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Ishii T, Tsuchida N, Hemelda NM, Saito K, Bao J, Watanabe M, Toyoda A, Matsubara T, Sato M, Toyooka K, Ishihama N, Shirasu K, Matsui H, Toyoda K, Ichinose Y, Hayashi T, Kawaguchi A, Noutoshi Y. Rhizoviticin is an alphaproteobacterial tailocin that mediates biocontrol of grapevine crown gall disease. THE ISME JOURNAL 2024; 18:wrad003. [PMID: 38365227 PMCID: PMC10811719 DOI: 10.1093/ismejo/wrad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 02/18/2024]
Abstract
Tailocins are headless phage tail structures that mediate interbacterial antagonism. Although the prototypical tailocins, R- and F-pyocins, in Pseudomonas aeruginosa, and other predominantly R-type tailocins have been studied, their presence in Alphaproteobacteria remains unexplored. Here, we report the first alphaproteobacterial F-type tailocin, named rhizoviticin, as a determinant of the biocontrol activity of Allorhizobium vitis VAR03-1 against crown gall. Rhizoviticin is encoded by a chimeric prophage genome, one providing transcriptional regulators and the other contributing to tail formation and cell lysis, but lacking head formation genes. The rhizoviticin genome retains a nearly intact early phage region containing an integrase remnant and replication-related genes critical for downstream gene transcription, suggesting an ongoing transition of this locus from a prophage to a tailocin-coding region. Rhizoviticin is responsible for the most antagonistic activity in VAR03-1 culture supernatant against pathogenic A. vitis strain, and rhizoviticin deficiency resulted in a significant reduction in the antitumorigenic activity in planta. We identified the rhizoviticin-coding locus in eight additional A. vitis strains from diverse geographical locations, highlighting a unique survival strategy of certain Rhizobiales bacteria in the rhizosphere. These findings advance our understanding of the evolutionary dynamics of tailocins and provide a scientific foundation for employing rhizoviticin-producing strains in plant disease control.
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Affiliation(s)
- Tomoya Ishii
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Natsuki Tsuchida
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
- Present address: Division of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Niarsi Merry Hemelda
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Department of Biology, University of Indonesia, Depok 16424, Indonesia
| | - Kirara Saito
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Present address: Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki 885-0091, Japan
| | - Jiyuan Bao
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Megumi Watanabe
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiro Matsubara
- Okayama University Hospital Biobank, Okayama University Hospital, Okayama 700-8558, Japan
| | - Mayuko Sato
- Mass Spectrometry and Microscopy Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Kiminori Toyooka
- Mass Spectrometry and Microscopy Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Nobuaki Ishihama
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Graduate School of Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hidenori Matsui
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Yuki Ichinose
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Kawaguchi
- Western Region Agricultural Research Center (WARC), National Agricultural and Food Research Organization (NARO), Fukuyama, Hiroshima 721-8514, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
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Brown PJB, Chang JH, Fuqua C. Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology. J Bacteriol 2023; 205:e0000523. [PMID: 36892285 PMCID: PMC10127608 DOI: 10.1128/jb.00005-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.
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Affiliation(s)
- Pamela J. B. Brown
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Xi H, Grist J, Ryder M, Searle IR. Complete Genome Sequence Data for the Grapevine Crown Gall-Inhibiting Bacteria Allorhizobium vitis F2/5. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:174-176. [PMID: 34713721 DOI: 10.1094/mpmi-09-21-0223-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Hangwei Xi
- School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Josh Grist
- School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Maarten Ryder
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, 5064, Australia
| | - Iain R Searle
- School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
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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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Hao L, Kemmenoe DJ, Orel DC, Burr T. The Impacts of Tumorigenic and Nontumorigenic Agrobacterium vitis Strains on Graft Strength and Growth of Grapevines. PLANT DISEASE 2018; 102:375-381. [PMID: 30673517 DOI: 10.1094/pdis-07-17-0952-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The effects of tumorigenic and nontumorigenic strains of Agrobacterium vitis on graft strength and growth of grapevines was studied. A procedure was developed for inoculating graft interface surfaces with A. vitis and for measuring the force required to break grafts at different time points. Cuttings were soaked in an aqueous suspension of bacteria, about 106 CFU/ml, and bacteria were spread onto the graft interface during the grafting procedure. Tumorigenic strain CG49 caused reduced bud germination and increased callus (crown gall) at the graft union and at the base of cuttings at 30 days postinoculation (dpi) and significantly reduced shoot growth by 60 dpi whereas, at the same time points, nontumorigenic strain F2/5 inhibited callus formation but did not affect bud germination or shoot growth. Graft strength was enhanced at 30 dpi with CG49, presumably because the crown gall callus served to secure the union; graft strength was weakened by F2/5 over the same period. Between 30 and 60 dpi, the greatest increase in graft strength was observed in the water control. Following graft union inoculations, the A. vitis population increased more than 1,000-fold within 5 days.
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Affiliation(s)
- Lingyun Hao
- College of Life Sciences and Oceanography, Shenzhen University, Guang Dong 518060, P.R. China, and Section of Plant Pathology and Plant-Microbe Biology, SIPS, Cornell University-New York State Agricultural Experiment Station, Geneva, NY, 14456
| | - David J Kemmenoe
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850
| | - Didem Canik Orel
- Department of Plant Protection, Ankara University, Ankara, Turkey
| | - Thomas Burr
- Section of Plant Pathology and Plant-Microbe Biology, SIPS, Cornell University-New York State Agricultural Experiment Station
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Barton IS, Fuqua C, Platt TG. Ecological and evolutionary dynamics of a model facultative pathogen: Agrobacterium and crown gall disease of plants. Environ Microbiol 2018; 20:16-29. [PMID: 29105274 PMCID: PMC5764771 DOI: 10.1111/1462-2920.13976] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 01/09/2023]
Abstract
Many important pathogens maintain significant populations in highly disparate disease and non-disease environments. The consequences of this environmental heterogeneity in shaping the ecological and evolutionary dynamics of these facultative pathogens are incompletely understood. Agrobacterium tumefaciens, the causative agent for crown gall disease of plants has proven a productive model for many aspects of interactions between pathogens and their hosts and with other microbes. In this review, we highlight how this past work provides valuable context for the use of this system to examine how heterogeneity and transitions between disease and non-disease environments influence the ecology and evolution of facultative pathogens. We focus on several features common among facultative pathogens, such as the physiological remodelling required to colonize hosts from environmental reservoirs and the consequences of competition with host and non-host associated microbiota. In addition, we discuss how the life history of facultative pathogens likely often results in ecological tradeoffs associated with performance in disease and non-disease environments. These pathogens may therefore have different competitive dynamics in disease and non-disease environments and are subject to shifting selective pressures that can result in pathoadaptation or the within-host spread of avirulent phenotypes.
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Affiliation(s)
- Ian S. Barton
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Thomas G. Platt
- Division of Biology, Kansas State University, Manhattan, KS, USA
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Grapevine (Vitis vinifera) Crown Galls Host Distinct Microbiota. Appl Environ Microbiol 2016; 82:5542-52. [PMID: 27371584 DOI: 10.1128/aem.01131-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/27/2016] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED Crown gall disease of grapevine is caused by virulent Agrobacterium strains and establishes a suitable habitat for agrobacteria and, potentially, other bacteria. The microbial community associated with grapevine plants has not been investigated with respect to this disease, which frequently results in monetary losses. This study compares the endophytic microbiota of organs from grapevine plants with or without crown gall disease and the surrounding vineyard soil over the growing seasons of 1 year. Amplicon-based community profiling revealed that the dominating factor causing differences between the grapevine microbiota is the sample site, not the crown gall disease. The soil showed the highest microbial diversity, which decreased with the distance from the soil over the root and the graft union of the trunk to the cane. Only the graft union microbiota was significantly affected by crown gall disease. The bacterial community of graft unions without a crown gall hosted transient microbiota, with the three most abundant bacterial species changing from season to season. In contrast, graft unions with a crown gall had a higher species richness, which in every season was dominated by the same three bacteria (Pseudomonas sp., Enterobacteriaceae sp., and Agrobacterium vitis). For in vitro-cultivated grapevine plantlets, A. vitis infection alone was sufficient to cause crown gall disease. Our data show that microbiota in crown galls is more stable over time than microbiota in healthy graft unions and that the microbial community is not essential for crown gall disease outbreak. IMPORTANCE The characterization of bacterial populations in animal and human diseases using high-throughput deep-sequencing technologies, such as 16S amplicon sequencing, will ideally result in the identification of disease-specific microbiota. We analyzed the microbiota of the crown gall disease of grapevine, which is caused by infection with the bacterial pathogen Agrobacterium vitis. All other Agrobacterium species were found to be avirulent, even though they lived together with A. vitis in the same crown gall tumor. As has been reported for human cancer, the crown gall tumor also hosted opportunistic bacteria that are adapted to the tumor microenvironment. Characterization of the microbiota in various diseases using amplicon sequencing may help in early diagnosis, to serve as a preventative measure of disease in the future.
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