151
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Cabezón E, Ripoll-Rozada J, Peña A, de la Cruz F, Arechaga I. Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev 2014; 39:81-95. [PMID: 25154632 DOI: 10.1111/1574-6976.12085] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial conjugation is one of the main mechanisms for horizontal gene transfer. It constitutes a key element in the dissemination of antibiotic resistance and virulence genes to human pathogenic bacteria. DNA transfer is mediated by a membrane-associated macromolecular machinery called Type IV secretion system (T4SS). T4SSs are involved not only in bacterial conjugation but also in the transport of virulence factors by pathogenic bacteria. Thus, the search for specific inhibitors of different T4SS components opens a novel approach to restrict plasmid dissemination. This review highlights recent biochemical and structural findings that shed new light on the molecular mechanisms of DNA and protein transport by T4SS. Based on these data, a model for pilus biogenesis and substrate transfer in conjugative systems is proposed. This model provides a renewed view of the mechanism that might help to envisage new strategies to curb the threating expansion of antibiotic resistance.
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Affiliation(s)
- Elena Cabezón
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
| | - Jorge Ripoll-Rozada
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
| | - Alejandro Peña
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
| | - Ignacio Arechaga
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
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152
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Abstract
Plasmid-encoded virulence factors are important in the pathogenesis of diseases caused by spore-forming bacteria. Unlike many other bacteria, the most common virulence factors encoded by plasmids in Clostridium and Bacillus species are protein toxins. Clostridium perfringens causes several histotoxic and enterotoxin diseases in both humans and animals and produces a broad range of toxins, including many pore-forming toxins such as C. perfringens enterotoxin, epsilon-toxin, beta-toxin, and NetB. Genetic studies have led to the determination of the role of these toxins in disease pathogenesis. The genes for these toxins are generally carried on large conjugative plasmids that have common core replication, maintenance, and conjugation regions. There is considerable functional information available about the unique tcp conjugation locus carried by these plasmids, but less is known about plasmid maintenance. The latter is intriguing because many C. perfringens isolates stably maintain up to four different, but closely related, toxin plasmids. Toxin genes may also be plasmid-encoded in the neurotoxic clostridia. The tetanus toxin gene is located on a plasmid in Clostridium tetani, but the botulinum toxin genes may be chromosomal, plasmid-determined, or located on bacteriophages in Clostridium botulinum. In Bacillus anthracis it is well established that virulence is plasmid determined, with anthrax toxin genes located on pXO1 and capsule genes on a separate plasmid, pXO2. Orthologs of these plasmids are also found in other members of the Bacillus cereus group such as B. cereus and Bacillus thuringiensis. In B. thuringiensis these plasmids may carry genes encoding one or more insecticidal toxins.
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153
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Garcillán-Barcia MP, Ruiz del Castillo B, Alvarado A, de la Cruz F, Martínez-Martínez L. Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones. Plasmid 2014; 77:17-27. [PMID: 25463772 DOI: 10.1016/j.plasmid.2014.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/08/2014] [Accepted: 11/17/2014] [Indexed: 11/25/2022]
Abstract
Degenerate Primer MOB Typing is a PCR-based protocol for the classification of γ-proteobacterial transmissible plasmids in five phylogenetic relaxase MOB families. It was applied to a multiresistant E. coli collection, previously characterized by PCR-based replicon-typing, in order to compare both methods. Plasmids from 32 clinical isolates of multiresistant E. coli (19 extended spectrum beta-lactamase producers and 13 non producers) and their transconjugants were analyzed. A total of 95 relaxases were detected, at least one per isolate, underscoring the high potential of these strains for antibiotic-resistance transmission. MOBP12 and MOBF12 plasmids were the most abundant. Most MOB subfamilies detected were present in both subsets of the collection, indicating a shared mobilome among multiresistant E. coli. The plasmid profile obtained by both methods was compared, which provided useful data upon which decisions related to the implementation of detection methods in the clinic could be based. The phylogenetic depth at which replicon and MOB-typing classify plasmids is different. While replicon-typing aims at plasmid replication regions with non-degenerate primers, MOB-typing classifies plasmids into relaxase subfamilies using degenerate primers. As a result, MOB-typing provides a deeper phylogenetic depth than replicon-typing and new plasmid groups are uncovered. Significantly, MOB typing identified 17 plasmids and an integrative and conjugative element, which were not detected by replicon-typing. Four of these backbones were different from previously reported elements.
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Affiliation(s)
- M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, España.
| | - Belén Ruiz del Castillo
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla y Fundación Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, España
| | - Andrés Alvarado
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, España
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, España
| | - Luis Martínez-Martínez
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla y Fundación Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, España; Departamento de Biología Molecular, Universidad de Cantabria, Santander, España
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154
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Abstract
ABSTRACT
Whole-genome sequencing is revolutionizing the analysis of bacterial genomes. It leads to a massive increase in the amount of available data to be analyzed. Bacterial genomes are usually composed of one main chromosome and a number of accessory chromosomes, called plasmids. A recently developed methodology called PLACNET (for
pla
smid
c
onstellation
net
works) allows the reconstruction of the plasmids of a given genome. Thus, it opens an avenue for plasmidome analysis on a global scale. This work reviews our knowledge of the genetic determinants for plasmid propagation (conjugation and related functions), their diversity, and their prevalence in the variety of plasmids found by whole-genome sequencing. It focuses on the results obtained from a collection of 255
Escherichia coli
plasmids reconstructed by PLACNET. The plasmids found in
E. coli
represent a nonaleatory subset of the plasmids found in proteobacteria. Potential reasons for the prevalence of some specific plasmid groups will be discussed and, more importantly, additional questions will be posed.
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155
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Miyazaki R, van der Meer JR. How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element? Mob Genet Elements 2014; 1:82-84. [PMID: 22016851 DOI: 10.4161/mge.1.1.15744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 11/19/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are particularly interesting model systems for horizontal gene transfer, because they normally reside in an integrated state in the host chromosome but can excise and self-transfer under particular conditions, typically requiring exquisite regulatory cascades. Despite important advances in our understanding of the transfer mechanisms of a number of ICE, many essential details are lacking. Recently we reported that ICEclc, a 103 kb ICE of Pseudomonas knackmussii B13, has two active origins of transfer (oriTs), which is very much unlike conjugative plasmids that usually employ a single oriT. We discuss here how this dual oriT system could function and how it actually could have presented an evolutionary advantage for ICEclc distribution.
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Affiliation(s)
- Ryo Miyazaki
- Department of Fundamental Microbiology; University of Lausanne; Bâtiment Biophore; Quartier UNIL-Sorge; Lausanne, Switzerland
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156
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Bordeleau E, Ghinet MG, Burrus V. Diversity of integrating conjugative elements in actinobacteria: Coexistence of two mechanistically different DNA-translocation systems. Mob Genet Elements 2014; 2:119-124. [PMID: 22934248 PMCID: PMC3429521 DOI: 10.4161/mge.20498] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Conjugation is certainly the most widespread and promiscuous mechanism of horizontal gene transfer in bacteria. During conjugation, DNA translocation across membranes of two cells forming a mating pair is mediated by two types of mobile genetic elements: conjugative plasmids and integrating conjugative elements (ICEs). The vast majority of conjugative plasmids and ICEs employ a sophisticated protein secretion apparatus called type IV secretion system to transfer to a recipient cell. Yet another type of conjugative DNA translocation machinery exists and to date appears to be unique to conjugative plasmids and ICEs of the Actinomycetales order, a sub-group of high G + C Gram-positive bacteria. This conjugative system is reminiscent of the machinery that allows segregation of chromosomal DNA during bacterial cell division and sporulation, and relies on a single FtsK-homolog protein to translocate double-stranded DNA molecules to the recipient cell. Recent thorough sequence analyses reveal that while this latter strategy appears to be used by the majority of ICEs in Actinomycetales, the former is also predicted to be important in exchange of genetic material in actinobacteria.
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Affiliation(s)
- Eric Bordeleau
- Département de biologie; Faculté des sciences; Université de Sherbrooke; QC, Canada
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157
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Maindola P, Raina R, Goyal P, Atmakuri K, Ojha A, Gupta S, Christie PJ, Iyer LM, Aravind L, Arockiasamy A. Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids. Nat Commun 2014; 5:5322. [PMID: 25358815 PMCID: PMC4241021 DOI: 10.1038/ncomms6322] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/19/2014] [Indexed: 02/06/2023] Open
Abstract
Conjugative plasmids are typically locked in intergenomic and sexual conflicts with coresident rivals, whose translocation they block using fertility inhibition factors (FINs). We describe here the first crystal structure of an enigmatic FIN Osa deployed by the proteobacterial plasmid pSa. Osa contains a catalytically active version of the ParB/Sulfiredoxin fold with both ATPase and DNase activity, the latter being regulated by an ATP-dependent switch. Using the Agrobacterium tumefaciens VirB/D4 type-IV secretion system (T4SS), a relative of the conjugative T4SS, we demonstrate that catalytically active Osa blocks T-DNA transfer into plants. With a partially reconstituted T4SS in vitro, we show that Osa degrades T-DNA in the T-DNA-VirD2 complex prior to its translocation. Further, we present evidence for conservation and interplay between ATPase and DNase activities throughout the ParB/Sulfiredoxin fold, using other members of the family, namely P1 ParB and RK2 KorB, which have general functional implications across diverse biological contexts.
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Affiliation(s)
- Priyank Maindola
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Rahul Raina
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Parveen Goyal
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Krishnamohan Atmakuri
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, USA
| | - Abhishek Ojha
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sourabh Gupta
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894-6075, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894-6075, USA
| | - Arulandu Arockiasamy
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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158
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Rahube TO, Viana LS, Koraimann G, Yost CK. Characterization and comparative analysis of antibiotic resistance plasmids isolated from a wastewater treatment plant. Front Microbiol 2014; 5:558. [PMID: 25389419 PMCID: PMC4211555 DOI: 10.3389/fmicb.2014.00558] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/06/2014] [Indexed: 11/13/2022] Open
Abstract
A wastewater treatment plant (WWTP) is an environment high in nutrient concentration with diverse bacterial populations and can provide an ideal environment for the proliferation of mobile elements such as plasmids. WWTPs have also been identified as reservoirs for antibiotic resistance genes that are associated with human pathogens. The objectives of this study were to isolate and characterize self-transmissible or mobilizable resistance plasmids associated with effluent from WWTP. An enrichment culture approach designed to capture plasmids conferring resistance to high concentrations of erythromycin was used to capture plasmids from an urban WWTP servicing a population of ca. 210,000. DNA sequencing of the plasmids revealed diversity of plasmids represented by incompatibility groups IncU, col-E, IncFII and IncP-1β. Genes coding resistance to clinically relevant antibiotics (macrolide, tetracycline, beta-lactam, trimethoprim, chloramphenicol, sulphonamide), quaternary ammonium compounds and heavy metals were co-located on these plasmids, often within transposable and integrative mobile elements. Several of the plasmids were self-transmissible or mobilizable and could be maintained in the absence of antibiotic selection. The IncFII plasmid pEFC36a showed the highest degree of sequence identity to plasmid R1 which has been isolated in England more than 50 years ago from a patient suffering from a Salmonella infection. Functional conservation of key regulatory features of this F-like conjugation module were demonstrated by the finding that the conjugation frequency of pEFC36a could be stimulated by the positive regulator of plasmid R1 DNA transfer genes, TraJ.
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Affiliation(s)
- Teddie O Rahube
- Department of Biology, University of Regina Regina, SK, Canada ; Department of Biology and Biotechnological Sciences, Botswana International University of Science and Technology Palapye, Botswana
| | - Laia S Viana
- Institute of Molecular Biosciences, University of Graz Graz, Austria
| | - Günther Koraimann
- Institute of Molecular Biosciences, University of Graz Graz, Austria
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159
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Garcillán-Barcia MP, de la Cruz F. Ordering the bestiary of genetic elements transmissible by conjugation. Mob Genet Elements 2014; 3:e24263. [PMID: 23734300 PMCID: PMC3661145 DOI: 10.4161/mge.24263] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic reconstruction of three highly conserved proteins involved in bacterial conjugation (relaxase, coupling protein and a type IV secretion system ATPase) allowed the classification of transmissible elements in relaxase MOB families and mating pair formation MPF groups. These evolutionary studies point to the existence of a limited number of module combinations in transmissible elements, preferentially associated with specific genetic or environmental backgrounds. A practical protocol based on the MOB classification was implemented to detect and assort transmissible plasmids and integrative elements from γ-Proteobacteria. It was called “Degenerate Primer MOB Typing” or DPMT. It resulted in a powerful technique that discovers not only backbones related to previously classified elements (typically by PCR-based replicon typing or PBRT), but also distant new members sharing a common evolutionary ancestor. The DPMT method, conjointly with PBRT, promises to be useful to gain information on plasmid backbones and helpful to investigate the dissemination routes of transmissible elements in microbial ecosystems.
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Affiliation(s)
- Maria Pilar Garcillán-Barcia
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC); Universidad de Cantabria-CSIC-SODERCAN; Santander, Cantabria Spain
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160
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Noncanonical cell-to-cell DNA transfer in Thermus spp. is insensitive to argonaute-mediated interference. J Bacteriol 2014; 197:138-46. [PMID: 25331432 DOI: 10.1128/jb.02113-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Horizontal gene transfer drives the rapid evolution of bacterial populations. Classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. However, some species have nonconserved transfer mechanisms that are not well known. This is the case for the ancient extreme thermophile Thermus thermophilus. In this work, we show that T. thermophilus strains are capable of exchanging large DNA fragments by a novel mechanism that requires cell-to-cell contacts and employs components of the natural transformation machinery. This process facilitates the bidirectional transfer of virtually any DNA locus but favors by 10-fold loci found in the megaplasmid over those in the chromosome. In contrast to naked DNA acquisition by transformation, the system does not activate the recently described DNA-DNA interference mechanism mediated by the prokaryotic Argonaute protein, thus allowing the organism to distinguish between DNA transferred from a mate and exogenous DNA acquired from unknown hosts. This Argonaute-mediated discrimination may be tentatively viewed as a strategy for safe sharing of potentially "useful" traits by the components of a given population of Thermus spp. without increasing the genome sizes of its individuals.
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161
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Freedman JC, Theoret JR, Wisniewski JA, Uzal FA, Rood JI, McClane BA. Clostridium perfringens type A-E toxin plasmids. Res Microbiol 2014; 166:264-79. [PMID: 25283728 DOI: 10.1016/j.resmic.2014.09.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/04/2014] [Accepted: 09/09/2014] [Indexed: 12/26/2022]
Abstract
Clostridium perfringens relies upon plasmid-encoded toxin genes to cause intestinal infections. These toxin genes are associated with insertion sequences that may facilitate their mobilization and transfer, giving rise to new toxin plasmids with common backbones. Most toxin plasmids carry a transfer of clostridial plasmids locus mediating conjugation, which likely explains the presence of similar toxin plasmids in otherwise unrelated C. perfringens strains. The association of many toxin genes with insertion sequences and conjugative plasmids provides virulence flexibility when causing intestinal infections. However, incompatibility issues apparently limit the number of toxin plasmids maintained by a single cell.
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Affiliation(s)
- John C Freedman
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James R Theoret
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Francisco A Uzal
- California Animal Health and Food Safety Laboratory, San Bernadino Branch, School of Veterinary Medicine, University of California-Davis, San Bernadino, CA, USA
| | - Julian I Rood
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Bruce A McClane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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162
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Mobilizable Rolling-Circle Replicating Plasmids from Gram-Positive Bacteria: A Low-Cost Conjugative Transfer. Microbiol Spectr 2014; 2:8. [PMID: 25606350 DOI: 10.1128/microbiolspec.plas-0008-2013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Conjugation is a key mechanism for horizontal gene transfer in bacteria. Some plasmids are not self-transmissible but can be mobilized by functions encoded in trans provided by other auxiliary conjugative elements. Although the transfer efficiency of mobilizable plasmids is usually lower than that of conjugative elements, mobilizable plasmidsare more frequently found in nature. In this sense, replication and mobilization can be considered as important mechanisms influencing plasmid promiscuity. Here we review the present available information on two families of small mobilizable plasmids from Gram-positive bacteria that replicate via the rolling-circle mechanism. One of these families, represented by the streptococcal plasmid pMV158, is an interesting model since it contains a specific mobilization module (MOBV) that is widely distributed among mobilizable plasmids. We discuss a mechanism in which the promiscuity of the pMV158 replicon is based on the presence of two origins of lagging strand synthesis. The current strategies to assess plasmid transfer efficiency as well as to inhibit conjugative plasmid transfer are presented. Some applications of these plasmids as biotechnological tools are also reviewed.
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163
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Godziszewska J, Kulińska A, Jagura-Burdzy G. MobC of conjugative RA3 plasmid from IncU group autoregulates the expression of bicistronic mobC-nic operon and stimulates conjugative transfer. BMC Microbiol 2014; 14:235. [PMID: 25187417 PMCID: PMC4175270 DOI: 10.1186/s12866-014-0235-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/19/2014] [Indexed: 11/28/2022] Open
Abstract
Background The IncU conjugative transfer module represents highly efficient promiscuous system widespread among conjugative plasmids of different incompatibility groups. Despite its frequent occurrence the mechanisms of relaxosome formation/action are far from understood. Here we analyzed the putative transfer auxiliary protein MobC of the conjugative plasmid RA3 from the IncU incompatibility group. Results MobC is a protein of 176 amino acids encoded in the bicistronic operon mobC-nic adjacent to oriT. MobC is homologous to prokaryotic transcription factors of the ribbon-helix-helix (RHH) superfamily. Conserved LxxugxNlNQiaxxLn motif clusters MobC with the clade of conjugative transfer auxilliary proteins of MobP relaxases. MobC forms dimers in solution and autoregulates the expression of mobCp by binding to an imperfect palindromic sequence (OM) located between putative -35 and -10 motifs of the promoter. Medium-copy number test plasmid containing the oriT-mobCp region is mobilized with a high frequency by the RA3 conjugative system. The mutations introduced into OM that abolished MobC binding in vitro decreased 2-3 fold the frequency of mobilization of the test plasmids. The deletion of OM within the RA3 conjugative module had no effect on transfer if the mobC-nic operon was expressed from the heterologous promoter. If only nic was expressed from the heterologous promoter (no mobC) the conjugative transfer frequency of such plasmid was 1000-fold lower. Conclusion The MobC is an auxiliary transfer protein of dual function. It autoregulates the expression of mobC-nic operon while its presence significantly stimulates transfer efficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0235-1) contains supplementary material, which is available to authorized users.
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164
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Goessweiner-Mohr N, Eder M, Hofer G, Fercher C, Arends K, Birner-Gruenberger R, Grohmann E, Keller W. Structure of the double-stranded DNA-binding type IV secretion protein TraN from Enterococcus. ACTA ACUST UNITED AC 2014; 70:2376-89. [PMID: 25195751 DOI: 10.1107/s1399004714014187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/17/2014] [Indexed: 11/10/2022]
Abstract
Conjugative transfer through type IV secretion multiprotein complexes is the most important means of spreading antimicrobial resistance. Plasmid pIP501, frequently found in clinical Enterococcus faecalis and Enterococcus faecium isolates, is the first Gram-positive (G+) conjugative plasmid for which self-transfer to Gram-negative (G-) bacteria has been demonstrated. The pIP501-encoded type IV secretion system (T4SS) protein TraN localizes to the cytoplasm and shows specific DNA binding. The specific DNA-binding site upstream of the pIP501 origin of transfer (oriT) was identified by a novel footprinting technique based on exonuclease digestion and sequencing, suggesting TraN to be an accessory protein of the pIP501 relaxase TraA. The structure of TraN was determined to 1.35 Å resolution. It revealed an internal dimer fold with antiparallel β-sheets in the centre and a helix-turn-helix (HTH) motif at both ends. Surprisingly, structurally related proteins (excisionases from T4SSs of G+ conjugative transposons and transcriptional regulators of the MerR family) resembling only one half of TraN were found. Thus, TraN may be involved in the early steps of pIP501 transfer, possibly triggering pIP501 TraA relaxase activity by recruiting the relaxosome to the assembled mating pore.
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Affiliation(s)
| | - Markus Eder
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Gerhard Hofer
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Christian Fercher
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Karsten Arends
- Robert Koch Institute Berlin, Nordufer 20, 13353 Berlin, Germany
| | - Ruth Birner-Gruenberger
- Institute for Pathology and Omics Center Graz, Medical University Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Walter Keller
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
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165
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Carballeira JD, González-Pérez B, Moncalián G, de la Cruz F. A high security double lock and key mechanism in HUH relaxases controls oriT-processing for plasmid conjugation. Nucleic Acids Res 2014; 42:10632-43. [PMID: 25123661 PMCID: PMC4176350 DOI: 10.1093/nar/gku741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Relaxases act as DNA selection sieves in conjugative plasmid transfer. Most plasmid relaxases belong to the HUH endonuclease family. TrwC, the relaxase of plasmid R388, is the prototype of the HUH relaxase family, which also includes TraI of plasmid F. In this article we demonstrate that TrwC processes its target nic-site by means of a highly secure double lock and key mechanism. It is controlled both by TrwC–DNA intermolecular interactions and by intramolecular DNA interactions between several nic nucleotides. The sequence specificity map of the interaction between TrwC and DNA was determined by systematic mutagenesis using degenerate oligonucleotide libraries. The specificity map reveals the minimal nic sequence requirements for R388-based conjugation. Some nic-site sequence variants were still able to form the U-turn shape at the nic-site necessary for TrwC processing, as observed by X-ray crystallography. Moreover, purified TrwC relaxase effectively cleaved ssDNA as well as dsDNA substrates containing these mutant sequences. Since TrwC is able to catalyze DNA integration in a nic-site-containing DNA molecule, characterization of nic-site functionally active sequence variants should improve the search quality of potential target sequences for relaxase-mediated integration in any target genome.
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Affiliation(s)
- José Daniel Carballeira
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011 Santander, Spain
| | - Blanca González-Pérez
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011 Santander, Spain
| | - Gabriel Moncalián
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011 Santander, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011 Santander, Spain
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166
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Juhas M. Type IV secretion systems and genomic islands-mediated horizontal gene transfer in Pseudomonas and Haemophilus. Microbiol Res 2014; 170:10-7. [PMID: 25183653 DOI: 10.1016/j.micres.2014.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/28/2014] [Accepted: 06/30/2014] [Indexed: 11/16/2022]
Abstract
Bacterial secretion systems, such as type IV secretion systems (T4SSs) are multi-subunit machines transferring macromolecules across membranes. Besides proteins, T4SSs also transfer nucleoprotein complexes, thus having a significant impact on the evolution of bacterial species. By T4SS-mediated horizontal gene transfer bacteria can acquire a broad spectrum of fitness genes allowing them to thrive in the wide variety of environments. Furthermore, acquisition of antibiotic-resistance and virulence genes can lead to the emergence of novel 'superbugs'. This review provides an update on the investigation of T4SSs. It highlights the role T4SSs play in the horizontal gene transfer, particularly in the evolution of catabolic pathways, antibiotic-resistance and virulence in Haemophilus and Pseudomonas.
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Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP Cambridge, UK.
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167
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Bellanger X, Payot S, Leblond-Bourget N, Guédon G. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev 2014; 38:720-60. [DOI: 10.1111/1574-6976.12058] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/15/2013] [Accepted: 12/19/2013] [Indexed: 11/28/2022] Open
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168
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Lorenzo-Díaz F, Fernández-López C, Garcillán-Barcia MP, Espinosa M. Bringing them together: plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective. Plasmid 2014; 74:15-31. [PMID: 24942190 PMCID: PMC7103276 DOI: 10.1016/j.plasmid.2014.05.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 11/29/2022]
Abstract
Rolling circle-replicating plasmids constitute a vast family that is particularly abundant in, but not exclusive of, Gram-positive bacteria. These plasmids are constructed as cassettes that harbor genes involved in replication and its control, mobilization, resistance determinants and one or two origins of lagging strand synthesis. Any given plasmid may contain all, some, or just only the replication cassette. We discuss here the family of the promiscuous streptococcal plasmid pMV158, with emphasis on its mobilization functions: the product of the mobM gene, prototype of the MOBV relaxase family, and its cognate origin of transfer, oriT. Amongst the subfamily of MOBV1 plasmids, three groups of oriT sequences, represented by plasmids pMV158, pT181, and p1414 were identified. In the same subfamily, we found four types of single-strand origins, namely ssoA, ssoU, ssoW, and ssoT. We found that plasmids of the rolling-circle Rep_2 family (to which pMV158 belongs) are more frequently found in Lactobacillales than in any other bacterial order, whereas Rep_1 initiators seemed to prefer hosts included in the Bacillales order. In parallel, MOBV1 relaxases associated with Rep_2 initiators tended to cluster separately from those linked to Rep_1 plasmids. The updated inventory of MOBV1 plasmids still contains exclusively mobilizable elements, since no genes associated with conjugative transfer (other than the relaxase) were detected. These plasmids proved to have a great plasticity at using a wide variety of conjugative apparatuses. The promiscuous recognition of non-cognate oriT sequences and the role of replication origins for lagging-strand origin in the host range of these plasmids are also discussed.
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Affiliation(s)
- Fabián Lorenzo-Díaz
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria and Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Centro de Investigaciones Biomédicas de Canarias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
| | - Cris Fernández-López
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, E-28040 Madrid, Spain.
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria - CSIC-SODERCAN, Santander, Cantabria, Spain.
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, E-28040 Madrid, Spain.
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169
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Unique helicase determinants in the essential conjugative TraI factor from Salmonella enterica serovar Typhimurium plasmid pCU1. J Bacteriol 2014; 196:3082-90. [PMID: 24936053 DOI: 10.1128/jb.01496-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The widespread development of multidrug-resistant bacteria is a major health emergency. Conjugative DNA plasmids, which harbor a wide range of antibiotic resistance genes, also encode the protein factors necessary to orchestrate the propagation of plasmid DNA between bacterial cells through conjugative transfer. Successful conjugative DNA transfer depends on key catalytic components to nick one strand of the duplex DNA plasmid and separate the DNA strands while cell-to-cell transfer occurs. The TraI protein from the conjugative Salmonella plasmid pCU1 fulfills these key catalytic roles, as it contains both single-stranded DNA-nicking relaxase and ATP-dependent helicase domains within a single, 1,078-residue polypeptide. In this work, we unraveled the helicase determinants of Salmonella pCU1 TraI through DNA binding, ATPase, and DNA strand separation assays. TraI binds DNA substrates with high affinity in a manner influenced by nucleic acid length and the presence of a DNA hairpin structure adjacent to the nick site. TraI selectively hydrolyzes ATP, and mutations in conserved helicase motifs eliminate ATPase activity. Surprisingly, the absence of a relatively short (144-residue) domain at the extreme C terminus of the protein severely diminishes ATP-dependent strand separation. Collectively, these data define the helicase motifs of the conjugative factor TraI from Salmonella pCU1 and reveal a previously uncharacterized C-terminal functional domain that uncouples ATP hydrolysis from strand separation activity.
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170
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Clark NJ, Raththagala M, Wright NT, Buenger EA, Schildbach JF, Krueger S, Curtis JE. Structures of TraI in solution. J Mol Model 2014; 20:2308. [PMID: 24898939 DOI: 10.1007/s00894-014-2308-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Bacterial conjugation, a DNA transfer mechanism involving transport of one plasmid strand from donor to recipient, is driven by plasmid-encoded proteins. The F TraI protein nicks one F plasmid strand, separates cut and uncut strands, and pilots the cut strand through a secretion pore into the recipient. TraI is a modular protein with identifiable nickase, ssDNA-binding, helicase and protein-protein interaction domains. While domain structures corresponding to roughly 1/3 of TraI have been determined, there has been no comprehensive structural study of the entire TraI molecule, nor an examination of structural changes to TraI upon binding DNA. Here, we combine solution studies using small-angle scattering and circular dichroism spectroscopy with molecular Monte Carlo and molecular dynamics simulations to assess solution behavior of individual and groups of domains. Despite having several long (>100 residues) apparently disordered or highly dynamic regions, TraI folds into a compact molecule. Based on the biophysical characterization, we have generated models of intact TraI. These data and the resulting models have provided clues to the regulation of TraI function.
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Affiliation(s)
- Nicholas J Clark
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD, 20899, USA
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171
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Koraimann G, Wagner MA. Social behavior and decision making in bacterial conjugation. Front Cell Infect Microbiol 2014; 4:54. [PMID: 24809026 PMCID: PMC4010749 DOI: 10.3389/fcimb.2014.00054] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/09/2014] [Indexed: 01/05/2023] Open
Abstract
Bacteria frequently acquire novel genes by horizontal gene transfer (HGT). HGT through the process of bacterial conjugation is highly efficient and depends on the presence of conjugative plasmids (CPs) or integrated conjugative elements (ICEs) that provide the necessary genes for DNA transmission. This review focuses on recent advancements in our understanding of ssDNA transfer systems and regulatory networks ensuring timely and spatially controlled DNA transfer (tra) gene expression. As will become obvious by comparing different systems, by default, tra genes are shut off in cells in which conjugative elements are present. Only when conditions are optimal, donor cells—through epigenetic alleviation of negatively acting roadblocks and direct stimulation of DNA transfer genes—become transfer competent. These transfer competent cells have developmentally transformed into specialized cells capable of secreting ssDNA via a T4S (type IV secretion) complex directly into recipient cells. Intriguingly, even under optimal conditions, only a fraction of the population undergoes this transition, a finding that indicates specialization and cooperative, social behavior. Thereby, at the population level, the metabolic burden and other negative consequences of tra gene expression are greatly reduced without compromising the ability to horizontally transfer genes to novel bacterial hosts. This undoubtedly intelligent strategy may explain why conjugative elements—CPs and ICEs—have been successfully kept in and evolved with bacteria to constitute a major driving force of bacterial evolution.
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Affiliation(s)
- Günther Koraimann
- Institute of Molecular Biosciences, University of Graz Graz, Austria
| | - Maria A Wagner
- Max von Pettenkofer-Institut, Ludwig-Maximilians-Universität München Munich, Germany
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172
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Torres Tejerizo G, Pistorio M, Althabegoiti MJ, Cervantes L, Wibberg D, Schlüter A, Pühler A, Lagares A, Romero D, Brom S. Rhizobial plasmid pLPU83a is able to switch between different transfer machineries depending on its genomic background. FEMS Microbiol Ecol 2014; 88:565-78. [PMID: 24646299 DOI: 10.1111/1574-6941.12325] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/20/2014] [Accepted: 03/07/2014] [Indexed: 12/01/2022] Open
Abstract
Plasmids have played a major role in bacterial evolution, mainly by their capacity to perform horizontal gene transfer (HGT). Their conjugative transfer (CT) properties are usually described in terms of the plasmid itself. In this work, we analyzed structural and functional aspects of the CT of pLPU83a, an accessory replicon from Rhizobium sp. LPU83, able to transfer from its parental strain, from Ensifer meliloti, or from Rhizobium etli. pLPU83a contains a complete set of transfer genes, featuring a particular organization, shared with only two other rhizobial plasmids. These plasmids contain a TraR quorum-sensing (QS) transcriptional regulator, but lack an acyl-homoserine lactone (AHL) synthase gene. We also determined that the ability of pLPU83a to transfer from R. etli CFN42 genomic background was mainly achieved through mobilization, employing the machinery of the endogenous plasmid pRetCFN42a, falling under control of the QS regulators from pRetCFN42a. In contrast, from its native or from the E. meliloti background, pLPU83a utilized its own machinery for conjugation, requiring the plasmid-encoded traR. Activation of TraR seemed to be AHL independent. The results obtained indicate that the CT phenotype of a plasmid is dictated not only by the genes it carries, but by their interaction with its genomic context.
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Affiliation(s)
- Gonzalo Torres Tejerizo
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México; Instituto de Biotecnología y Biología Molecular, CCT-La Plata-CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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173
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Trokter M, Felisberto-Rodrigues C, Christie PJ, Waksman G. Recent advances in the structural and molecular biology of type IV secretion systems. Curr Opin Struct Biol 2014; 27:16-23. [PMID: 24709394 PMCID: PMC4182333 DOI: 10.1016/j.sbi.2014.02.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 02/28/2014] [Indexed: 11/28/2022]
Abstract
We describe the first structure of a type IV secretion (T4S) system. The previously reported core complex is mostly an outer membrane complex. We describe the newly discovered inner membrane complex and the stalk. We discuss proposed translocation mechanisms of T4S systems. We discuss the regulation of pilus biogenesis and substrate transfer by T4S systems.
Bacteria use type IV secretion (T4S) systems to deliver DNA and protein substrates to a diverse range of prokaryotic and eukaryotic target cells. T4S systems have great impact on human health, as they are a major source of antibiotic resistance spread among bacteria and are central to infection processes of many pathogens. Therefore, deciphering the structure and underlying translocation mechanism of T4S systems is crucial to facilitate development of new drugs. The last five years have witnessed considerable progress in unraveling the structure of T4S system subassemblies, notably that of the T4S system core complex, a large 1 MegaDalton (MDa) structure embedded in the double membrane of Gram-negative bacteria and made of 3 of the 12 T4S system components. However, the recent determination of the structure of ∼3 MDa assembly of 8 of these components has revolutionized our views of T4S system architecture and opened up new avenues of research, which are discussed in this review.
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Affiliation(s)
- Martina Trokter
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Catarina Felisberto-Rodrigues
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, 6431 Fannin Street, Houston, TX 77030, USA
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK.
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174
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Fernandez-Gonzalez E, Backert S. DNA transfer in the gastric pathogen Helicobacter pylori. J Gastroenterol 2014; 49:594-604. [PMID: 24515309 DOI: 10.1007/s00535-014-0938-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/16/2014] [Indexed: 02/08/2023]
Abstract
The gastric pathogen Helicobacter pylori is one of the most genetically diverse bacteria. Recombination and DNA transfer contribute to its genetic variability and enhance host adaptation. Among the strategies described to increase genetic diversity in bacteria, DNA transfer by conjugation is one of the best characterized. Using this mechanism, a fragment of DNA from a donor cell can be transferred to a recipient, always mediated by a conjugative nucleoprotein complex, which is evolutionarily related to type IV secretion systems (T4SSs). Interestingly, the H. pylori chromosomes can encode up to four T4SSs, including the cagPAI, comB, tfs3, and tfs4 genes, some of which are known to promote chronic H. pylori infection. The T4SS encoded by the cagPAI mediates the injection of the effector protein CagA and proinflammatory signaling, and the comB system is involved in DNA uptake from the environment. However, the role of tfs3 and tfs4 is not yet clear. The presence of a functional XerD tyrosine recombinase and 5'AAAGAATG-3' border sequences as well as two putative conjugative relaxases (Rlx1 and Rlx2), a coupling protein (TraG), and a chromosomal region carrying a putative origin of transfer (oriT) suggest the existence of a DNA transfer apparatus in tfs4. Moreover, a conjugation-like DNA transfer mechanism in H. pylori has already been described in vitro, but whether this occurs in vivo is still unknown. Some extrachromosomal plasmids and phages are also present in various H. pylori strains. Genetic exchange among plasmids and chromosomes, and involved DNA mobilization events, could explain part of H. pylori's genetic diversity. Here, we review our knowledge about the possible DNA transfer mechanisms in H. pylori and its implications in bacterial adaptation to the host environment.
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Affiliation(s)
- Esther Fernandez-Gonzalez
- Division of Microbiology, Department of Biology, Friedrich Alexander University Erlangen/Nuremberg, Staudtstr. 5, 91058, Erlangen, Germany
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175
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Common requirement for the relaxosome of plasmid R1 in multiple activities of the conjugative type IV secretion system. J Bacteriol 2014; 196:2108-21. [PMID: 24682328 DOI: 10.1128/jb.00045-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Macromolecular transport by bacterial type IV secretion systems involves regulated uptake of (nucleo)protein complexes by the cell envelope-spanning transport channel. A coupling protein receptor is believed to recognize the specific proteins destined for transfer, but the steps initiating their translocation remain unknown. Here, we investigate the contribution of a complex of transfer initiation proteins, the relaxosome, of plasmid R1 to translocation of competing transferable substrates from mobilizable plasmids ColE1 and CloDF13 or the bacteriophage R17. We found that not only does the R1 translocation machinery engage the R1 relaxosome during conjugative self-transfer and during infection by R17 phage but it is also activated by its cognate relaxosome to mediate the export of an alternative plasmid. Transporter activity was optimized by the R1 relaxosome even when this complex itself could not be transferred, i.e., when the N-terminal activation domain (amino acids 1 to 992 [N1-992]) of TraI was present without the C-terminal conjugative helicase domain. We propose that the functional dependence of the transfer machinery on the R1 relaxosome for initiating translocation ensures that dissemination of heterologous plasmids does not occur at the expense of self-transfer.
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176
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Goessweiner-Mohr N, Fercher C, Arends K, Birner-Gruenberger R, Laverde-Gomez D, Huebner J, Grohmann E, Keller W. The type IV secretion protein TraK from the Enterococcus conjugative plasmid pIP501 exhibits a novel fold. ACTA ACUST UNITED AC 2014; 70:1124-35. [PMID: 24699656 DOI: 10.1107/s1399004714001606] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 01/22/2014] [Indexed: 11/11/2022]
Abstract
Conjugative plasmid transfer presents a serious threat to human health as the most important means of spreading antibiotic resistance and virulence genes among bacteria. The required direct cell-cell contact is established by a multi-protein complex, the conjugative type IV secretion system (T4SS). The conjugative core complex spans the cellular envelope and serves as a channel for macromolecular secretion. T4SSs of Gram-negative (G-) origin have been studied in great detail. In contrast, T4SSs of Gram-positive (G+) bacteria have only received little attention thus far, despite the medical relevance of numerous G+ pathogens (e.g. enterococci, staphylococci and streptococci). This study provides structural information on the type IV secretion (T4S) protein TraK of the G+ broad host range Enterococcus conjugative plasmid pIP501. The crystal structure of the N-terminally truncated construct TraKΔ was determined to 3.0 Å resolution and exhibits a novel fold. Immunolocalization demonstrated that the protein localizes to the cell wall facing towards the cell exterior, but does not exhibit surface accessibility. Circular dichroism, dynamic light scattering and size-exclusion chromatography confirmed the protein to be a monomer. With the exception of proteins from closely related T4SSs, no significant sequence or structural relatives were found. This observation marks the protein as a very exclusive, specialized member of the pIP501 T4SS.
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Affiliation(s)
- Nikolaus Goessweiner-Mohr
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Christian Fercher
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | | | - Ruth Birner-Gruenberger
- Institute for Pathology and Center of Medical Research, Medical University Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Diana Laverde-Gomez
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Johannes Huebner
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Walter Keller
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
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177
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Guglielmini J, Néron B, Abby SS, Garcillán-Barcia MP, de la Cruz F, Rocha EPC. Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. Nucleic Acids Res 2014; 42:5715-27. [PMID: 24623814 PMCID: PMC4027160 DOI: 10.1093/nar/gku194] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Conjugation of DNA through a type IV secretion system (T4SS) drives horizontal gene transfer. Yet little is known on the diversity of these nanomachines. We previously found that T4SS can be divided in eight classes based on the phylogeny of the only ubiquitous protein of T4SS (VirB4). Here, we use an ab initio approach to identify protein families systematically and specifically associated with VirB4 in each class. We built profiles for these proteins and used them to scan 2262 genomes for the presence of T4SS. Our analysis led to the identification of thousands of occurrences of 116 protein families for a total of 1623 T4SS. Importantly, we could identify almost always in our profiles the essential genes of well-studied T4SS. This allowed us to build a database with the largest number of T4SS described to date. Using profile–profile alignments, we reveal many new cases of homology between components of distant classes of T4SS. We mapped these similarities on the T4SS phylogenetic tree and thus obtained the patterns of acquisition and loss of these protein families in the history of T4SS. The identification of the key VirB4-associated proteins paves the way toward experimental analysis of poorly characterized T4SS classes.
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Affiliation(s)
- Julien Guglielmini
- Microbial Evolutionary Genomics, Institut Pasteur, Paris 75015, France UMR3525, CNRS, Paris 75015, France
| | - Bertrand Néron
- Centre d'Informatique pour les Biologistes, Institut Pasteur, Paris 75015, France
| | - Sophie S Abby
- Microbial Evolutionary Genomics, Institut Pasteur, Paris 75015, France UMR3525, CNRS, Paris 75015, France
| | - María Pilar Garcillán-Barcia
- Institute of Biomedicine and Biotechnology of Cantabria (CSIC-Sodercan-University of Cantabria), Santander 39011, Spain
| | - Fernando de la Cruz
- Institute of Biomedicine and Biotechnology of Cantabria (CSIC-Sodercan-University of Cantabria), Santander 39011, Spain
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris 75015, France UMR3525, CNRS, Paris 75015, France
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178
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Rolloos M, Dohmen MHC, Hooykaas PJJ, van der Zaal BJ. Involvement of Rad52 in T-DNA circle formation duringAgrobacterium tumefaciens-mediated transformation ofSaccharomyces cerevisiae. Mol Microbiol 2014; 91:1240-51. [DOI: 10.1111/mmi.12531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Martijn Rolloos
- Department of Molecular and Developmental Genetics; nstitute of Biology Leiden; Leiden Sylviusweg 72, 2333 BE The Netherlands
| | - Marius H. C. Dohmen
- Department of Molecular and Developmental Genetics; nstitute of Biology Leiden; Leiden Sylviusweg 72, 2333 BE The Netherlands
| | - Paul J. J. Hooykaas
- Department of Molecular and Developmental Genetics; nstitute of Biology Leiden; Leiden Sylviusweg 72, 2333 BE The Netherlands
| | - Bert J. van der Zaal
- Department of Molecular and Developmental Genetics; nstitute of Biology Leiden; Leiden Sylviusweg 72, 2333 BE The Netherlands
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179
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Schuurmans JM, van Hijum SAFT, Piet JR, Händel N, Smelt J, Brul S, ter Kuile BH. Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains. Plasmid 2014; 72:1-8. [PMID: 24525238 DOI: 10.1016/j.plasmid.2014.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
Abstract
Antibiotic resistance increases costs for health care and causes therapy failure. An important mechanism for spreading resistance is transfer of plasmids containing resistance genes and subsequent selection. Yet the factors that influence the rate of transfer are poorly known. Rates of plasmid transfer were measured in co-cultures in chemostats of a donor and a acceptor strain under various selective pressures. To document whether specific mutations in either plasmid or acceptor genome are associated with the plasmid transfer, whole genome sequencing was performed. The DM0133 TetR tetracycline resistance plasmid was transferred between Escherichia coli K-12 strains during co-culture at frequencies that seemed higher at increased growth rate. Modeling of the take-over of the culture by the transformed strain suggests that in reality more transfer events occurred at low growth rates. At moderate selection pressure due to an antibiotic concentration that still allowed growth, a maximum transfer frequency was determined of once per 10(11) cell divisions. In the absence of tetracycline or in the presence of high concentrations the frequency of transfer was sometimes zero, but otherwise reduced by at least a factor of 5. Whole genome sequencing showed that the plasmid was transferred without mutations, but two functional mutations in the genome of the recipient strain accompanied this transfer. Exposure to concentrations of antibiotics that fall within the mutant selection window stimulated transfer of the resistance plasmid most.
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Affiliation(s)
- Jasper M Schuurmans
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sacha A F T van Hijum
- NIZO Food Research B.V., Kernhemseweg 2, 6718 ZB Ede, The Netherlands; Centre for Molecular and Biomolecular Informatics (CMBI), NCMLS, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jurgen R Piet
- Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, 1100 DD Amsterdam, The Netherlands
| | - Nadine Händel
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jan Smelt
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Benno H ter Kuile
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Office for Risk Assessment and Research, Netherlands Food and Consumer Product Safety Authority, Catharijnesingel 59, 3511 GG Utrecht, The Netherlands.
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180
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Chen L, Chavda KD, Melano RG, Hong T, Rojtman AD, Jacobs MR, Bonomo RA, Kreiswirth BN. Molecular survey of the dissemination of two blaKPC-harboring IncFIA plasmids in New Jersey and New York hospitals. Antimicrob Agents Chemother 2014; 58:2289-94. [PMID: 24492370 PMCID: PMC4023724 DOI: 10.1128/aac.02749-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/26/2014] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae strains have spread worldwide and become a major threat in health care facilities. Transmission of blaKPC, the plasmid-borne KPC gene, can be mediated by clonal spread and horizontal transfer. Here, we report the complete nucleotide sequences of two novel blaKPC-3-harboring IncFIA plasmids, pBK30661 and pBK30683. pBK30661 is 74 kb in length, with a mosaic plasmid structure; it exhibits homologies to several other plasmids but lacks the plasmid transfer operon (tra) and the origin of transfer (oriT) that are required for plasmid transfer. pBK30683 is a conjugative plasmid with a cointegrated plasmid structure, comprising a 72-kb element that highly resembles pBK30661 (>99.9% nucleotide identities) and an extra 68-kb element that harbors tra and oriT. A PCR scheme was designed to detect the distribution of blaKPC-harboring IncFIA (pBK30661-like and pBK30683-like) plasmids in a collection of clinical Enterobacteriaceae isolates from 10 hospitals in New Jersey and New York. KPC-harboring IncFIA plasmids were found in 20% of 491 K. pneumoniae isolates, and all carried blaKPC-3. pBK30661-like plasmids were identified mainly in the epidemic sequence type 258 (ST258) K. pneumoniae clone, while pBK30683-like plasmids were widely distributed in ST258 and other K. pneumoniae sequence types and among non-K. pneumoniae Enterobacteriaceae species. This suggests that both clonal spread and horizontal plasmid transfer contributed to the dissemination of blaKPC-harboring IncFIA plasmids in our area. Further studies are needed to understand the distribution of this plasmid group in other health care regions and to decipher the origins of pBK30661-like and pBK30683-like plasmids.
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Affiliation(s)
- Liang Chen
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Kalyan D. Chavda
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Roberto G. Melano
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Tao Hong
- Department of Pathology, Hackensack Medical Center, Hackensack, New Jersey, USA
| | - Albert D. Rojtman
- Department of Pathology, Jersey Shore University Medical Center, Neptune, New Jersey, USA
| | - Michael R. Jacobs
- Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Medicine, Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Barry N. Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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181
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Sakai Y, Ogawa N, Shimomura Y, Fujii T. A 2,4-dichlorophenoxyacetic acid degradation plasmid pM7012 discloses distribution of an unclassified megaplasmid group across bacterial species. MICROBIOLOGY-SGM 2014; 160:525-536. [PMID: 24440834 DOI: 10.1099/mic.0.074369-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analysis of the complete nucleotide sequence of plasmid pM7012 from 2,4-dichlorophenoxyacetic-acid (2,4-D)-degrading bacterium Burkholderia sp. M701 revealed that the plasmid had 582 142 bp, with 541 putative protein-coding sequences and 39 putative tRNA genes for the transport of the standard 20 aa. pM7012 contains sequences homologous to the regions involved in conjugal transfer and plasmid maintenance found in plasmids byi_2p from Burkholderia sp. YI23 and pBVIE01 from Burkholderia sp. G4. No relaxase gene was found in any of these plasmids, although genes for a type IV secretion system and type IV coupling proteins were identified. Plasmids with no relaxase gene have been classified as non-mobile plasmids. However, nucleotide sequences with a high level of similarity to the genes for plasmid transfer, plasmid maintenance, 2,4-D degradation and arsenic resistance contained on pM7012 were also detected in eight other megaplasmids (~600 or 900 kb) found in seven Burkholderia strains and a strain of Cupriavidus, which were isolated as 2,4-D-degrading bacteria in Japan and the United States. These results suggested that the 2,4-D degradation megaplasmids related to pM7012 are mobile and distributed across various bacterial species worldwide, and that the plasmid group could be distinguished from known mobile plasmid groups.
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Affiliation(s)
- Yoriko Sakai
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Naoto Ogawa
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Surugaku, Shizuoka 422-8529, Japan
| | - Yumi Shimomura
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Takeshi Fujii
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
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182
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Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria. Microbiol Spectr 2014; 2:MGM2-0022-2013. [PMID: 25505644 DOI: 10.1128/microbiolspec.mgm2-0022-2013] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The last decade has seen an explosion in the application of genomic tools across all biological disciplines. This is also true for mycobacteria, where whole genome sequences are now available for pathogens and non-pathogens alike. Genomes within the Mycobacterium tuberculosis Complex (MTBC) bear the hallmarks of horizontal gene transfer (HGT). Conjugation is the form of HGT with the highest potential capacity and evolutionary influence. Donor and recipient strains of Mycobacterium smegmatis actively conjugate upon co-culturing in biofilms and on solid media. Whole genome sequencing of the transconjugant progeny demonstrated the incredible scale and range of genomic variation that conjugation generates. Transconjugant genomes are complex mosaics of the parental strains. Some transconjugant genomes are up to one-quarter donor-derived, distributed over 30 segments. Transferred segments range from ~50 bp to ~225,000 bp in length, and are exchanged with their recipient orthologs all around the genome. This unpredictable genome-wide infusion of DNA sequences is called Distributive Conjugal Transfer (DCT), to distinguish it from traditional oriT-based conjugation. The mosaicism generated in a single transfer event resembles that seen from meiotic recombination in sexually reproducing organisms, and contrasts with traditional models of HGT. This similarity allowed the application of a GWAS-like approach to map the donor genes that confer a donor mating identity phenotype. The mating identity genes map to the esx1 locus, expanding the central role of ESX-1 function in conjugation. The potential for DCT to instantaneously blend genomes will affect how we view mycobacterial evolution, and provide new tools for the facile manipulation of mycobacterial genomes.
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183
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Christie PJ, Whitaker N, González-Rivera C. Mechanism and structure of the bacterial type IV secretion systems. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1578-91. [PMID: 24389247 DOI: 10.1016/j.bbamcr.2013.12.019] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 01/25/2023]
Abstract
The bacterial type IV secretion systems (T4SSs) translocate DNA and protein substrates to bacterial or eukaryotic target cells generally by a mechanism dependent on direct cell-to-cell contact. The T4SSs encompass two large subfamilies, the conjugation systems and the effector translocators. The conjugation systems mediate interbacterial DNA transfer and are responsible for the rapid dissemination of antibiotic resistance genes and virulence determinants in clinical settings. The effector translocators are used by many Gram-negative bacterial pathogens for delivery of potentially hundreds of virulence proteins to eukaryotic cells for modulation of different physiological processes during infection. Recently, there has been considerable progress in defining the structures of T4SS machine subunits and large machine subassemblies. Additionally, the nature of substrate translocation sequences and the contributions of accessory proteins to substrate docking with the translocation channel have been elucidated. A DNA translocation route through the Agrobacterium tumefaciens VirB/VirD4 system was defined, and both intracellular (DNA ligand, ATP energy) and extracellular (phage binding) signals were shown to activate type IV-dependent translocation. Finally, phylogenetic studies have shed light on the evolution and distribution of T4SSs, and complementary structure-function studies of diverse systems have identified adaptations tailored for novel functions in pathogenic settings. This review summarizes the recent progress in our understanding of the architecture and mechanism of action of these fascinating machines, with emphasis on the 'archetypal' A. tumefaciens VirB/VirD4 T4SS and related conjugation systems. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Peter J Christie
- Department of Microbiology and Molecular Genetics, UT-Houston Medical School, 6431 Fannin, JFB1.765, Houston, TX 77030, USA.
| | - Neal Whitaker
- Department of Microbiology and Molecular Genetics, UT-Houston Medical School, 6431 Fannin, JFB1.765, Houston, TX 77030, USA
| | - Christian González-Rivera
- Department of Microbiology and Molecular Genetics, UT-Houston Medical School, 6431 Fannin, JFB1.765, Houston, TX 77030, USA
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184
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Wee BA, Woolfit M, Beatson SA, Petty NK. A distinct and divergent lineage of genomic island-associated Type IV Secretion Systems in Legionella. PLoS One 2013; 8:e82221. [PMID: 24358157 PMCID: PMC3864950 DOI: 10.1371/journal.pone.0082221] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 10/25/2013] [Indexed: 12/21/2022] Open
Abstract
Legionella encodes multiple classes of Type IV Secretion Systems (T4SSs), including the Dot/Icm protein secretion system that is essential for intracellular multiplication in amoebal and human hosts. Other T4SSs not essential for virulence are thought to facilitate the acquisition of niche-specific adaptation genes including the numerous effector genes that are a hallmark of this genus. Previously, we identified two novel gene clusters in the draft genome of Legionella pneumophila strain 130b that encode homologues of a subtype of T4SS, the genomic island-associated T4SS (GI-T4SS), usually associated with integrative and conjugative elements (ICE). In this study, we performed genomic analyses of 14 homologous GI-T4SS clusters found in eight publicly available Legionella genomes and show that this cluster is unusually well conserved in a region of high plasticity. Phylogenetic analyses show that Legionella GI-T4SSs are substantially divergent from other members of this subtype of T4SS and represent a novel clade of GI-T4SSs only found in this genus. The GI-T4SS was found to be under purifying selection, suggesting it is functional and may play an important role in the evolution and adaptation of Legionella. Like other GI-T4SSs, the Legionella clusters are also associated with ICEs, but lack the typical integration and replication modules of related ICEs. The absence of complete replication and DNA pre-processing modules, together with the presence of Legionella-specific regulatory elements, suggest the Legionella GI-T4SS-associated ICE is unique and may employ novel mechanisms of regulation, maintenance and excision. The Legionella GI-T4SS cluster was found to be associated with several cargo genes, including numerous antibiotic resistance and virulence factors, which may confer a fitness benefit to the organism. The in-silico characterisation of this new T4SS furthers our understanding of the diversity of secretion systems involved in the frequent horizontal gene transfers that allow Legionella to adapt to and exploit diverse environmental niches.
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Affiliation(s)
- Bryan A. Wee
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Megan Woolfit
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Scott A. Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (NKP); (SAB)
| | - Nicola K. Petty
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, Australia
- * E-mail: (NKP); (SAB)
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185
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Wagner MA, Bischof K, Kati D, Koraimann G. Silencing and activating type IV secretion genes of the F-like conjugative resistance plasmid R1. Microbiology (Reading) 2013; 159:2481-2491. [DOI: 10.1099/mic.0.071738-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Maria Anna Wagner
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - Karin Bischof
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - Dominiki Kati
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - Günther Koraimann
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Humboldtstrasse 50, A-8010 Graz, Austria
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186
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Goessweiner-Mohr N, Arends K, Keller W, Grohmann E. Conjugative type IV secretion systems in Gram-positive bacteria. Plasmid 2013; 70:289-302. [PMID: 24129002 PMCID: PMC3913187 DOI: 10.1016/j.plasmid.2013.09.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 09/21/2013] [Accepted: 09/30/2013] [Indexed: 01/17/2023]
Abstract
The conjugative transfer mechanism of broad-host-range, Enterococcus sex pheromone and Clostridium plasmids is reviewed. Comparisons with Gram-negative type IV secretion systems are presented. The current understanding of the unique Streptomyces double stranded DNA transfer mechanism is reviewed.
Bacterial conjugation presents the most important means to spread antibiotic resistance and virulence factors among closely and distantly related bacteria. Conjugative plasmids are the mobile genetic elements mainly responsible for this task. All the genetic information required for the horizontal transmission is encoded on the conjugative plasmids themselves. Two distinct concepts for horizontal plasmid transfer in Gram-positive bacteria exist, the most prominent one transports single stranded plasmid DNA via a multi-protein complex, termed type IV secretion system, across the Gram-positive cell envelope. Type IV secretion systems have been found in virtually all unicellular Gram-positive bacteria, whereas multicellular Streptomycetes seem to have developed a specialized system more closely related to the machinery involved in bacterial cell division and sporulation, which transports double stranded DNA from donor to recipient cells. This review intends to summarize the state of the art of prototype systems belonging to the two distinct concepts; it focuses on protein key players identified so far and gives future directions for research in this emerging field of promiscuous interbacterial transport.
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187
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Smits TH, Rezzonico F, López MM, Blom J, Goesmann A, Frey JE, Duffy B. Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics. Syst Appl Microbiol 2013; 36:449-56. [DOI: 10.1016/j.syapm.2013.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/18/2013] [Accepted: 04/18/2013] [Indexed: 10/26/2022]
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188
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Segura RL, Águila-Arcos S, Ugarte-Uribe B, Vecino AJ, de la Cruz F, Goñi FM, Alkorta I. The transmembrane domain of the T4SS coupling protein TrwB and its role in protein–protein interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2015-25. [DOI: 10.1016/j.bbamem.2013.05.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/14/2013] [Accepted: 05/22/2013] [Indexed: 11/15/2022]
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189
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TraG encoded by the pIP501 type IV secretion system is a two-domain peptidoglycan-degrading enzyme essential for conjugative transfer. J Bacteriol 2013; 195:4436-44. [PMID: 23913323 DOI: 10.1128/jb.02263-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
pIP501 is a conjugative broad-host-range plasmid frequently present in nosocomial Enterococcus faecalis and Enterococcus faecium isolates. We focus here on the functional analysis of the type IV secretion gene traG, which was found to be essential for pIP501 conjugative transfer between Gram-positive bacteria. The TraG protein, which localizes to the cell envelope of E. faecalis harboring pIP501, was expressed and purified without its N-terminal transmembrane helix (TraGΔTMH) and shown to possess peptidoglycan-degrading activity. TraGΔTMH was inhibited by specific lytic transglycosylase inhibitors hexa-N-acetylchitohexaose and bulgecin A. Analysis of the TraG sequence suggested the presence of two domains which both could contribute to the observed cell wall-degrading activity: an N-terminal soluble lytic transglycosylase domain (SLT) and a C-terminal cysteine-, histidine-dependent amidohydrolases/peptidases (CHAP) domain. The protein domains were expressed separately, and both degraded peptidoglycan. A change of the conserved glutamate residue in the putative catalytic center of the SLT domain (E87) to glycine resulted in almost complete inactivity, which is consistent with this part of TraG being a predicted lytic transglycosylase. Based on our findings, we propose that TraG locally opens the peptidoglycan to facilitate insertion of the Gram-positive bacterial type IV secretion machinery into the cell envelope.
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190
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A cointegrate-like plasmid that facilitates dissemination by conjugation of the extended-spectrum β-lactamase CTX-M-17. Antimicrob Agents Chemother 2013; 57:5191-2. [PMID: 23877684 DOI: 10.1128/aac.01365-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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191
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Gray TA, Krywy JA, Harold J, Palumbo MJ, Derbyshire KM. Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus. PLoS Biol 2013; 11:e1001602. [PMID: 23874149 PMCID: PMC3706393 DOI: 10.1371/journal.pbio.1001602] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 05/24/2013] [Indexed: 01/01/2023] Open
Abstract
We find that genome-wide DNA transfer by conjugation in mycobacteria affords bacteria that reproduce by binary fission the same advantages of sexual reproduction, and may explain the genomic evolution of Mycobacterium tuberculosis. Horizontal gene transfer (HGT) in bacteria generates variation and drives evolution, and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species. We previously described a novel form of chromosomal conjugation in mycobacteria that does not conform to classic oriT-based conjugation models, and whose potential evolutionary significance has not been evaluated. Here, we determined the genome sequences of 22 F1-generation transconjugants, providing the first genome-wide view of conjugal HGT in bacteria at the nucleotide level. Remarkably, mycobacterial recipients acquired multiple, large, unlinked segments of donor DNA, far exceeding expectations for any bacterial HGT event. Consequently, conjugal DNA transfer created extensive genome-wide mosaicism within individual transconjugants, which generated large-scale sibling diversity approaching that seen in meiotic recombination. We exploited these attributes to perform genome-wide mapping and introgression analyses to map a locus that determines conjugal mating identity in M. smegmatis. Distributive conjugal transfer offers a plausible mechanism for the predicted HGT events that created the genome mosaicism observed among extant Mycobacterium tuberculosis and Mycobacterium canettii species. Mycobacterial distributive conjugal transfer permits innovative genetic approaches to map phenotypic traits and confers the evolutionary benefits of sexual reproduction in an asexual organism. Bacteria reproduce by binary fission, generating two clones of the original; this restricts the genomic diversity of the population, which brings with it inherent evolutionary drawbacks. This problem can be eased by conjugation, which transfers DNA from a donor to a recipient bacterium. Understanding the potential of conjugal DNA transfer for generating genetic diversity is necessary for estimating gene flow through populations and for predicting rates of bacterial evolution. The influence of chromosomal conjugal DNA transfer on mycobacterial diversity has not been previously addressed. Here, we determine and compare the complete genome sequences of independent progeny from bacterial matings between defined donor and recipient strains of Mycobacterium smegmatis. We find the resulting hybrid bacteria to be extremely diverse blends of the parental strains, reminiscent of the genetic mixing that occurs through meiotic recombination in sexual organisms. This novel mechanism of conjugation can create genome-wide mosaicism in a single event, generating segments of donor DNA that range from small (∼0.05 kb) to large (∼250 kb), widely distributed around the recipient chromosome. We exploit this mixing by using genetic tools originally developed for finding mammalian disease genes to locate the genes that confer a donor phenotype in M. smegmatis. We speculate that similar genomic mosaicism observed in pathogenic mycobacteria arose from conjugation between ancestral progenitor strains.
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Affiliation(s)
- Todd A Gray
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.
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192
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Abstract
HUH endonucleases are numerous and widespread in all three domains of life. The major function of these enzymes is processing a range of mobile genetic elements by catalysing cleavage and rejoining of single-stranded DNA using an active-site Tyr residue to make a transient 5'-phosphotyrosine bond with the DNA substrate. These enzymes have a key role in rolling-circle replication of plasmids and bacteriophages, in plasmid transfer, in the replication of several eukaryotic viruses and in various types of transposition. They have also been appropriated for cellular processes such as intron homing and the processing of bacterial repeated extragenic palindromes. Here, we provide an overview of these fascinating enzymes and their functions, using well-characterized examples of Rep proteins, relaxases and transposases, and we explore the molecular mechanisms used in their diverse activities.
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193
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Redzej A, Ilangovan A, Lang S, Gruber CJ, Topf M, Zangger K, Zechner EL, Waksman G. Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems. Mol Microbiol 2013; 89:324-33. [PMID: 23710762 PMCID: PMC3912908 DOI: 10.1111/mmi.12275] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2013] [Indexed: 01/26/2023]
Abstract
Relaxases are proteins responsible for the transfer of plasmid and chromosomal DNA from one bacterium to another during conjugation. They covalently react with a specific phosphodiester bond within DNA origin of transfer sequences, forming a nucleo-protein complex which is subsequently recruited for transport by a plasmid-encoded type IV secretion system. In previous work we identified the targeting translocation signals presented by the conjugative relaxase TraI of plasmid R1. Here we report the structure of TraI translocation signal TSA. In contrast to known translocation signals we show that TSA is an independent folding unit and thus forms a bona fide structural domain. This domain can be further divided into three subdomains with striking structural homology with helicase subdomains of the SF1B family. We also show that TSA is part of a larger vestigial helicase domain which has lost its helicase activity but not its single-stranded DNA binding capability. Finally, we further delineate the binding site responsible for translocation activity of TSA by targeting single residues for mutations. Overall, this study provides the first evidence that translocation signals can be part of larger structural scaffolds, overlapping with translocation-independent activities.
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Affiliation(s)
- Adam Redzej
- Institute of Structural and Molecular Biology, UCL and BirkbeckMalet Street, London, WC1E 7HX, UK
| | - Aravindan Ilangovan
- Institute of Structural and Molecular Biology, UCL and BirkbeckMalet Street, London, WC1E 7HX, UK
| | - Silvia Lang
- University of Graz, Institute of Molecular BiosciencesHumboldtstrasse 50, 8010, Graz, Austria
| | - Christian J Gruber
- University of Graz, Institute of Molecular BiosciencesHumboldtstrasse 50, 8010, Graz, Austria
| | - Maya Topf
- Institute of Structural and Molecular Biology, UCL and BirkbeckMalet Street, London, WC1E 7HX, UK
| | - Klaus Zangger
- University of Graz, Institute of ChemistryHeinrichstrasse 28, 8010, Graz, Austria
| | - Ellen L Zechner
- University of Graz, Institute of Molecular BiosciencesHumboldtstrasse 50, 8010, Graz, Austria
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, UCL and BirkbeckMalet Street, London, WC1E 7HX, UK
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194
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F conjugation: Back to the beginning. Plasmid 2013; 70:18-32. [DOI: 10.1016/j.plasmid.2013.03.010] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 11/19/2022]
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195
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Goñi-Moreno A, Amos M, de la Cruz F. Multicellular computing using conjugation for wiring. PLoS One 2013; 8:e65986. [PMID: 23840385 PMCID: PMC3688716 DOI: 10.1371/journal.pone.0065986] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/01/2013] [Indexed: 12/24/2022] Open
Abstract
Recent efforts in synthetic biology have focussed on the implementation of logical functions within living cells. One aim is to facilitate both internal "re-programming" and external control of cells, with potential applications in a wide range of domains. However, fundamental limitations on the degree to which single cells may be re-engineered have led to a growth of interest in multicellular systems, in which a "computation" is distributed over a number of different cell types, in a manner analogous to modern computer networks. Within this model, individual cell type perform specific sub-tasks, the results of which are then communicated to other cell types for further processing. The manner in which outputs are communicated is therefore of great significance to the overall success of such a scheme. Previous experiments in distributed cellular computation have used global communication schemes, such as quorum sensing (QS), to implement the "wiring" between cell types. While useful, this method lacks specificity, and limits the amount of information that may be transferred at any one time. We propose an alternative scheme, based on specific cell-cell conjugation. This mechanism allows for the direct transfer of genetic information between bacteria, via circular DNA strands known as plasmids. We design a multi-cellular population that is able to compute, in a distributed fashion, a Boolean XOR function. Through this, we describe a general scheme for distributed logic that works by mixing different strains in a single population; this constitutes an important advantage of our novel approach. Importantly, the amount of genetic information exchanged through conjugation is significantly higher than the amount possible through QS-based communication. We provide full computational modelling and simulation results, using deterministic, stochastic and spatially-explicit methods. These simulations explore the behaviour of one possible conjugation-wired cellular computing system under different conditions, and provide baseline information for future laboratory implementations.
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Affiliation(s)
- Angel Goñi-Moreno
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain.
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196
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Juhas M, Dimopoulou I, Robinson E, Elamin A, Harding R, Hood D, Crook D. Identification of another module involved in the horizontal transfer of the Haemophilus genomic island ICEHin1056. Plasmid 2013; 70:277-83. [PMID: 23764277 PMCID: PMC3739013 DOI: 10.1016/j.plasmid.2013.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/24/2013] [Accepted: 05/30/2013] [Indexed: 12/04/2022]
Abstract
The investigated module on the 5′ extremity of ICEHin1056 consists of 15 genes. Genes of this module are homologues of DNA replication and stabilization genes. This module is well conserved in a number of genomic islands. This module is important for the conjugal transfer of ICEHin1056.
A significant part of horizontal gene transfer is facilitated by genomic islands. Haemophilus influenzae genomic island ICEHin1056 is an archetype of a genomic island that accounts for pandemic spread of antibiotics resistance. ICEHin1056 has modular structure and harbors modules involved in type IV secretion and integration. Previous studies have shown that ICEHin1056 encodes a functional type IV secretion system; however, other modules have not been characterized yet. Here we show that the module on the 5′ extremity of ICEHin1056 consists of 15 genes that are well conserved in a number of related genomic islands. Furthermore by disrupting six genes of the investigated module of ICEHin1056 by site-specific mutagenesis we demonstrate that in addition to type IV secretion system module, the investigated module is also important for the successful conjugal transfer of ICEHin1056 from donor to recipient cells.
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Affiliation(s)
- Mario Juhas
- Clinical Microbiology and Infectious Diseases, NDCLS, University of Oxford, OX3 9DU, UK.
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197
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Cascales E, Atmakuri K, Sarkar MK, Christie PJ. DNA substrate-induced activation of the Agrobacterium VirB/VirD4 type IV secretion system. J Bacteriol 2013; 195:2691-704. [PMID: 23564169 PMCID: PMC3676061 DOI: 10.1128/jb.00114-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/29/2013] [Indexed: 11/20/2022] Open
Abstract
The bitopic membrane protein VirB10 of the Agrobacterium VirB/VirD4 type IV secretion system (T4SS) undergoes a structural transition in response to sensing of ATP binding or hydrolysis by the channel ATPases VirD4 and VirB11. This transition, detectable as a change in protease susceptibility, is required for DNA substrate passage through the translocation channel. Here, we present evidence that DNA substrate engagement with VirD4 and VirB11 also is required for activation of VirB10. Several DNA substrates (oncogenic T-DNA and plasmids RSF1010 and pCloDF13) induced the VirB10 conformational change, each by mechanisms requiring relaxase processing at cognate oriT sequences. VirD2 relaxase deleted of its translocation signal or any of the characterized relaxases produced in the absence of cognate DNA substrates did not induce the structural transition. Translocated effector proteins, e.g., VirE2, VirE3, and VirF, also did not induce the transition. By mutational analyses, we supplied evidence that the N-terminal periplasmic loop of VirD4, in addition to its catalytic site, is essential for early-stage DNA substrate transfer and the VirB10 conformational change. Further studies of VirB11 mutants established that three T4SS-mediated processes, DNA transfer, protein transfer, and pilus production, can be uncoupled and that the latter two processes proceed independently of the VirB10 conformational change. Our findings support a general model whereby DNA ligand binding with VirD4 and VirB11 stimulates ATP binding/hydrolysis, which in turn activates VirB10 through a structural transition. This transition confers an open-channel configuration enabling passage of the DNA substrate to the cell surface.
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Affiliation(s)
- Eric Cascales
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, Houston, Texas, USA
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198
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van Wolferen M, Ajon M, Driessen AJM, Albers SV. How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions. Extremophiles 2013; 17:545-63. [PMID: 23712907 DOI: 10.1007/s00792-013-0552-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/12/2013] [Indexed: 01/24/2023]
Abstract
Transfer of DNA has been shown to be involved in genome evolution. In particular with respect to the adaptation of bacterial species to high temperatures, DNA transfer between the domains of bacteria and archaea seems to have played a major role. In addition, DNA exchange between similar species likely plays a role in repair of DNA via homologous recombination, a process that is crucial under DNA damaging conditions such as high temperatures. Several mechanisms for the transfer of DNA have been described in prokaryotes, emphasizing its general importance. However, until recently, not much was known about this process in prokaryotes growing in highly thermophilic environments. This review describes the different mechanisms of DNA transfer in hyperthermophiles, and how this may contribute to the survival and adaptation of hyperthermophilic archaea and bacteria to extreme environments.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
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199
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Westra ER, Staals RH, Gort G, Høgh S, Neumann S, de la Cruz F, Fineran PC, Brouns SJ. CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biol 2013; 10:749-61. [PMID: 23535265 PMCID: PMC3737333 DOI: 10.4161/rna.24202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/28/2013] [Accepted: 03/05/2013] [Indexed: 12/21/2022] Open
Abstract
Most prokaryotes contain CRISPR-Cas immune systems that provide protection against mobile genetic elements. We have focused on the ability of CRISPR-Cas to block plasmid conjugation, and analyzed the position of target sequences (protospacers) on conjugative plasmids. The analysis reveals that protospacers are non-uniformly distributed over plasmid regions in a pattern that is determined by the plasmid's mobilization type (MOB). While MOBP plasmids are most frequently targeted in the region entering the recipient cell last (lagging region), MOBF plasmids are mostly targeted in the region entering the recipient cell first (leading region). To explain this protospacer distribution bias, we propose two mutually non-exclusive hypotheses: (1) spacers are acquired more frequently from either the leading or lagging region depending on the MOB type (2) CRISPR-interference is more efficient when spacers target these preferred regions. To test the latter hypothesis, we analyzed Type I-E CRISPR-interference against MOBF prototype plasmid F in Escherichia coli. Our results show that plasmid conjugation is effectively inhibited, but the level of immunity is not affected by targeting the plasmid in the leading or lagging region. Moreover, CRISPR-immunity levels do not depend on whether the incoming single-stranded plasmid DNA, or the DNA strand synthesized in the recipient is targeted. Our findings indicate that single-stranded DNA may not be a target for Type I-E CRISPR-Cas systems, and suggest that the protospacer distribution bias might be due to spacer acquisition preferences.
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Affiliation(s)
- Edze R. Westra
- Laboratory of Microbiology; Department of Agrotechnology and Food Sciences; Wageningen University; Wageningen, The Netherlands
| | - Raymond H.J. Staals
- Laboratory of Microbiology; Department of Agrotechnology and Food Sciences; Wageningen University; Wageningen, The Netherlands
| | - Gerrit Gort
- Biometris; Wageningen University and Research Center; Wageningen, The Netherlands
| | - Søren Høgh
- Laboratory of Microbiology; Department of Agrotechnology and Food Sciences; Wageningen University; Wageningen, The Netherlands
| | - Sarah Neumann
- Laboratory of Microbiology; Department of Agrotechnology and Food Sciences; Wageningen University; Wageningen, The Netherlands
| | - Fernando de la Cruz
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria; Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN; Santander, Spain
| | - Peter C. Fineran
- Laboratory of Microbiology; Department of Agrotechnology and Food Sciences; Wageningen University; Wageningen, The Netherlands
- Department of Microbiology and Immunology; University of Otago; Dunedin, New Zealand
| | - Stan J.J. Brouns
- Laboratory of Microbiology; Department of Agrotechnology and Food Sciences; Wageningen University; Wageningen, The Netherlands
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200
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Functional properties and structural requirements of the plasmid pMV158-encoded MobM relaxase domain. J Bacteriol 2013; 195:3000-8. [PMID: 23625844 DOI: 10.1128/jb.02264-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A crucial element in the horizontal transfer of mobilizable and conjugative plasmids is the relaxase, a single-stranded endonuclease that nicks the origin of transfer (oriT) of the plasmid DNA. The relaxase of the pMV158 mobilizable plasmid is MobM (494 residues). In solution, MobM forms a dimer through its C-terminal domain, which is proposed to anchor the protein to the cell membrane and to participate in type 4 secretion system (T4SS) protein-protein interactions. In order to gain a deeper insight into the structural MobM requirements for efficient DNA catalysis, we studied two endonuclease domain variants that include the first 199 or 243 amino acid residues (MobMN199 and MobMN243, respectively). Our results confirmed that the two proteins behaved as monomers in solution. Interestingly, MobMN243 relaxed supercoiled DNA and cleaved single-stranded oligonucleotides harboring oriTpMV158, whereas MobMN199 was active only on supercoiled DNA. Protein stability studies using gel electrophoresis and mass spectrometry showed increased susceptibility to degradation at the domain boundary between the N- and C-terminal domains, suggesting that the domains change their relative orientation upon DNA binding. Overall, these results demonstrate that MobMN243 is capable of nicking the DNA substrate independently of its topology and that the amino acids 200 to 243 modulate substrate specificity but not the nicking activity per se. These findings suggest that these amino acids are involved in positioning the DNA for the nuclease reaction rather than in the nicking mechanism itself.
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