to produce a ready to transfer circular form. The adaptation modules of ICEXTD represent a unique combination of gene clusters for aerobic (tod genes) and anaerobic (bss-bbs and mbd genes) degradation of certain aromatic hydrocarbons, e.g., toluene, m-xylene and cumene. Transfer of ICEXTD to other Azoarcus strains, e.g., A. evansii, confers them the ability to degrade aromatic hydrocarbons both aerobically and anaerobically. Interestingly, ICEXTD allows Cupriavidus pinatubonensis, a bacterium unable to degrade anaerobically aromatic compounds, to grow with m-xylene under anoxic conditions. Thus, ICEXTD constitutes the first mobile genetic element able to expand the catabolic abilities of certain bacteria for the removal of aromatic hydrocarbons either in the presence or absence of oxygen.
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Affiliation(s)
- María Teresa Zamarro
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Zaira Martín-Moldes
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
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168
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Depluverez S, Devos S, Devreese B. The Role of Bacterial Secretion Systems in the Virulence of Gram-Negative Airway Pathogens Associated with Cystic Fibrosis. Front Microbiol 2016; 7:1336. [PMID: 27625638 PMCID: PMC5003817 DOI: 10.3389/fmicb.2016.01336] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/12/2016] [Indexed: 11/16/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal inherited disorder in Caucasians. It is caused by mutation of the CF transmembrane conductance regulator (CFTR) gene. A defect in the CFTR ion channel causes a dramatic change in the composition of the airway surface fluid, leading to a highly viscous mucus layer. In healthy individuals, the majority of bacteria trapped in the mucus layer are removed and destroyed by mucociliary clearance. However, in the lungs of patients with CF, the mucociliary clearance is impaired due to dehydration of the airway surface fluid. As a consequence, patients with CF are highly susceptible to chronic or intermittent pulmonary infections, often causing extensive lung inflammation and damage, accompanied by a decreased life expectancy. This mini review will focus on the different secretion mechanisms used by the major bacterial CF pathogens to release virulence factors, their role in resistance and discusses the potential for therapeutically targeting secretion systems.
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Affiliation(s)
- Sofie Depluverez
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Simon Devos
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Bart Devreese
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
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169
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Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis. Sci Rep 2016; 6:30379. [PMID: 27461509 PMCID: PMC4961963 DOI: 10.1038/srep30379] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/04/2016] [Indexed: 02/01/2023] Open
Abstract
Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.
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170
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Auchtung JM, Aleksanyan N, Bulku A, Berkmen MB. Biology of ICEBs1, an integrative and conjugative element in Bacillus subtilis. Plasmid 2016; 86:14-25. [PMID: 27381852 DOI: 10.1016/j.plasmid.2016.07.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/21/2016] [Accepted: 07/01/2016] [Indexed: 10/21/2022]
Abstract
Horizontal gene transfer plays a profound role in bacterial evolution by propelling the rapid transfer of genes and gene cassettes. Integrative and conjugative elements (ICEs) are one important mechanism driving horizontal gene transfer. ICEs, also known as conjugative transposons, reside on the host chromosome but can excise to form a conjugative DNA circle that is capable of transfer to other cells. Analysis of the large number of completed bacterial genome sequences has revealed many previously unrecognized ICEs, including ICEBs1, found in the Gram-positive model bacterium Bacillus subtilis. The discovery of ICEBs1 in an organism with such an impressive array of molecular tools for genetics and molecular biology was fortuitous. Significant insights into ICE biology have resulted since its discovery <15years ago. In this review, we describe aspects of ICEBs1 biology, such as excision, conjugative transfer, and reintegration, likely to be conserved across many ICEs. We will also highlight some of the more unexpected aspects of ICEBs1 biology, such as its ability to undergo plasmid-like replication after excision and its ability to mobilize plasmids lacking dedicated mobilization functions. A molecular understanding of ICEBs1 has led to additional insights into signals and mechanisms that promote horizontal gene transfer and shape bacterial evolution.
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Affiliation(s)
- Jennifer M Auchtung
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Naira Aleksanyan
- Department of Chemistry and Biochemistry, Suffolk University, 8 Ashburton Place, Boston, MA 02108, USA.
| | - Artemisa Bulku
- Department of Chemistry and Biochemistry, Suffolk University, 8 Ashburton Place, Boston, MA 02108, USA.
| | - Melanie B Berkmen
- Department of Chemistry and Biochemistry, Suffolk University, 8 Ashburton Place, Boston, MA 02108, USA.
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171
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Hanage WP. Not So Simple After All: Bacteria, Their Population Genetics, and Recombination. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a018069. [PMID: 27091940 DOI: 10.1101/cshperspect.a018069] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The pervasive nature of bacterial recombination has become clear. Despite this, the population genetics of bacteria persist in being viewed as simple. Here, I argue against that characterization. After summarizing the history of the topic, I survey the evidence for remarkable and unexplained variation in recombination rate among and within bacterial species. I finally argue that despite recent assertions that recombination means bacterial genes are "public goods," in bacteria the level of selection is the gene, and genes can be understood to have niches with dimensions including the other contents of the genome in which they find themselves.
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Affiliation(s)
- William P Hanage
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
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172
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Zheng Q, Lin W, Liu Y, Chen C, Jiao N. A Comparison of 14 Erythrobacter Genomes Provides Insights into the Genomic Divergence and Scattered Distribution of Phototrophs. Front Microbiol 2016; 7:984. [PMID: 27446024 PMCID: PMC4919336 DOI: 10.3389/fmicb.2016.00984] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/08/2016] [Indexed: 11/15/2022] Open
Abstract
Aerobic anoxygenic phototrophic bacteria (AAPB) are bacteriochlorophyll a (Bchl a)-containing microbial functional population. Erythrobacter is the first genus that was identified to contain AAPB species. Here, we compared 14 Erythrobacter genomes: seven phototrophic strains and seven non- phototrophic strains. Interestingly, AAPB strains are scattered in this genus based on their phylogenetic relationships. All 14 strains could be clustered into three groups based on phylo-genomic analysis, average genomic nucleotide identity and the phylogeny of signature genes (16S rRNA and virB4 genes). The AAPB strains were distributed in three groups, and gain and loss of phototrophic genes co-occurred in the evolutionary history of the genus Erythrobacter. The organization and structure of photosynthesis gene clusters (PGCs) in seven AAPB genomes displayed high synteny of major regions except for few insertions. The 14 Erythrobacter genomes had a large range of genome sizes, from 2.72 to 3.60 M, and the sizes of the core and pan- genomes were 1231 and 8170 orthologous clusters, respectively. Integrative and conjugative elements (ICEs) were frequently identified in genomes we studied, which might play significant roles in shaping or contributing to the pan-genome of Erythrobacter. Our findings suggest the ongoing evolutionary divergence of Erythrobacter genomes and the scattered distribution characteristic of PGC.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Wenxin Lin
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Yanting Liu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Chang Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhou, China
- Xisha Deep Sea Marine Environment Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of SciencesSansha, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
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173
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Martini MC, Wibberg D, Lozano M, Torres Tejerizo G, Albicoro FJ, Jaenicke S, van Elsas JD, Petroni A, Garcillán-Barcia MP, de la Cruz F, Schlüter A, Pühler A, Pistorio M, Lagares A, Del Papa MF. Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Sci Rep 2016; 6:28284. [PMID: 27321040 PMCID: PMC4913263 DOI: 10.1038/srep28284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/31/2016] [Indexed: 12/02/2022] Open
Abstract
The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.
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Affiliation(s)
- María C Martini
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Mauricio Lozano
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Gonzalo Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Francisco J Albicoro
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Sebastian Jaenicke
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | | | - Alejandro Petroni
- Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas (CSIC), 39011 Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas (CSIC), 39011 Santander, Spain
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - María F Del Papa
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
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174
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Bossé JT, Li Y, Fernandez Crespo R, Chaudhuri RR, Rogers J, Holden MTG, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR. ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae. Front Microbiol 2016; 7:810. [PMID: 27379024 PMCID: PMC4908127 DOI: 10.3389/fmicb.2016.00810] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/12/2016] [Indexed: 12/26/2022] Open
Abstract
ICEApl1 was identified in the whole genome sequence of MIDG2331, a tetracycline-resistant (MIC = 8 mg/L) serovar 8 clinical isolate of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. PCR amplification of virB4, one of the core genes involved in conjugation, was used to identify other A. pleuropneumoniae isolates potentially carrying ICEApl1. MICs for tetracycline were determined for virB4 positive isolates, and shotgun whole genome sequence analysis was used to confirm presence of the complete ICEApl1. The sequence of ICEApl1 is 56083 bp long and contains 67 genes including a Tn10 element encoding tetracycline resistance. Comparative sequence analysis was performed with similar integrative conjugative elements (ICEs) found in other members of the Pasteurellaceae. ICEApl1 is most similar to the 59393 bp ICEHin1056, from Haemophilus influenzae strain 1056. Although initially identified only in serovar 8 isolates of A. pleuropneumoniae (31 from the UK and 1 from Cyprus), conjugal transfer of ICEApl1 to representative isolates of other serovars was confirmed. All isolates carrying ICEApl1 had a MIC for tetracycline of 8 mg/L. This is, to our knowledge, the first description of an ICE in A. pleuropneumoniae, and the first report of a member of the ICEHin1056 subfamily in a non-human pathogen. ICEApl1 confers resistance to tetracycline, currently one of the more commonly used antibiotics for treatment and control of porcine pleuropneumonia.
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Affiliation(s)
- Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London London, UK
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London London, UK
| | | | - Roy R Chaudhuri
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Jon Rogers
- Animal and Plant Health Agency Bury St Edmunds Suffolk, UK
| | - Matthew T G Holden
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine London, UK
| | - Andrew N Rycroft
- Department of Pathology and Pathogen Biology, The Royal Veterinary College Hatfield, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London London, UK
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175
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Gonzalez-Rivera C, Bhatty M, Christie PJ. Mechanism and Function of Type IV Secretion During Infection of the Human Host. Microbiol Spectr 2016; 4:10.1128/microbiolspec.VMBF-0024-2015. [PMID: 27337453 PMCID: PMC4920089 DOI: 10.1128/microbiolspec.vmbf-0024-2015] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Indexed: 02/07/2023] Open
Abstract
Bacterial pathogens employ type IV secretion systems (T4SSs) for various purposes to aid in survival and proliferation in eukaryotic hosts. One large T4SS subfamily, the conjugation systems, confers a selective advantage to the invading pathogen in clinical settings through dissemination of antibiotic resistance genes and virulence traits. Besides their intrinsic importance as principle contributors to the emergence of multiply drug-resistant "superbugs," detailed studies of these highly tractable systems have generated important new insights into the mode of action and architectures of paradigmatic T4SSs as a foundation for future efforts aimed at suppressing T4SS machine function. Over the past decade, extensive work on the second large T4SS subfamily, the effector translocators, has identified a myriad of mechanisms employed by pathogens to subvert, subdue, or bypass cellular processes and signaling pathways of the host cell. An overarching theme in the evolution of many effectors is that of molecular mimicry. These effectors carry domains similar to those of eukaryotic proteins and exert their effects through stealthy interdigitation of cellular pathways, often with the outcome not of inducing irreversible cell damage but rather of reversibly modulating cellular functions. This article summarizes the major developments for the actively studied pathogens with an emphasis on the structural and functional diversity of the T4SSs and the emerging common themes surrounding effector function in the human host.
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Affiliation(s)
- Christian Gonzalez-Rivera
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, Phone: 713-500-5440 (P. J. Christie); 713-500-5441 (C. Gonzalez-Rivera, M. Bhatty)
| | - Minny Bhatty
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, Phone: 713-500-5440 (P. J. Christie); 713-500-5441 (C. Gonzalez-Rivera, M. Bhatty)
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, Phone: 713-500-5440 (P. J. Christie); 713-500-5441 (C. Gonzalez-Rivera, M. Bhatty)
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176
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Ryan MP, Armshaw P, Pembroke JT. SXT/R391 Integrative and Conjugative Elements (ICEs) Encode a Novel 'Trap-Door' Strategy for Mobile Element Escape. Front Microbiol 2016; 7:829. [PMID: 27303400 PMCID: PMC4885824 DOI: 10.3389/fmicb.2016.00829] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/17/2016] [Indexed: 11/18/2022] Open
Abstract
Integrative conjugative elements (ICEs) are a class of bacterial mobile elements that have the ability to mediate their own integration, excision, and transfer from one host genome to another by a mechanism of site-specific recombination, self-circularisation, and conjugative transfer. Members of the SXT/R391 ICE family of enterobacterial mobile genetic elements display an unusual UV-inducible sensitization function which results in stress induced killing of bacterial cells harboring the ICE. This sensitization has been shown to be associated with a stress induced overexpression of a mobile element encoded conjugative transfer gene, orf43, a traV homolog. This results in cell lysis and release of a circular form of the ICE. Induction of this novel system may allow transfer of an ICE, enhancing its survival potential under conditions not conducive to conjugative transfer.
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Affiliation(s)
- Michael P Ryan
- Molecular and Structural Biochemistry Group, Department of Chemical and Environmental Sciences, Materials and Surface Science Institute, University of Limerick Limerick, Ireland
| | - Patricia Armshaw
- Molecular and Structural Biochemistry Group, Department of Chemical and Environmental Sciences, Materials and Surface Science Institute, University of Limerick Limerick, Ireland
| | - J Tony Pembroke
- Molecular and Structural Biochemistry Group, Department of Chemical and Environmental Sciences, Materials and Surface Science Institute, University of Limerick Limerick, Ireland
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177
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Rodríguez-Blanco A, Lemos ML, Osorio CR. Unveiling the pan-genome of the SXT/R391 family of ICEs: molecular characterisation of new variable regions of SXT/R391-like ICEs detected in Pseudoalteromonas sp. and Vibrio scophthalmi. Antonie van Leeuwenhoek 2016; 109:1141-52. [DOI: 10.1007/s10482-016-0716-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/17/2016] [Indexed: 11/30/2022]
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178
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Regulation of genetic flux between bacteria by restriction-modification systems. Proc Natl Acad Sci U S A 2016; 113:5658-63. [PMID: 27140615 DOI: 10.1073/pnas.1603257113] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Restriction-modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.
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179
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Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene. Antimicrob Agents Chemother 2016; 60:3032-40. [PMID: 26953198 DOI: 10.1128/aac.00124-16] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/02/2016] [Indexed: 11/20/2022] Open
Abstract
The species Acinetobacter baumannii is one of the most important multidrug-resistant human pathogens. To determine its virulence and antibiotic resistance determinants, the genome of the nosocomial blaNDM-1-positive A. baumannii strain R2090 originating from Egypt was completely sequenced. Genome analysis revealed that strain R2090 is highly related to the community-acquired Australian A. baumannii strain D1279779. The two strains belong to sequence type 267 (ST267). Isolate R2090 harbored the chromosomally integrated transposon Tn125 carrying the carbapenemase gene blaNDM-1 that is not present in the D1279779 genome. To test the transferability of the metallo-β-lactamase (MBL) gene region, the clinical isolate R2090 was mated with the susceptible A. baumannii recipient CIP 70.10, and the carbapenem-resistant derivative R2091 was obtained. Genome sequencing of the R2091 derivative revealed that it had received an approximately 66-kb region comprising the transposon Tn125 embedding the blaNDM-1 gene. This region had integrated into the chromosome of the recipient strain CIP 70.10. From the four known mechanisms for horizontal gene transfer (conjugation, outer membrane vesicle-mediated transfer, transformation, and transduction), conjugation could be ruled out, since strain R2090 lacks any plasmid, and a type IV secretion system is not encoded in its chromosome. However, strain R2090 possesses three putative prophages, two of which were predicted to be complete and therefore functional. Accordingly, it was supposed that the transfer of the resistance gene region from the clinical isolate R2090 to the recipient occurred by general transduction facilitated by one of the prophages present in the R2090 genome. Hence, phage-mediated transduction has to be taken into account for the dissemination of antibiotic resistance genes within the species A. baumannii.
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180
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Complete Genome Sequence of Streptococcus mitis Strain SVGS_061 Isolated from a Neutropenic Patient with Viridans Group Streptococcal Shock Syndrome. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00259-16. [PMID: 27056234 PMCID: PMC4824267 DOI: 10.1128/genomea.00259-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Streptococcus mitisfrequently causes invasive infections in neutropenic cancer patients, with a subset of patients developing viridans group streptococcal (VGS) shock syndrome. We report here the first complete genome sequence ofS. mitisstrain SVGS_061, which caused VGS shock syndrome, to help elucidate the pathogenesis of severe VGS infection.
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181
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Carraro N, Libante V, Morel C, Charron-Bourgoin F, Leblond P, Guédon G. Plasmid-like replication of a minimal streptococcal integrative and conjugative element. MICROBIOLOGY-SGM 2016; 162:622-632. [PMID: 26825653 DOI: 10.1099/mic.0.000219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements encoding their own excision from a replicon of their bacterial host, transfer by conjugation to a recipient bacterium and reintegration for maintenance. The conjugation, recombination and regulation modules of ICEs of the ICESt3 family are grouped together in a region called the ICE 'core region'. In addition to this core region, elements belonging to this family carry a highly variable region including cargo genes that could be involved in bacterial adaptation or in the maintenance of the element. Although ICEs are a major class of mobile elements through bacterial genomes, the functionality of an element encoding only its excision, transfer, integration and regulation has never been demonstrated experimentally. We engineered MiniICESt3, an artificial ICE derived from ICESt3, devoid of its cargo genes and thus only harbouring the core region. The functionality of this minimal element was assessed. MiniICESt3 was found to be able to excise at a rate of 3.1 %, transfer with a frequency of 1.0 × 10- 5 transconjugants per donor cell and stably maintain by site-specific integration into the 3' end of the fda gene, the same as ICESt3. Furthermore, MiniICESt3 was found in ∼10 copies per chromosome, this multicopy state likely contributing to its stability for >100 generations even in the absence of selection. Therefore, although ICEs were primarily assumed to only replicate along with the chromosome, our results uncovered extrachromosomal rolling-circle replicating plasmid-like forms of MiniICESt3.
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Affiliation(s)
- Nicolas Carraro
- INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Virginie Libante
- INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Catherine Morel
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Florence Charron-Bourgoin
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Pierre Leblond
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Gérard Guédon
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
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182
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The Composition of the Cell Envelope Affects Conjugation in Bacillus subtilis. J Bacteriol 2016; 198:1241-9. [PMID: 26833415 DOI: 10.1128/jb.01044-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 01/27/2016] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED Conjugation in bacteria is the contact-dependent transfer of DNA from one cell to another via donor-encoded conjugation machinery. It is a major type of horizontal gene transfer between bacteria. Conjugation of the integrative and conjugative element ICEBs1 into Bacillus subtilis is affected by the composition of phospholipids in the cell membranes of the donor and recipient. We found that reduction (or elimination) of lysyl-phosphatidylglycerol caused by loss of mpr F caused a decrease in conjugation efficiency. Conversely, alterations that caused an increase in lysyl-phosphatidylglycerol, including loss of ugtP or overproduction of mprF, caused an increase in conjugation efficiency. In addition, we found that mutations that alter production of other phospholipids, e.g., loss of clsA and yfnI, also affected conjugation, apparently without substantively altering levels of lysyl-phosphatidylglycerol, indicating that there are multiple pathways by which changes to the cell envelope affect conjugation. We found that the contribution of mprF to conjugation was affected by the chemical environment. Wild-type cells were generally more responsive to addition of anions that enhanced conjugation, whereas mprF mutant cells were more sensitive to combinations of anions that inhibited conjugation at pH 7. Our results indicate that mprF and lysyl-phosphatidylglycerol allow cells to maintain relatively consistent conjugation efficiencies under a variety of ionic conditions. IMPORTANCE Horizontal gene transfer is a driving force in microbial evolution, enabling cells that receive DNA to acquire new genes and phenotypes. Conjugation, the contact-dependent transfer of DNA from a donor to a recipient by a donor-encoded secretion machine, is a prevalent type of horizontal gene transfer. Although critically important, it is not well understood how the recipient influences the success of conjugation. We found that the composition of phospholipids in the membranes of donors and recipients influences the success of transfer of the integrative and conjugative element ICEBs1 in Bacillus subtilis Specifically, the presence of lysyl-phosphatidylglycerol enables relatively constant conjugation efficiencies in a range of diverse chemical environments.
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183
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Identification of protein secretion systems in bacterial genomes. Sci Rep 2016; 6:23080. [PMID: 26979785 PMCID: PMC4793230 DOI: 10.1038/srep23080] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/24/2016] [Indexed: 01/08/2023] Open
Abstract
Bacteria with two cell membranes (diderms) have evolved complex systems for protein secretion. These systems were extensively studied in some model bacteria, but the characterisation of their diversity has lagged behind due to lack of standard annotation tools. We built online and standalone computational tools to accurately predict protein secretion systems and related appendages in bacteria with LPS-containing outer membranes. They consist of models describing the systems’ components and genetic organization to be used with MacSyFinder to search for T1SS-T6SS, T9SS, flagella, Type IV pili and Tad pili. We identified ~10,000 candidate systems in bacterial genomes, where T1SS and T5SS were by far the most abundant and widespread. All these data are made available in a public database. The recently described T6SSiii and T9SS were restricted to Bacteroidetes, and T6SSii to Francisella. The T2SS, T3SS, and T4SS were frequently encoded in single-copy in one locus, whereas most T1SS were encoded in two loci. The secretion systems of diderm Firmicutes were similar to those found in other diderms. Novel systems may remain to be discovered, since some clades of environmental bacteria lacked all known protein secretion systems. Our models can be fully customized, which should facilitate the identification of novel systems.
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184
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The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials. Microbiol Spectr 2016; 3:PLAS-0039-2014. [PMID: 26104702 DOI: 10.1128/microbiolspec.plas-0039-2014] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The phylum Firmicutes is one of the most abundant groups of prokaryotes in the microbiota of humans and animals and includes genera of outstanding relevance in biomedicine, health care, and industry. Antimicrobial drug resistance is now considered a global health security challenge of the 21st century, and this heterogeneous group of microorganisms represents a significant part of this public health issue.The presence of the same resistant genes in unrelated bacterial genera indicates a complex history of genetic interactions. Plasmids have largely contributed to the spread of resistance genes among Staphylococcus, Enterococcus, and Streptococcus species, also influencing the selection and ecological variation of specific populations. However, this information is fragmented and often omits species outside these genera. To date, the antimicrobial resistance problem has been analyzed under a "single centric" perspective ("gene tracking" or "vehicle centric" in "single host-single pathogen" systems) that has greatly delayed the understanding of gene and plasmid dynamics and their role in the evolution of bacterial communities.This work analyzes the dynamics of antimicrobial resistance genes using gene exchange networks; the role of plasmids in the emergence, dissemination, and maintenance of genes encoding resistance to antimicrobials (antibiotics, heavy metals, and biocides); and their influence on the genomic diversity of the main Gram-positive opportunistic pathogens under the light of evolutionary ecology. A revision of the approaches to categorize plasmids in this group of microorganisms is given using the 1,326 fully sequenced plasmids of Gram-positive bacteria available in the GenBank database at the time the article was written.
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185
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Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD, Fraser C. Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict. PLoS Biol 2016; 14:e1002394. [PMID: 26934590 PMCID: PMC4774983 DOI: 10.1371/journal.pbio.1002394] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/29/2016] [Indexed: 01/21/2023] Open
Abstract
Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated.
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Affiliation(s)
- Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Rafal Mostowy
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Christopher Wymant
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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186
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Sapriel G, Konjek J, Orgeur M, Bouri L, Frézal L, Roux AL, Dumas E, Brosch R, Bouchier C, Brisse S, Vandenbogaert M, Thiberge JM, Caro V, Ngeow YF, Tan JL, Herrmann JL, Gaillard JL, Heym B, Wirth T. Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications. BMC Genomics 2016; 17:118. [PMID: 26884275 PMCID: PMC4756508 DOI: 10.1186/s12864-016-2448-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/08/2016] [Indexed: 11/16/2022] Open
Abstract
Background In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB). Results Multilocus sequence typing confirmed the existence of three M. abscessus subspecies, and unravelled extensive allelic exchange between them. Furthermore, an asymmetrical gene flow occurring between these main lineages was detected, resulting in highly admixed strains. Intriguingly, these mosaic strains were significantly associated with cystic fibrosis patients with lung infections or chronic colonization. Genome sequencing of those hybrid strains confirmed that half of their genomic content was remodelled in large genomic blocks, leading to original tri-modal ‘patchwork’ architecture. One of these hybrid strains acquired a locus conferring inducible macrolide resistance, and a large genomic insertion from a slowly growing pathogenic mycobacteria, suggesting an adaptive gene transfer. This atypical genomic architecture of the highly recombinogenic strains is consistent with the distributive conjugal transfer (DCT) observed in M. smegmatis. Intriguingly, no known DCT function was found in M. abscessus chromosome, however, a p-RAW-like genetic element was detected in one of the highly admixed strains. Conclusion Taken together, our results strongly suggest that MAB evolution is sporadically punctuated by dramatic genome wide remodelling events. These findings might have far reaching epidemiological consequences for emerging mycobacterial pathogens survey in the context of increasing numbers of rapidly growing mycobacteria and M. tuberculosis co-infections. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2448-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guillaume Sapriel
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,Laboratoire des Sciences du Climat et de l'Environnement, LSCE, UMR8212, Université de Versailles St. Quentin - CEA - CNRS, Saint-Aubin, France. .,Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, France.
| | - Julie Konjek
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Mickael Orgeur
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France.
| | - Laurent Bouri
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.
| | - Lise Frézal
- Institut of Biology of the Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris, Cedex 05, France.
| | | | - Emilie Dumas
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France.
| | | | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
| | | | | | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
| | - Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Joon Liang Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Jean-Louis Herrmann
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Raymond Poincaré, Service de Microbiologie et Hygiène, Garches, France.
| | - Jean-Louis Gaillard
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Beate Heym
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Thierry Wirth
- Laboratoire de Biologie intégrative des populations, Evolution moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. .,Institut de Systématique, Evolution, Biodiversité, ISYEB, UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 16 rue Buffon, F-75231, Paris, Cedex 05, France.
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187
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Abstract
Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely distributed among virtually all bacterial genera. Recent extensive studies have unraveled their high diversity and complexity. The present review depicts the general conserved features of ICEs and describes more precisely three major families of ICEs that have been extensively studied in the past decade for their biology, their evolution and their impact on genomes dynamics. First, the large SXT/R391 family of ICEs disseminates antibiotic resistance genes and drives the exchange of mobilizable genomic islands (MGIs) between many enteric pathogens such as Vibrio cholerae. Second, ICEBs1 of Bacillus subtilis is the most well understood ICE of Gram-positive bacteria, notably regarding the regulation of its dissemination and its initially unforeseen extrachromosomal replication, which could be a common feature of ICEs of both Gram-positive and Gram-negative bacteria. Finally, ICESt1 and ICESt3 of Streptococcus thermophilus are the prototypes of a large family of ICEs widely distributed among various streptococci. These ICEs carry an original regulation module that associates regulators related to those of both SXT/R391 and ICEBs1. Study of ICESt1 and ICESt3 uncovered the cis-mobilization of related genomic islands (CIMEs) by a mechanism called accretion-mobilization, which likely represents a paradigm for the evolution of many ICEs and genomic islands. These three major families of ICEs give a glimpse about ICEs dynamics and their high impact on bacterial adaptation.
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188
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Huang J, Liang Y, Guo D, Shang K, Ge L, Kashif J, Wang L. Comparative Genomic Analysis of the ICESa2603 Family ICEs and Spread of erm(B)- and tet(O)-Carrying Transferable 89K-Subtype ICEs in Swine and Bovine Isolates in China. Front Microbiol 2016; 7:55. [PMID: 26870017 PMCID: PMC4735348 DOI: 10.3389/fmicb.2016.00055] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
Integrative and conjugative elements (ICEs) of the ICESa2603 family have been isolated from several species of Streptococcus spp.; however, the comparative genomic and evolutionary analyses of these particular ICEs are currently only at their initial stages. By investigating 13 ICEs of the ICESa2603 family and two ICESa2603 family-like ICEs derived from diverse hosts and locations, we have determined that ICEs comprised a backbone of 30 identical syntenic core genes and accessory genes that were restricted to the intergenic sites or the 3′-end of the non-conserved domain of core genes to maintain its function. ICESa2603 family integrase IntICESa2603 specifically recognized a 15-bp att sequence (TTATTTAAGAGTAAC) at the 3′-end of rplL, which was highly conserved in genus Streptococcus. Phylogenetic analyses suggest that extensive recombination/insertion and the occurrence of a hybrid/mosaic in the ICESa2603 family were responsible for the significant increase in ICE diversity, thereby broadening its host range. Approximately 42.5 and 38.1% of the tested Streptococcus suis and Streptococcus agalactiae clinical isolates respectively contained ICESa2603 family Type IV secretion system (T4SS) genes, and 80.5 and 62.5% of which also respectively carried intICESa2603, indicating that ICESa2603 family is widely distributed across these bacteria. Sequencing and conjugation transfer of a novel sequence type ST303 clinical S. suis isolate HB1011 demonstrated that the 89K-subtype ICESsuHB1011 retained its transferrable function, thereby conferring tetracycline and macrolide resistance.
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Affiliation(s)
- Jinhu Huang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Yuan Liang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Dawei Guo
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Kexin Shang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Lin Ge
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Jam Kashif
- Department of Veterinary Pharmacology, Sindh Agricultural University Tandojam, Pakistan
| | - Liping Wang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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189
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Bisch G, Ogier JC, Médigue C, Rouy Z, Vincent S, Tailliez P, Givaudan A, Gaudriault S. Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species. Genome Biol Evol 2016; 8:148-60. [PMID: 26769959 PMCID: PMC4758244 DOI: 10.1093/gbe/evv248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Within Xenorhabdus bovienii species, the X. bovienii CS03 strain (Xb CS03) is nonvirulent when directly injected into lepidopteran insects, and displays a low virulence when associated with its Steinernema symbiont. The genome of Xb CS03 was sequenced and compared with the genome of a virulent strain, X. bovienii SS-2004 (Xb SS-2004). The genome size and content widely differed between the two strains. Indeed, Xb CS03 had a large genome containing several specific loci involved in the inhibition of competitors, including a few NRPS-PKS loci (nonribosomal peptide synthetases and polyketide synthases) producing antimicrobial molecules. Consistently, Xb CS03 had a greater antimicrobial activity than Xb SS-2004. The Xb CS03 strain contained more pseudogenes than Xb SS-2004. Decay of genes involved in the host invasion and exploitation (toxins, invasins, or extracellular enzymes) was particularly important in Xb CS03. This may provide an explanation for the nonvirulence of the strain when injected into an insect host. We suggest that Xb CS03 and Xb SS-2004 followed divergent evolutionary scenarios to cope with their peculiar life cycle. The fitness strategy of Xb CS03 would involve competitor inhibition, whereas Xb SS-2004 would quickly and efficiently kill the insect host. Hence, Xenorhabdus strains would have widely divergent host exploitation strategies, which impact their genome structure.
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Affiliation(s)
- Gaëlle Bisch
- Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Institut National De La Recherche Agronomique, Montpellier Cedex, France Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Université Montpellier, France
| | - Jean-Claude Ogier
- Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Institut National De La Recherche Agronomique, Montpellier Cedex, France Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Université Montpellier, France
| | - Claudine Médigue
- CEA, Genoscope & CNRS-UMR 8030, Laboratoire D'analyse Bioinformatique En Génomique Et Métabolisme, Evry Cedex, France
| | - Zoé Rouy
- CEA, Genoscope & CNRS-UMR 8030, Laboratoire D'analyse Bioinformatique En Génomique Et Métabolisme, Evry Cedex, France
| | - Stéphanie Vincent
- CEA, Genoscope & CNRS-UMR 8030, Laboratoire D'analyse Bioinformatique En Génomique Et Métabolisme, Evry Cedex, France
| | - Patrick Tailliez
- Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Institut National De La Recherche Agronomique, Montpellier Cedex, France Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Université Montpellier, France
| | - Alain Givaudan
- Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Institut National De La Recherche Agronomique, Montpellier Cedex, France Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Université Montpellier, France
| | - Sophie Gaudriault
- Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Institut National De La Recherche Agronomique, Montpellier Cedex, France Diversité, Génomes Et Interactions Microorganismes-Insectes (DGIMI), Université Montpellier, France
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190
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Ambroset C, Coluzzi C, Guédon G, Devignes MD, Loux V, Lacroix T, Payot S, Leblond-Bourget N. New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration. Front Microbiol 2016; 6:1483. [PMID: 26779141 PMCID: PMC4701971 DOI: 10.3389/fmicb.2015.01483] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/08/2015] [Indexed: 12/30/2022] Open
Abstract
Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.
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Affiliation(s)
- Chloé Ambroset
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Charles Coluzzi
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Marie-Dominique Devignes
- Laboratoire Lorrain de Recherche en Informatique et ses Applications, Faculté des Sciences et Technologies, Université de Lorraine, UMR 7503Vandœuvre-lès-Nancy, France; CNRS, Laboratoire Lorrain de Recherche en Informatique et ses Applications, UMR 7503Vandśuvre-lès-Nancy, France
| | - Valentin Loux
- UR 1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique Jouy-en-Josas, France
| | - Thomas Lacroix
- UR 1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique Jouy-en-Josas, France
| | - Sophie Payot
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Nathalie Leblond-Bourget
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
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191
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Genome Analysis of Kingella kingae Strain KWG1 Reveals How a β-Lactamase Gene Inserted in the Chromosome of This Species. Antimicrob Agents Chemother 2015; 60:703-8. [PMID: 26574009 DOI: 10.1128/aac.02192-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/08/2015] [Indexed: 11/20/2022] Open
Abstract
We describe the genome of a penicillinase-producing Kingella kingae strain (KWG1), the first to be isolated in continental Europe, whose bla(TEM-1) gene was, for the first time in this species, found to be chromosomally inserted. The bla(TEM) gene is located in an integrative and conjugative element (ICE) inserted in Met-tRNA and comprising genes that encode resistance to sulfonamides, streptomycin, and tetracycline. This ICE is homologous to resistance-conferring plasmids of K. kingae and other Gram-negative bacteria.
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192
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Carraro N, Burrus V. The dualistic nature of integrative and conjugative elements. Mob Genet Elements 2015; 5:98-102. [PMID: 26942046 PMCID: PMC4755238 DOI: 10.1080/2159256x.2015.1102796] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 09/26/2015] [Indexed: 11/23/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that play a key role in bacterial adaptation. Such elements are found in almost every bacterial genera and species, and often code for adaptive traits conferring selective advantages to their host. ICEs maintain by integrating into and replicating along with a replicon of the host genome. ICEs can propagate by conjugative transfer toward a recipient cell following excision from the replicon as a circular covalently-closed molecule. For a long time, the excised form of ICEs was assumed to be non-replicative. This assumption predicts that excised ICEs are sensitive to loss during cell division, unless they carry stabilization systems such as addiction modules or antibiotic resistance genes. Over the past few years, growing evidence have been presented that support conditional replication of the circular intermediate as an intrinsic feature of ICEs. We recently confirmed this feature in the large family of SXT/R391 ICEs, which thrive in several species of Enterobacteriaceae and Vibrionaceae. Furthermore, we demonstrated that SXT/R391 ICEs encode a functional plasmid-like type II partition system that enhances their stability, such systems being probably encoded by other ICEs. The lifecycle of ICEs is therefore much more complex than initially thought as many ICEs may use plasmid-like features to improve their stability and dissemination.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of Bacterial Molecular Genetics; Département de Biologie; Université de Sherbrooke ; Sherbrooke, Canada
| | - Vincent Burrus
- Laboratory of Bacterial Molecular Genetics; Département de Biologie; Université de Sherbrooke ; Sherbrooke, Canada
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193
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Abstract
Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. Induction of ICE gene expression leads to excision, production of the conserved conjugation machinery (a type IV secretion system), and the potential to transfer DNA to appropriate recipients. ICEs typically contain cargo genes that are not usually related to the ICE life cycle and that confer phenotypes to host cells. We summarize the life cycle and discovery of ICEs, some of the regulatory mechanisms, and how the types of cargo have influenced our view of ICEs. We discuss how ICEs can acquire new cargo genes and describe challenges to the field and various perspectives on ICE biology.
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Affiliation(s)
- Christopher M Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; ,
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194
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Abstract
Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in Escherichia coli for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the E. coli genome.
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195
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Wright LD, Johnson CM, Grossman AD. Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis. PLoS Genet 2015; 11:e1005556. [PMID: 26440206 PMCID: PMC4595007 DOI: 10.1371/journal.pgen.1005556] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/07/2015] [Indexed: 11/24/2022] Open
Abstract
We identified a functional single strand origin of replication (sso) in the integrative and conjugative element ICEBs1 of Bacillus subtilis. Integrative and conjugative elements (ICEs, also known as conjugative transposons) are DNA elements typically found integrated into a bacterial chromosome where they are transmitted to daughter cells by chromosomal replication and cell division. Under certain conditions, ICEs become activated and excise from the host chromosome and can transfer to neighboring cells via the element-encoded conjugation machinery. Activated ICEBs1 undergoes autonomous rolling circle replication that is needed for the maintenance of the excised element in growing and dividing cells. Rolling circle replication, used by many plasmids and phages, generates single-stranded DNA (ssDNA). In many cases, the presence of an sso enhances the conversion of the ssDNA to double-stranded DNA (dsDNA) by enabling priming of synthesis of the second DNA strand. We initially identified sso1 in ICEBs1 based on sequence similarity to the sso of an RCR plasmid. Several functional assays confirmed Sso activity. Genetic analyses indicated that ICEBs1 uses sso1 and at least one other region for second strand DNA synthesis. We found that Sso activity was important for two key aspects of the ICEBs1 lifecycle: 1) maintenance of the plasmid form of ICEBs1 in cells after excision from the chromosome, and 2) stable acquisition of ICEBs1 following transfer to a new host. We identified sequences similar to known plasmid sso's in several other ICEs. Together, our results indicate that many other ICEs contain at least one single strand origin of replication, that these ICEs likely undergo autonomous replication, and that replication contributes to the stability and spread of these elements. Mobile genetic elements facilitate movement of genes, including those conferring antibiotic resistance and other traits, between bacteria. Integrative and conjugative elements (ICEs) are a large family of mobile genetic elements that are typically found integrated in the chromosome of their host bacterium. Under certain conditions (e.g., DNA damage, high cell density, stationary phase) an ICE excises from the host chromosome to form a circle. A linear single strand of ICE DNA can be transferred to an appropriate recipient through the ICE-encoded conjugation machinery. In addition, following excision from the chromosome, at least some (perhaps most) ICEs undergo autonomous rolling circle replication, a mechanism used by many plasmids and phages. Rolling circle replication generates single-stranded DNA (ssDNA). We found that ICEBs1, from Bacillus subtilis, contains at least two regions that enable conversion of ssDNA to double-stranded DNA. At least one of these regions functions as an sso (single strand origin of replication). ICEBs1 Sso activity was important for the ability of transferred ICEBs1 to be acquired by recipients and for the ability of ICEBs1 to replicate autonomously after excising from its host’s chromosome. We identified putative sso's in several other ICEs, indicating that Sso activity is likely important for the replication, stability and spread of these elements.
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Affiliation(s)
- Laurel D. Wright
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Christopher M. Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Alan D. Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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196
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Abstract
Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic resistance genes among human pathogens. Antibiotic resistance spread could be halted or diminished by molecules that interfere with the conjugation process. In this work, synthetic 2-alkynoic fatty acids were identified as a novel class of conjugation inhibitors. Their chemical properties were investigated by using the prototype 2-hexadecynoic acid and its derivatives. Essential features of effective inhibitors were the carboxylic group, an optimal long aliphatic chain of 16 carbon atoms, and one unsaturation. Chemical modification of these groups led to inactive or less-active derivatives. Conjugation inhibitors were found to act on the donor cell, affecting a wide number of pathogenic bacterial hosts, including Escherichia, Salmonella, Pseudomonas, and Acinetobacter spp. Conjugation inhibitors were active in inhibiting transfer of IncF, IncW, and IncH plasmids, moderately active against IncI, IncL/M, and IncX plasmids, and inactive against IncP and IncN plasmids. Importantly, the use of 2-hexadecynoic acid avoided the spread of a derepressed IncF plasmid into a recipient population, demonstrating the feasibility of abolishing the dissemination of antimicrobial resistances by blocking bacterial conjugation. Diseases caused by multidrug-resistant bacteria are taking an important toll with respect to human morbidity and mortality. The most relevant antibiotic resistance genes come to human pathogens carried by plasmids, mainly using conjugation as a transmission mechanism. Here, we identified and characterized a series of compounds that were active against several plasmid groups of clinical relevance, in a wide variety of bacterial hosts. These inhibitors might be used for fighting antibiotic-resistance dissemination by inhibiting conjugation. Potential inhibitors could be used in specific settings (e.g., farm, fish factory, or even clinical settings) to investigate their effect in the eradication of undesired resistances.
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197
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Poulin-Laprade D, Carraro N, Burrus V. The extended regulatory networks of SXT/R391 integrative and conjugative elements and IncA/C conjugative plasmids. Front Microbiol 2015; 6:837. [PMID: 26347724 PMCID: PMC4542580 DOI: 10.3389/fmicb.2015.00837] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/31/2015] [Indexed: 12/14/2022] Open
Abstract
Nowadays, healthcare systems are challenged by a major worldwide drug resistance crisis caused by the massive and rapid dissemination of antibiotic resistance genes and associated emergence of multidrug resistant pathogenic bacteria, in both clinical and environmental settings. Conjugation is the main driving force of gene transfer among microorganisms. This mechanism of horizontal gene transfer mediates the translocation of large DNA fragments between two bacterial cells in direct contact. Integrative and conjugative elements (ICEs) of the SXT/R391 family (SRIs) and IncA/C conjugative plasmids (ACPs) are responsible for the dissemination of a broad spectrum of antibiotic resistance genes among diverse species of Enterobacteriaceae and Vibrionaceae. The biology, diversity, prevalence and distribution of these two families of conjugative elements have been the subject of extensive studies for the past 15 years. Recently, the transcriptional regulators that govern their dissemination through the expression of ICE- or plasmid-encoded transfer genes have been described. Unrelated repressors control the activation of conjugation by preventing the expression of two related master activator complexes in both types of elements, i.e., SetCD in SXT/R391 ICEs and AcaCD in IncA/C plasmids. Finally, in addition to activating ICE- or plasmid-borne genes, these master activators have been shown to specifically activate phylogenetically unrelated mobilizable genomic islands (MGIs) that also disseminate antibiotic resistance genes and other adaptive traits among a plethora of pathogens such as Vibrio cholerae and Salmonella enterica.
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Affiliation(s)
- Dominic Poulin-Laprade
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke , Sherbrooke, QC, Canada
| | - Nicolas Carraro
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke , Sherbrooke, QC, Canada
| | - Vincent Burrus
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke , Sherbrooke, QC, Canada
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198
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Kingston AW, Roussel-Rossin C, Dupont C, Raleigh EA. Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12. PLoS One 2015; 10:e0130813. [PMID: 26162088 PMCID: PMC4498929 DOI: 10.1371/journal.pone.0130813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/27/2015] [Indexed: 01/19/2023] Open
Abstract
In bacteria, mechanisms that incorporate DNA into a genome without strand-transfer proteins such as RecA play a major role in generating novelty by horizontal gene transfer. We describe a new illegitimate recombination event in Escherichia coli K-12: RecA-independent homologous replacements, with very large (megabase-length) donor patches replacing recipient DNA. A previously uncharacterized gene (yjiP) increases the frequency of RecA-independent replacement recombination. To show this, we used conjugal DNA transfer, combining a classical conjugation donor, HfrH, with modern genome engineering methods and whole genome sequencing analysis to enable interrogation of genetic dependence of integration mechanisms and characterization of recombination products. As in classical experiments, genomic DNA transfer begins at a unique position in the donor, entering the recipient via conjugation; antibiotic resistance markers are then used to select recombinant progeny. Different configurations of this system were used to compare known mechanisms for stable DNA incorporation, including homologous recombination, F'-plasmid formation, and genome duplication. A genome island of interest known as the immigration control region was specifically replaced in a minority of recombinants, at a frequency of 3 X 10(-12) CFU/recipient per hour.
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Affiliation(s)
- Anthony W. Kingston
- New England Biolabs, Ipswich, Massachusetts, 01938, United States of America
| | | | - Claire Dupont
- New England Biolabs, Ipswich, Massachusetts, 01938, United States of America
| | - Elisabeth A. Raleigh
- New England Biolabs, Ipswich, Massachusetts, 01938, United States of America
- * E-mail:
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199
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Carraro N, Poulin D, Burrus V. Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner. PLoS Genet 2015; 11:e1005298. [PMID: 26061412 PMCID: PMC4489591 DOI: 10.1371/journal.pgen.1005298] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/23/2015] [Indexed: 02/07/2023] Open
Abstract
Integrative and Conjugative Elements (ICEs) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae. SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugation. Conjugative transfer of SXT/R391 ICEs involves a transient extrachromosomal circular plasmid-like form that is thought to be the substrate for single-stranded DNA translocation to the recipient cell through the mating pore. This plasmid-like form is thought to be non-replicative and is consequently expected to be highly unstable. We report here that the ICE R391 of Providencia rettgeri is impervious to loss upon cell division. We have investigated the genetic determinants contributing to R391 stability. First, we found that a hipAB-like toxin/antitoxin system improves R391 stability as its deletion resulted in a tenfold increase of R391 loss. Because hipAB is not a conserved feature of SXT/R391 ICEs, we sought for alternative and conserved stabilization mechanisms. We found that conjugation itself does not stabilize R391 as deletion of traG, which abolishes conjugative transfer, did not influence the frequency of loss. However, deletion of either the relaxase-encoding gene traI or the origin of transfer (oriT) led to a dramatic increase of R391 loss correlated with a copy number decrease of its plasmid-like form. This observation suggests that replication initiated at oriT by TraI is essential not only for conjugative transfer but also for stabilization of SXT/R391 ICEs. Finally, we uncovered srpMRC, a conserved locus coding for two proteins distantly related to the type II (actin-type ATPase) parMRC partitioning system of plasmid R1. R391 and plasmid stabilization assays demonstrate that srpMRC is active and contributes to reducing R391 loss. While partitioning systems usually stabilizes low-copy plasmids, srpMRC is the first to be reported that stabilizes a family of ICEs.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Poulin
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
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200
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Abstract
UNLABELLED Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells. Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions. IMPORTANCE Plasmids and other episomes are an integral part of bacterial biology in all environments, yet their study is heavily biased toward their role as vectors for antibiotic resistance genes. This study presents a comprehensive analysis of all episomes within several coexisting bacterial populations of Vibrionaceae from the coastal ocean and represents the largest-yet genomic survey of episomes from a single bacterial family. The host population framework allows analysis of the eco-evolutionary dynamics at unprecedented resolution, yielding several unexpected results. These include (i) discovery of novel, nonintegrative temperate phages, (ii) revision of a class of episomes, previously termed "nontransmissible," as highly transmissible, and (iii) surprisingly high evolutionary turnover of episomes, manifest as frequent birth, spread, and loss.
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