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Shapiro JA. A very brief note on why bacterial evolution has physiology. J Physiol 2024; 602:2395-2399. [PMID: 37641409 DOI: 10.1113/jp284409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
The majority of bacteria live and evolve in surface biofilms. Both growth in biofilms and horizontal transfer of DNA are regulated by quorum-sensing pheromone signals. The common regulation of bacterial surface growth and DNA transfers illustrates how physiology contributes to bacterial evolution.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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2
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Moréra S, Vigouroux A, Aumont-Nicaise M, Ahmar M, Meyer T, El Sahili A, Deicsics G, González-Mula A, Li S, Doré J, Sirigu S, Legrand P, Penot C, André F, Faure D, Soulère L, Queneau Y, Vial L. A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity. Biochem J 2024; 481:93-117. [PMID: 38058289 DOI: 10.1042/bcj20230273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/08/2023]
Abstract
Plants genetically modified by the pathogenic Agrobacterium strain C58 synthesize agrocinopines A and B, whereas those modified by the pathogenic strain Bo542 produce agrocinopines C and D. The four agrocinopines (A, B, C and D) serve as nutrients by agrobacteria and signaling molecule for the dissemination of virulence genes. They share the uncommon pyranose-2-phosphate motif, represented by the l-arabinopyranose moiety in agrocinopines A/B and the d-glucopyranose moiety in agrocinopines C/D, also found in the antibiotic agrocin 84. They are imported into agrobacterial cytoplasm via the Acc transport system, including the solute-binding protein AccA coupled to an ABC transporter. We have previously shown that unexpectedly, AccA from strain C58 (AccAC58) recognizes the pyranose-2-phosphate motif present in all four agrocinopines and agrocin 84, meaning that strain C58 is able to import agrocinopines C/D, originating from the competitor strain Bo542. Here, using agrocinopine derivatives and combining crystallography, affinity and stability measurements, modeling, molecular dynamics, in vitro and vivo assays, we show that AccABo542 and AccAC58 behave differently despite 75% sequence identity and a nearly identical ligand binding site. Indeed, strain Bo542 imports only compounds containing the d-glucopyranose-2-phosphate moiety, and with a lower affinity compared with strain C58. This difference in import efficiency makes C58 more competitive than Bo542 in culture media. We can now explain why Agrobacterium/Allorhizobium vitis strain S4 is insensitive to agrocin 84, although its genome contains a conserved Acc transport system. Overall, our work highlights AccA proteins as a case study, for which stability and dynamics drive specificity.
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Affiliation(s)
- Solange Moréra
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Armelle Vigouroux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Magali Aumont-Nicaise
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mohammed Ahmar
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Thibault Meyer
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
| | - Abbas El Sahili
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Grégory Deicsics
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Almudena González-Mula
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sizhe Li
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Jeanne Doré
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
| | - Serena Sirigu
- Synchrotron SOLEIL, HelioBio Group, 91190 Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio Group, 91190 Saint-Aubin, France
| | - Camille Penot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - François André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Denis Faure
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Laurent Soulère
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Yves Queneau
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Ludovic Vial
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
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Zhou J, Ma H, Zhang L. Mechanisms of Virulence Reprogramming in Bacterial Pathogens. Annu Rev Microbiol 2023; 77:561-581. [PMID: 37406345 DOI: 10.1146/annurev-micro-032521-025954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Bacteria are single-celled organisms that carry a comparatively small set of genetic information, typically consisting of a few thousand genes that can be selectively activated or repressed in an energy-efficient manner and transcribed to encode various biological functions in accordance with environmental changes. Research over the last few decades has uncovered various ingenious molecular mechanisms that allow bacterial pathogens to sense and respond to different environmental cues or signals to activate or suppress the expression of specific genes in order to suppress host defenses and establish infections. In the setting of infection, pathogenic bacteria have evolved various intelligent mechanisms to reprogram their virulence to adapt to environmental changes and maintain a dominant advantage over host and microbial competitors in new niches. This review summarizes the bacterial virulence programming mechanisms that enable pathogens to switch from acute to chronic infection, from local to systemic infection, and from infection to colonization. It also discusses the implications of these findings for the development of new strategies to combat bacterial infections.
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Affiliation(s)
- Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
| | - Hongmei Ma
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
| | - Lianhui Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
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Kuzmanović N, Wolf J, Will SE, Smalla K, diCenzo GC, Neumann-Schaal M. Diversity and Evolutionary History of Ti Plasmids of "tumorigenes" Clade of Rhizobium spp. and Their Differentiation from Other Ti and Ri Plasmids. Genome Biol Evol 2023; 15:evad133. [PMID: 37463407 PMCID: PMC10410297 DOI: 10.1093/gbe/evad133] [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: 06/21/2023] [Revised: 07/05/2023] [Accepted: 07/13/2023] [Indexed: 07/20/2023] Open
Abstract
Agrobacteria are important plant pathogens responsible for crown/cane gall and hairy root diseases. Crown/cane gall disease is associated with strains carrying tumor-inducing (Ti) plasmids, while hairy root disease is caused by strains harboring root-inducing (Ri) plasmids. In this study, we analyzed the sequences of Ti plasmids of the novel "tumorigenes" clade of the family Rhizobiaceae ("tumorigenes" Ti plasmids), which includes two species, Rhizobium tumorigenes and Rhizobium rhododendri. The sequences of reference Ti/Ri plasmids were also included, which was followed by a comparative analysis of their backbone and accessory regions. The "tumorigenes" Ti plasmids have novel opine signatures compared with other Ti/Ri plasmids characterized so far. The first group exemplified by pTi1078 is associated with production of agrocinopine, nopaline, and ridéopine in plant tumors, while the second group comprising pTi6.2 is responsible for synthesis of leucinopine. Bioinformatic and chemical analyses, including opine utilization assays, indicated that leucinopine associated with pTi6.2 most likely has D,L stereochemistry, unlike the L,L-leucinopine produced in tumors induced by reference strains Chry5 and Bo542. Most of the "tumorigenes" Ti plasmids have conjugative transfer system genes that are unusual for Ti plasmids, composed of avhD4/avhB and traA/mobC/parA regions. Next, our results suggested that "tumorigenes" Ti plasmids have a common origin, but they diverged through large-scale recombination events, through recombination with single or multiple distinct Ti/Ri plasmids. Lastly, we showed that Ti/Ri plasmids could be differentiated based on pairwise Mash or average amino-acid identity distance clustering, and we supply a script to facilitate application of the former approach by other researchers.
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Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Urban Green, Braunschweig, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Eva Will
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Chakraborty S, Bashir Y, Sirotiya V, Ahirwar A, Das S, Vinayak V. Role of bacterial quorum sensing and quenching mechanism in the efficient operation of microbial electrochemical technologies: A state-of-the-art review. Heliyon 2023; 9:e16205. [PMID: 37215776 PMCID: PMC10199210 DOI: 10.1016/j.heliyon.2023.e16205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Microbial electrochemical technologies (METs) are a group of innovative technologies that produce valuables like bioelectricity and biofuels with the simultaneous treatment of wastewater from microorganisms known as electroactive microorganisms. The electroactive microorganisms are capable of transferring electrons to the anode of a MET through various metabolic pathways such as direct (via cytochrome or pili) or indirect (through transporters) transfer. Though this technology is promising, the inferior yield of valuables and the high cost of reactor fabrication are presently impeding the large-scale application of this technology. Therefore, to overcome these major bottlenecks, a lot of research has been dedicated to the application of bacterial signalling, for instance, quorum sensing (QS) and quorum quenching (QQ) mechanisms in METs to improve its efficacy in order to achieve a higher power density and to make it more cost-effective. The QS circuit in bacteria produces auto-inducer signal molecules, which enhances the biofilm-forming ability and regulates the bacterial attachment on the electrode of METs. On the other hand, the QQ circuit can effectively function as an antifouling agent for the membranes used in METs and microbial membrane bioreactors, which is imperative for their stable long-term operation. This state-of-the-art review thus distinctly describes in detail the interaction between the QQ and QS systems in bacteria employed in METs to generate value-added by-products, antifouling strategies, and the recent applications of the signalling mechanisms in METs to improve their yield. Further, the article also throws some light on the recent advancements and the challenges faced while incorporating QS and QQ mechanisms in various types of METs. Thus, this review article will help budding researchers in upscaling METs with the integration of the QS signalling mechanism in METs.
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Affiliation(s)
- Sukanya Chakraborty
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
| | - Yasser Bashir
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Vandana Sirotiya
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
| | - Ankesh Ahirwar
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
- Metabolism, Bioengineering of Microalgal Metabolism and Applications (MIMMA), Mer Molecules Santé, Le Mans University, IUML - FR 3473 CNRS, Le Mans, France
| | - Sovik Das
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Vandana Vinayak
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
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Hooykaas PJJ. The Ti Plasmid, Driver of Agrobacterium Pathogenesis. PHYTOPATHOLOGY 2023; 113:594-604. [PMID: 37098885 DOI: 10.1094/phyto-11-22-0432-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The phytopathogenic bacterium Agrobacterium tumefaciens causes crown gall disease in plants, characterized by the formation of tumor-like galls where wounds were present. Nowadays, however, the bacterium and its Ti (tumor-inducing) plasmid is better known as an effective vector for the genetic manipulation of plants and fungi. In this review, I will briefly summarize some of the major discoveries that have led to this bacterium now playing such a prominent role worldwide in plant and fungal research at universities and research institutes and in agricultural biotechnology for the production of genetically modified crops. I will then delve a little deeper into some aspects of Agrobacterium biology and discuss the diversity among agrobacteria and the taxonomic position of these bacteria, the diversity in Ti plasmids, the molecular mechanism used by the bacteria to transform plants, and the discovery of protein translocation from the bacteria to host cells as an essential feature of Agrobacterium-mediated transformation.
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7
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Tiwari M, Mishra AK, Chakrabarty D. Agrobacterium-mediated gene transfer: recent advancements and layered immunity in plants. PLANTA 2022; 256:37. [PMID: 35819629 PMCID: PMC9274631 DOI: 10.1007/s00425-022-03951-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/19/2022] [Indexed: 05/15/2023]
Abstract
Plant responds to Agrobacterium via three-layered immunity that determines its susceptibility or resistance to Agrobacterium infection. Agrobacterium tumefaciens is a soil-borne Gram-negative bacterium that causes crown gall disease in plants. The remarkable feat of interkingdom gene transfer has been extensively utilised in plant biotechnology to transform plant as well as non-host systems. In the past two decades, the molecular mode of the pathogenesis of A. tumefaciens has been extensively studied. Agrobacterium has also been utilised as a premier model to understand the defence response of plants during plant-Agrobacterium interaction. Nonetheless, the threat of Agrobacterium-mediated crown gall disease persists and is associated with a huge loss of plant vigour in agriculture. Understanding the molecular dialogues between these two interkingdom species might provide a cure for crown gall disease. Plants respond to A. tumefaciens by mounting a three-layered immune response, which is manipulated by Agrobacterium via its virulence effector proteins. Comparative studies on plant defence proteins versus the counter-defence of Agrobacterium have shed light on plant susceptibility and tolerance. It is possible to manipulate a plant's immune system to overcome the crown gall disease and increase its competence via A. tumefaciens-mediated transformation. This review summarises the recent advances in the molecular mode of Agrobacterium pathogenesis as well as the three-layered immune response of plants against Agrobacterium infection.
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Affiliation(s)
- Madhu Tiwari
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Debasis Chakrabarty
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Characterization of the Agrobacterium octopine-cucumopine catabolic plasmid pAtAg67. Plasmid 2022; 121:102629. [DOI: 10.1016/j.plasmid.2022.102629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/06/2022] [Accepted: 03/29/2022] [Indexed: 11/21/2022]
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Asenstorfer RE, Ryder MH, Jones GP. Agrocinopine C, a Ti-plasmid-coded enzyme-product, is a 2-O, 6-O linked phosphodiester of D-Glucose and sucrose. PHYTOCHEMISTRY 2022; 194:113013. [PMID: 34839131 DOI: 10.1016/j.phytochem.2021.113013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/06/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Agrocinopine C is a small molecule found in crown gall tumours induced by pathogenic Agrobacterium radiobacter carrying the tumour-inducing plasmid pTi Bo542. This phosphodiester opine was isolated (at 0.02 g/100 g fresh wt.) from sunflower (Helianthus annuus L.) galls. It is structurally related to agrocinopine A and is a glucose-2-phosphodiester linked to the C6-hydroxy-methyl group of the glucose moiety of sucrose. Sugar-2-phosphates are uncommon in plant tissues, whether transformed by Agrobacterium or not. 1H and 31P NMR signal multiplicity indicates five-fold anomeric complexity of agrocinopine C in solution, implying that the permeases taking up these sucrose-phosphodiesters could recognise any one of the five anomers. Data suggests that the open chain aldehyde forms of the 2-phosphorylated opines agrocinopine C and agrocinopine A and the corresponding phosphorylated glucose-2-phosphoramidate component of the antibiotic agrocin 84 play a central role in agrocin's selective toxicity to certain strains of Agrobacterium after uptake via Ti plasmid-encoded permeases.
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Affiliation(s)
- Robert E Asenstorfer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia
| | - Maarten H Ryder
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia.
| | - Graham P Jones
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia
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Nabi N, Ben Hafsa A, Gaillard V, Nesme X, Chaouachi M, Vial L. Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions. Mol Phylogenet Evol 2022; 169:107388. [PMID: 35017066 DOI: 10.1016/j.ympev.2022.107388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 11/15/2020] [Accepted: 12/08/2021] [Indexed: 11/19/2022]
Abstract
Tumor-inducing (Ti) and root-inducing (Ri) plasmids of Agrobacterium that display a large diversity are involved in crown gall and hairy root plant diseases. Their phylogenetic relationships were inferred from an exhaustive set of Ti and Ri plasmids (including 36 new complete Ti plasmids) by focusing on T-DNA and virulence regions. The opine synthase gene content of T-DNAs revealed 13 opine types corresponding to former classifications based on opines detected in diseased plants, while the T-DNA gene content more finely separate opine types in 18 T-DNA organizations. This classification was supported by the phylogeny of T-DNA oncogenes of Ti plasmids. The five gene organizations found in Ti/Ri vir regions was supported by the phylogeny of common vir genes. The vir organization was found to be likely an ancestral plasmid trait separating "classic" Ti plasmids (with one or two T-DNAs) and "Ri and vine-Ti" plasmids. A scenario generally supported by the repABC phylogeny. T-DNAs likely evolved later with the acquisition of opine characteristics as last steps in the Ti/Ri plasmid evolution. This novel evolutionary classification of Ti/Ri plasmids was found to be relevant for accurate crown gall and hairy root epidemiology.
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Affiliation(s)
- Nesrine Nabi
- Unité de Recherche UR17ES30 Génomique, Biotechnologie et Stratégies Antivirales, Institut Supérieur de Biotechnologie, Université de Monastir, Monastir, Tunisie.
| | - Ahmed Ben Hafsa
- Unité de Recherche UR17ES30 Génomique, Biotechnologie et Stratégies Antivirales, Institut Supérieur de Biotechnologie, Université de Monastir, Monastir, Tunisie
| | - Vincent Gaillard
- Laboratoire d'Ecologie Microbienne (LEM), UCBL, CNRS, INRAE, VetAgro Sup, Univ Lyon, F-69622 Villeurbanne Cedex, France
| | - Xavier Nesme
- Laboratoire d'Ecologie Microbienne (LEM), UCBL, CNRS, INRAE, VetAgro Sup, Univ Lyon, F-69622 Villeurbanne Cedex, France
| | - Maher Chaouachi
- Unité de Recherche UR17ES30 Génomique, Biotechnologie et Stratégies Antivirales, Institut Supérieur de Biotechnologie, Université de Monastir, Monastir, Tunisie
| | - Ludovic Vial
- Laboratoire d'Ecologie Microbienne (LEM), UCBL, CNRS, INRAE, VetAgro Sup, Univ Lyon, F-69622 Villeurbanne Cedex, France.
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11
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Hooykaas MJG, Hooykaas PJJ. Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid. BMC Microbiol 2021; 21:295. [PMID: 34711172 PMCID: PMC8554961 DOI: 10.1186/s12866-021-02358-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/06/2021] [Indexed: 01/18/2023] Open
Abstract
Background The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7012 genes (6948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in ridéopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02358-0.
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Otten L. T-DNA regions from 350 Agrobacterium genomes: maps and phylogeny. PLANT MOLECULAR BIOLOGY 2021; 106:239-258. [PMID: 33826062 DOI: 10.1007/s11103-021-01140-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/12/2021] [Indexed: 05/27/2023]
Abstract
Analysis of 350 Agrobacterium wgs sequences reveals complex evolutionary history of T-DNA regions Virulent Agrobacterium strains transfer one or more plasmid DNA fragments to plant cells during a well-characterized transformation process. The transferred DNA sequences (T-DNA regions) are delimited by 25 nucleotide long conserved border sequences. Until recently, relatively few T-DNA regions were known. However, due to increased whole genome sequencing efforts, about 400 Agrobacterium sequences have now become available, 350 of which contain T-DNA regions. Detailed analysis identified 92 different T-DNA regions and several new T-DNA genes. T-DNA regions can be divided into three groups. I. Typical Agrobacterium rhizogenes T-DNA regions with rol genes. II. A large group of T-DNA regions with iaa and ipt genes, which can be further subdivided into seven subgroups. III. A small group of unusual T-DNA regions. The evolutionary relation between the T-DNA regions could not be completely elucidated, because of the lack of evolutionary intermediates. Several clusters of highly related structures suggest that evolution of T-DNA regions proceeds by slow, progressive evolution of gene sequences, accompanied by rapid changes in overall structure, due to recombination between T-DNA regions of different origins, and insertion of bacterial insertion sequences (IS). Divergence values for T-DNA genes suggest that they were recruited at different times in evolution. An attempt was made to link T-DNA region evolution to plasmid evolution. The present study provides a solid basis for further studies on T-DNA region diversity and evolution.
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Affiliation(s)
- Léon Otten
- Institut de Biologie Moléculaire des Plantes, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
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13
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Hooykaas MJG, Hooykaas PJJ. The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402: Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid. Microbiologyopen 2021; 10:e1180. [PMID: 33970547 PMCID: PMC8087989 DOI: 10.1002/mbo3.1180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
We report here the complete genome sequence of the Rhizobium rhizogenes (formerly Agrobacterium rhizogenes) strain LBA9402 (NCPPB1855rifR), a pathogenic strain causing hairy root disease. To assemble a complete genome, we obtained short reads from Illumina sequencing and long reads from Oxford Nanopore Technology sequencing. The genome consists of a 3,958,212 bp chromosome, a 2,005,144 bp chromid (secondary chromosome) and a 252,168 bp Ri plasmid (pRi1855), respectively. The primary chromosome was very similar to that of the avirulent biocontrol strain K84, but the chromid showed a 724 kbp deletion accompanied by a large 1.8 Mbp inversion revealing the dynamic nature of these secondary chromosomes. The sequence of the agropine Ri plasmid was compared to other types of Ri and Ti plasmids. Thus, we identified the genes responsible for agropine catabolism, but also a unique segment adjacent to the TL region that has the signature of a new opine catabolic gene cluster including the three genes that encode the three subunits of an opine dehydrogenase. Our sequence analysis also revealed a novel gene at the very right end of the TL-DNA, which is unique for the agropine Ri plasmid. The protein encoded by this gene was most related to the succinamopine synthases of chrysopine and agropine Ti plasmids and thus may be involved in the synthesis of the unknown opine that can be degraded by the adjacent catabolic cluster. The available sequence will facilitate the use of R. rhizogenes and especially LBA9402 in both the laboratory and for biotechnological purposes.
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14
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Barton IS, Eagan JL, Nieves-Otero PA, Reynolds IP, Platt TG, Fuqua C. Co-dependent and Interdigitated: Dual Quorum Sensing Systems Regulate Conjugative Transfer of the Ti Plasmid and the At Megaplasmid in Agrobacterium tumefaciens 15955. Front Microbiol 2021; 11:605896. [PMID: 33552018 PMCID: PMC7856919 DOI: 10.3389/fmicb.2020.605896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Members of the Rhizobiaceae, often carry multiple secondary replicons in addition to the primary chromosome with compatible repABC-based replication systems. Unlike secondary chromosomes and chromids, repABC-based megaplasmids and plasmids can undergo copy number fluctuations and are capable of conjugative transfer in response to environmental signals. Several Agrobacterium tumefaciens lineages harbor three secondary repABC-based replicons, including a secondary chromosome (often linear), the Ti (tumor-inducing) plasmid and the At megaplasmid. The Ti plasmid is required for virulence and encodes a conjugative transfer (tra) system that is strictly regulated by a subset of plant-tumor released opines and a well-described acyl-homoserine lactone (AHL)-based quorum-sensing mechanism. The At plasmids are generally not required for virulence, but carry genes that enhance rhizosphere survival, and these plasmids are often conjugatively proficient. We report that the At megaplasmid of the octopine-type strain A. tumefaciens 15955 encodes a quorum-controlled conjugation system that directly interacts with the paralogous quorum sensing system on the co-resident Ti plasmid. Both the pAt15955 and pTi15955 plasmids carry homologs of a TraI-type AHL synthase, a TraR-type AHL-responsive transcription activator, and a TraM-type anti-activator. The traI genes from both pTi15955 and pAt15955 can direct production of the inducing AHL (3-octanoyl-L-homoserine lactone) and together contribute to the overall AHL pool. The TraR protein encoded on each plasmid activates AHL-responsive transcription of target tra gene promoters. The pAt15955 TraR can cross-activate tra genes on the Ti plasmid as strongly as its cognate tra genes, whereas the pTi15955 TraR is preferentially biased toward its own tra genes. Putative tra box elements are located upstream of target promoters, and comparing between plasmids, they are in similar locations and share an inverted repeat structure, but have distinct consensus sequences. The two AHL quorum sensing systems have a combinatorial effect on conjugative transfer of both plasmids. Overall, the interactions described here have implications for the horizontal transfer and evolutionary stability of both plasmids and, in a broad sense, are consistent with other repABC systems that often have multiple quorum-sensing controlled secondary replicons.
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Affiliation(s)
- Ian S Barton
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Justin L Eagan
- Department of Biology, Indiana University, Bloomington, IN, United States
| | | | - Ian P Reynolds
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Thomas G Platt
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN, United States
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15
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Weisberg AJ, Davis EW, Tabima J, Belcher MS, Miller M, Kuo CH, Loper JE, Grünwald NJ, Putnam ML, Chang JH. Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 2020; 368:368/6495/eaba5256. [PMID: 32499412 DOI: 10.1126/science.aba5256] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/28/2020] [Accepted: 04/27/2020] [Indexed: 12/21/2022]
Abstract
The accelerated evolution and spread of pathogens are threats to host species. Agrobacteria require an oncogenic Ti or Ri plasmid to transfer genes into plants and cause disease. We developed a strategy to characterize virulence plasmids and applied it to analyze hundreds of strains collected between 1927 and 2017, on six continents and from more than 50 host species. In consideration of prior evidence for prolific recombination, it was surprising that oncogenic plasmids are descended from a few conserved lineages. Characterization of a hierarchy of features that promote or constrain plasticity allowed inference of the evolutionary history across the plasmid lineages. We uncovered epidemiological patterns that highlight the importance of plasmid transmission in pathogen diversification as well as in long-term persistence and the global spread of disease.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
| | - Javier Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Michael S Belcher
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marilyn Miller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA.,Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR 97331, USA
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR 97331, USA
| | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA. .,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA.,Center for Genome Research and Biocomputing (CGRB), Oregon State University, Corvallis, OR 97331, USA
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16
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Cavassim MIA, Moeskjær S, Moslemi C, Fields B, Bachmann A, Vilhjálmsson BJ, Schierup MH, W. Young JP, Andersen SU. Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex. Microb Genom 2020; 6:e000351. [PMID: 32176601 PMCID: PMC7276703 DOI: 10.1099/mgen.0.000351] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/17/2020] [Indexed: 12/22/2022] Open
Abstract
Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.
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Affiliation(s)
- Maria Izabel A. Cavassim
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Sara Moeskjær
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Camous Moslemi
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Asger Bachmann
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | | | | | | | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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17
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Kuzmanović N, Puławska J. Evolutionary Relatedness and Classification of Tumor-Inducing and Opine-Catabolic Plasmids in Three Rhizobium rhizogenes Strains Isolated from the Same Crown Gall Tumor. Genome Biol Evol 2019; 11:1525-1540. [PMID: 31028704 PMCID: PMC6546132 DOI: 10.1093/gbe/evz091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/12/2022] Open
Abstract
Plasmids play a crucial role in the ecology of agrobacteria. In this study, we sequenced tumor-inducing (Ti) and opine-catabolic (OC) plasmids in three Rhizobium rhizogenes (Agrobacterium biovar 2) strains isolated from the same crown gall tumor on “Colt” cherry rootstock and conducted comparative genomic analyses. Tumorigenic strains C5.7 and C6.5 carry nopaline-type Ti plasmids pTiC5.7/pTiC6.5, whereas the nonpathogenic strain Colt5.8 carries the nopaline-type OC plasmid pOC-Colt5.8. Overall, comparative genomic analysis indicated that pTiC5.7/pTiC6.5 and related Ti plasmids described before (pTiC58 and pTi-SAKURA) originate from a common ancestor, although they have diverged during evolution. On the other hand, plasmid pOC-Colt5.8 was most closely related to the well-known OC plasmid pAtK84b; however, analysis suggested that they had different evolutionary histories and seem to share a more distant common ancestor. Although the reconstruction of the evolutionary history of Ti and OC plasmids is still speculative, we hypothesized that nopaline-type Ti plasmid might originate from the nopaline-type OC plasmid. Our results suggested that OC plasmids are widespread and closely associated with crown gall tumors. Finally, we proposed a thorough scheme for classification of Ti and OC plasmids that is based on separate comparative analysis of each functional element of the plasmid studied.
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Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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18
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The Ecology of Agrobacterium vitis and Management of Crown Gall Disease in Vineyards. Curr Top Microbiol Immunol 2019; 418:15-53. [PMID: 29556824 DOI: 10.1007/82_2018_85] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Agrobacterium vitis is the primary causal agent of grapevine crown gall worldwide. Symptoms of grapevine crown gall disease include tumor formation on the aerial plant parts, whereas both tumorigenic and nontumorigenic strains of A. vitis cause root necrosis. Genetic and genomic analyses indicated that A. vitis is distinguishable from the members of the Agrobacterium genus and its transfer to the genus Allorhizobium was suggested. A. vitis is genetically diverse, with respect to both chromosomal and plasmid DNA. Its pathogenicity is mainly determined by a large conjugal tumor-inducing (Ti) plasmid characterized by a mosaic structure with conserved and variable regions. Traditionally, A. vitis Ti plasmids and host strains were differentiated into octopine/cucumopine, nopaline, and vitopine groups, based on opine markers. However, tumorigenic and nontumorigenic strains of A. vitis may carry other ecologically important plasmids, such as tartrate- and opine-catabolic plasmids. A. vitis colonizes vines endophytically. It is also able to survive epiphytically on grapevine plants and is detected in soil exclusively in association with grapevine plants. Because A. vitis persists systemically in symptomless grapevine plants, it can be efficiently disseminated to distant geographical areas via international trade of propagation material. The use of healthy planting material in areas with no history of the crown gall represents the crucial measure of disease management. Moreover, biological control and production of resistant grape varieties are encouraging as future control measures.
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19
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Wetzel ME, Asenstorfer RE, Tate ME, Farrand SK. Quorum-dependent transfer of the opine-catabolic plasmid pAoF64/95 is regulated by a novel mechanism involving inhibition of the TraR antiactivator TraM. Microbiologyopen 2019; 8:e00625. [PMID: 29635848 PMCID: PMC6341043 DOI: 10.1002/mbo3.625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/27/2018] [Accepted: 01/30/2018] [Indexed: 11/06/2022] Open
Abstract
We previously described a plasmid of Agrobacterium spp., pAoF64/95, in which the quorum-sensing system that controls conjugative transfer is induced by the opine mannopine. We also showed that the quorum-sensing regulators TraR, TraM, and TraI function similarly to their counterparts in other repABC plasmids. However, traR, unlike its counterpart on Ti plasmids, is monocistronic and not located in an operon that is inducible by the conjugative opine. Here, we report that both traR and traM are expressed constitutively and not regulated by growth with mannopine. We report two additional regulatory genes, mrtR and tmsP, that are involved in a novel mechanism of control of TraR activity. Both genes are located in the distantly linked region of pAoF64/95 encoding mannopine utilization. MrtR, in the absence of mannopine, represses the four-gene mocC operon as well as tmsP, which is the distal gene of the eight-gene motA operon. As judged by a bacterial two-hybrid analysis, TmsP, which shows amino acid sequence relatedness with the TraM-binding domain of TraR, interacts with the antiactivator. We propose a model in which mannopine, acting through the repressor MrtR, induces expression of TmsP which then titrates the levels of TraM thereby freeing TraR to activate the tra regulon.
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Affiliation(s)
- Margaret E. Wetzel
- Department of MicrobiologyThe University of Illinois at Urbana‐ChampaignUrbanaILUSA
| | | | - Max E. Tate
- School of Agriculture, Food and WineThe University of AdelaideOsmondSAAustralia
| | - Stephen K. Farrand
- Department of MicrobiologyThe University of Illinois at Urbana‐ChampaignUrbanaILUSA
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20
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Yamamoto S, Agustina V, Sakai A, Moriguchi K, Suzuki K. An extra repABC locus in the incRh2 Ti plasmid pTiBo542 exerts incompatibility toward an incRh1 plasmid. Plasmid 2017; 90:20-29. [PMID: 28238706 DOI: 10.1016/j.plasmid.2017.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
Abstract
Ti/Ri plasmids in pathogenic Agrobacterium species are repABC replicons that are stably maintained by the function of repABC genes. Two Ti plasmids, pTiBo542 and pTiS4, belonging to incRh2 and incRh4 incompatibility groups, respectively, were reported to carry two repABC loci. In the present study, to reveal the roles of the two repABC loci in the two plasmids, we constructed mini-replicons carrying any one or both of the repABC loci (referred to as repABC1 and repABC2 here) and examined their replication and incompatibility properties. The introduction of mini-replicons into A. tumefaciens C58C1 strains suggested that repABC1 functions as replicator genes but repABC2 does not in both the Ti plasmids. Because the components of repABC2 of pTiBo542 have highly similar amino acid and nucleotide sequences to those of the incRh1-type repABC replicon, we introduced repABC2-containing replicons into cells harboring an incRh1 plasmid in order to check their incompatibility traits. As a result, the repABC2-containing replicon expelled the resident incRh1 plasmid, indicating that the extra repABC locus is dispensable for replication and could work as an incompatibility determinant against incRh1 group plasmids. We suggest that the locus contributes to plasmid retention by eliminating the burden of co-existing competitive plasmids in host cells through its incompatibility.
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Affiliation(s)
- Shinji Yamamoto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Vita Agustina
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Ayako Sakai
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Kazuki Moriguchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Katsunori Suzuki
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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