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Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, Christakis NA, Iqbal NT, Ali SA, Mathad JS, Brito IL. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nat Commun 2023; 14:7366. [PMID: 37963868 PMCID: PMC10645880 DOI: 10.1038/s41467-023-42998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.
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Affiliation(s)
- Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Matthew W Rhee
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Qiaojuan Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nguyen Vinh Trung
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
| | | | | | - Vandana Kulkarni
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Prasad Deshpande
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Mallika Alexander
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh city, Vietnam
| | | | | | | | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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Espaldon A, Oguma K. Conformation-dependent UV inactivation efficiency of a conjugative, multi-drug resistant plasmid. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132324. [PMID: 37647660 DOI: 10.1016/j.jhazmat.2023.132324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
A conjugative, multi-drug-resistant plasmid was irradiated in-vivo and in-vitro with a 265-nm UV-light emitting diode (UV-LED) to investigate the gene inactivation efficiency of a plasmid deoxyribonucleic acid (pDNA) carrying DNA transfer and replication genes. The clinical-isolate 60 kb RP4 plasmid of the IncPα group containing the traG gene, was irradiated intracellularly in E. coli DH5α and extracellularly in a water medium at pH 8.5. Real-time quantitative polymerase chain reaction (RT-qPCR) measurements of the UV-fluence response gene inactivation rate constants revealed a decreasing pattern via a pseudo-1st-order inactivation kinetics in all forms examined. Our findings showed that the intracellular-supercoiled conformation, with k = 6.1 × 10-3 cm2/mJ, has the lowest UV susceptibility (lowest inactivation rate). UV absorbance measurements and a computational approach showed that the host's RNA provides the photo-shielding, demonstrating this high UV resistance. When UV exposure was measured in-vitro, the condensed DNA exhibited a self-shielding effect over supercoiled and denatured DNA due to the hypochromic-hyperchromic effects. This study has shown that large-sized conjugative plasmids with conformation-dependent UV/UV-LED-based gene inactivation play a significant role in preventing the spread of antibiotic resistance.
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Affiliation(s)
- Achilles Espaldon
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kumiko Oguma
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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Nowak KP, Sobolewska-Ruta A, Jagiełło A, Bierczyńska-Krzysik A, Kierył P, Wawrzyniak P. Molecular and Functional Characterization of MobK Protein-A Novel-Type Relaxase Involved in Mobilization for Conjugational Transfer of Klebsiella pneumoniae Plasmid pIGRK. Int J Mol Sci 2021; 22:5152. [PMID: 34068033 PMCID: PMC8152469 DOI: 10.3390/ijms22105152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 02/01/2023] Open
Abstract
Conjugation, besides transformation and transduction, is one of the main mechanisms of horizontal transmission of genetic information among bacteria. Conjugational transfer, due to its essential role in shaping bacterial genomes and spreading of antibiotics resistance genes, has been widely studied for more than 70 years. However, new and intriguing facts concerning the molecular basis of this process are still being revealed. Most recently, a novel family of conjugative relaxases (Mob proteins) was distinguished. The characteristic feature of these proteins is that they are not related to any of Mobs described so far. Instead of this, they share significant similarity to tyrosine recombinases. In this study MobK-a tyrosine recombinase-like Mob protein, encoded by pIGRK cryptic plasmid from the Klebsiella pneumoniae clinical strain, was characterized. This study revealed that MobK is a site-specific nuclease and its relaxase activity is dependent on both a conserved catalytic tyrosine residue (Y179) that is characteristic of tyrosine recombinases and the presence of Mg2+ divalent cations. The pIGRK minimal origin of transfer sequence (oriT) was also characterized. This is one of the first reports presenting tyrosine recombinase-like conjugative relaxase protein. It also demonstrates that MobK is a convenient model for studying this new protein family.
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Affiliation(s)
- Katarzyna Paulina Nowak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Agnieszka Sobolewska-Ruta
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Agata Jagiełło
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
- Central Forensic Laboratory of the Police, Biology Department, Iwicka 14, 00-735 Warsaw, Poland
| | - Anna Bierczyńska-Krzysik
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
- Curiosity Diagnostics Sp. z o.o., Duchnicka 3, Building 16, Entrance A, 01-796 Warsaw, Poland
| | - Piotr Kierył
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Paweł Wawrzyniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
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4
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Lewicka E, Dolowy P, Godziszewska J, Litwin E, Ludwiczak M, Jagura-Burdzy G. Transcriptional Organization of the Stability Module of Broad-Host-Range Plasmid RA3, from the IncU Group. Appl Environ Microbiol 2020; 86:e00847-20. [PMID: 32532870 PMCID: PMC7414963 DOI: 10.1128/aem.00847-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/06/2020] [Indexed: 02/06/2023] Open
Abstract
The broad-host-range (BHR) conjugative plasmids have developed diverse adaptive mechanisms defining the range of their promiscuity. The BHR conjugative RA3 plasmid, the archetype of the IncU group, can transfer between, replicate in, and be maintained in representatives of Alpha-, Beta-, and Gammaproteobacteria Its stability module encompasses ten open reading frames (ORFs) apparently organized into five operons, all transcribed in the same direction from several strong promoters that are tightly regulated either by autorepressors or by global plasmid-encoded regulators. In this paper, we demonstrate that owing to an efficient RNA polymerase (RNAP) read-through, the transcription from the first promoter, orf02p, may continue through the whole module. Moreover, an analysis of mRNA produced from the wild-type (WT) stability module and its deletion variants deprived of particular internal transcription initiation sites reveals that in fact each operon may be transcribed from any upstream promoter, giving rise to multicistronic transcripts of variable length and creating an additional level of gene expression control by transcript dosage adjustment. The gene expression patterns differ among various hosts, indicating that promoter recognition, regulation, and the RNAP read-through mechanisms are modulated in a species-specific manner.IMPORTANCE The efficiently disseminating conjugative or mobilizable BHR plasmids play key roles in the horizontal spread of genetic information between closely related and phylogenetically distant species, which can be harmful from the medical, veterinary, or industrial point of view. Understanding the mechanisms determining the plasmid's ability to function in diverse hosts is essential to help limit the spread of undesirable plasmid-encoded traits, e.g., antibiotic resistance. The range of a plasmid's promiscuity depends on the adaptations of its transfer, replication, and stability functions to the various hosts. IncU plasmids, with the archetype plasmid RA3, are considered to constitute a reservoir of antibiotic resistance genes in aquatic environments; however, the molecular mechanisms determining their adaptability to a broad range of hosts are rather poorly characterized. Here, we present the transcriptional organization of the stability module and show that the gene transcript dosage effect is an important determinant of the stable maintenance of RA3 in different hosts.
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Affiliation(s)
- Ewa Lewicka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Patrycja Dolowy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jolanta Godziszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Emilia Litwin
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Ludwiczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Grazyna Jagura-Burdzy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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5
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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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Sarkar MK, Husnain SI, Jakubowski SJ, Christie PJ. Isolation of bacterial type IV machine subassemblies. Methods Mol Biol 2013; 966:187-204. [PMID: 23299736 DOI: 10.1007/978-1-62703-245-2_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The bacterial type IV secretion systems (T4SSs) deliver DNA and protein substrates to bacterial and eukaryotic target cells generally by a mechanism requiring direct contact between donor and target cells. Recent advances in defining the architectures of T4SSs have been made through isolation of machine subassemblies for further biochemical and ultrastructural analysis. Here, we describe a protocol for isolation and characterization of VirB protein complexes from the paradigmatic VirB/VirD4 T4SS of Agrobacterium tumefaciens. This protocol can be adapted for isolation of T4SS subassemblies from other gram-negative bacteria as well as gram-positive bacteria. The biological importance of isolated T4SS subcomplexes can be assessed by assaying for copurification of trapped or cross-linked substrates. This can be achieved with a modified form of the chromatin immunoprecipitation (ChIP) assay termed transfer DNA immunoprecipitation (TrIP). Here, a TrIP protocol is described for recovery of formaldehyde-cross-linked DNA substrate-channel subunit complexes from cells employing T4SSs for conjugative DNA transfer.
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Affiliation(s)
- Mayukh K Sarkar
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, Houston, TX, USA
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7
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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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Complete sequence of pBFUK1, a carbapenemase-harboring mobilizable plasmid from Bacteroides fragilis, and distribution of pBFUK1-like plasmids among carbapenem-resistant B. fragilis clinical isolates. J Antibiot (Tokyo) 2012; 66:239-42. [PMID: 23232931 DOI: 10.1038/ja.2012.109] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Wong JJW, Lu J, Glover JNM. Relaxosome function and conjugation regulation in F-like plasmids - a structural biology perspective. Mol Microbiol 2012; 85:602-17. [PMID: 22788760 DOI: 10.1111/j.1365-2958.2012.08131.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The tra operon of the prototypical F plasmid and its relatives enables transfer of a copy of the plasmid to other bacterial cells via the process of conjugation. Tra proteins assemble to form the transferosome, the transmembrane pore through which the DNA is transferred, and the relaxosome, a complex of DNA-binding proteins at the origin of DNA transfer. F-like plasmid conjugation is characterized by a high degree of plasmid specificity in the interactions of tra components, and is tightly regulated at the transcriptional, translational and post-translational levels. Over the past decade, X-ray crystallography of conjugative components has yielded insights into both specificity and regulatory mechanisms. Conjugation is repressed by FinO, an RNA chaperone which increases the lifetime of the small RNA, FinP. Recent work has resulted in a detailed model of FinO/FinP interactions and the discovery of a family of FinO-like RNA chaperones. Relaxosome components include TraI, a relaxase/helicase, and TraM, which mediates signalling between the transferosome and relaxosome for transfer initiation. The structures of TraI and TraM bound to oriT DNA reveal the basis of specific recognition of DNA for their cognate plasmid. Specificity also exists in TraI and TraM interactions with the transferosome protein TraD.
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Affiliation(s)
- Joyce J W Wong
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
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Varsaki A, Lamb HK, Eleftheriadou O, Vandera E, Thompson P, Moncalián G, de la Cruz F, Hawkins AR, Drainas C. Interaction between relaxase MbeA and accessory protein MbeC of the conjugally mobilizable plasmid ColE1. FEBS Lett 2012; 586:675-9. [DOI: 10.1016/j.febslet.2012.01.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/24/2012] [Accepted: 01/27/2012] [Indexed: 02/01/2023]
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Alvarez-Martinez CE, Christie PJ. Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 2009; 73:775-808. [PMID: 19946141 PMCID: PMC2786583 DOI: 10.1128/mmbr.00023-09] [Citation(s) in RCA: 524] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Type IV secretion systems (T4SS) translocate DNA and protein substrates across prokaryotic cell envelopes generally by a mechanism requiring direct contact with a target cell. Three types of T4SS have been described: (i) conjugation systems, operationally defined as machines that translocate DNA substrates intercellularly by a contact-dependent process; (ii) effector translocator systems, functioning to deliver proteins or other macromolecules to eukaryotic target cells; and (iii) DNA release/uptake systems, which translocate DNA to or from the extracellular milieu. Studies of a few paradigmatic systems, notably the conjugation systems of plasmids F, R388, RP4, and pKM101 and the Agrobacterium tumefaciens VirB/VirD4 system, have supplied important insights into the structure, function, and mechanism of action of type IV secretion machines. Information on these systems is updated, with emphasis on recent exciting structural advances. An underappreciated feature of T4SS, most notably of the conjugation subfamily, is that they are widely distributed among many species of gram-negative and -positive bacteria, wall-less bacteria, and the Archaea. Conjugation-mediated lateral gene transfer has shaped the genomes of most if not all prokaryotes over evolutionary time and also contributed in the short term to the dissemination of antibiotic resistance and other virulence traits among medically important pathogens. How have these machines adapted to function across envelopes of distantly related microorganisms? A survey of T4SS functioning in phylogenetically diverse species highlights the biological complexity of these translocation systems and identifies common mechanistic themes as well as novel adaptations for specialized purposes relating to the modulation of the donor-target cell interaction.
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Affiliation(s)
- Cristina E. Alvarez-Martinez
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin, Houston, Texas 77030
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin, Houston, Texas 77030
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Plasmid r1 conjugative DNA processing is regulated at the coupling protein interface. J Bacteriol 2009; 191:6877-87. [PMID: 19767437 DOI: 10.1128/jb.00918-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Selective substrate uptake controls initiation of macromolecular secretion by type IV secretion systems in gram-negative bacteria. Type IV coupling proteins (T4CPs) are essential, but the molecular mechanisms governing substrate entry to the translocation pathway remain obscure. We report a biochemical approach to reconstitute a regulatory interface between the plasmid R1 T4CP and the nucleoprotein relaxosome dedicated to the initiation stage of plasmid DNA processing and substrate presentation. The predicted cytosolic domain of T4CP TraD was purified in a predominantly monomeric form, and potential regulatory effects of this protein on catalytic activities exhibited by the relaxosome during transfer initiation were analyzed in vitro. TraDDeltaN130 stimulated the TraI DNA transesterase activity apparently via interactions on both the protein and the DNA levels. TraM, a protein interaction partner of TraD, also increased DNA transesterase activity in vitro. The mechanism may involve altered DNA conformation as TraM induced underwinding of oriT plasmid DNA in vivo (DeltaL(k) = -4). Permanganate mapping of the positions of duplex melting due to relaxosome assembly with TraDDeltaN130 on supercoiled DNA in vitro confirmed localized unwinding at nic but ruled out formation of an open complex compatible with initiation of the TraI helicase activity. These data link relaxosome regulation to the T4CP and support the model that a committed step in the initiation of DNA export requires activation of TraI helicase loading or catalysis.
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