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Polidore ALA, Caserio AD, Zhu L, Metcalf WW. Complete Biochemical Characterization of Pantaphos Biosynthesis Highlights an Unusual Role for a SAM-Dependent Methyltransferase. Angew Chem Int Ed Engl 2024; 63:e202317262. [PMID: 38141166 PMCID: PMC10873477 DOI: 10.1002/anie.202317262] [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: 11/13/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/25/2023]
Abstract
Pantaphos is small molecule virulence factor made by the plant pathogen Pantoea ananatis. An 11 gene operon, designated hvr for high virulence, is required for production of this phosphonic acid natural product, but the metabolic steps used in its production have yet to be established. Herein, we determine the complete biosynthetic pathway using a combination of bioinformatics, in vitro biochemistry and in vivo heterologous expression. Only 6 of the 11 hvr genes are needed to produce pantaphos, while a seventh is likely to be required for export. Surprisingly, the pathway involves a series of O-methylated intermediates, which are then hydrolyzed to produce the final product. The methylated intermediates are produced by an irreversible S-adenosylmethione (SAM)-dependent methyltransferase that is required to drive a thermodynamically unfavorable dehydration in the preceding step, a function not previously attributed to members of this enzyme class. Methylation of pantaphos by the same enzyme is also likely to limit its toxicity in the producing organism. The pathway also involves a novel flavin-dependent monooxygenase that differs from homologous proteins due to its endogenous flavin-reductase activity. Heterologous production of pantaphos by Escherichia coli strains expressing the minimal gene set strongly supports the in vitro biochemical data.
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Affiliation(s)
- Alexander L A Polidore
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin, Urbana, IL 61874, USA
| | - Angelica D Caserio
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin, Urbana, IL 61874, USA
| | - Lingyang Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Ave, Urbana, IL 61874, USA
| | - William W Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin, Urbana, IL 61874, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61874, USA
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Crosby KC, Rojas M, Sharma P, Johnson MA, Mazloom R, Kvitko BH, Smits THM, Venter SN, Coutinho TA, Heath LS, Palmer M, Vinatzer BA. Genomic delineation and description of species and within-species lineages in the genus Pantoea. Front Microbiol 2023; 14:1254999. [PMID: 38029109 PMCID: PMC10665919 DOI: 10.3389/fmicb.2023.1254999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.
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Affiliation(s)
- Katherine C. Crosby
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Mariah Rojas
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Parul Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Marcela A. Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Theo H. M. Smits
- Environmental Genomics and System Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Teresa A. Coutinho
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Boris A. Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Zhao M, Shin GY, Stice S, Bown JL, Coutinho T, Metcalf WW, Gitaitis R, Kvitko B, Dutta B. A Novel Biosynthetic Gene Cluster Across the Pantoea Species Complex Is Important for Pathogenicity in Onion. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:176-188. [PMID: 36534063 PMCID: PMC10433531 DOI: 10.1094/mpmi-08-22-0165-r] [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] [Indexed: 06/01/2023]
Abstract
Onion center rot is caused by at least four species of genus Pantoea (P. ananatis, P. agglomerans, P. allii, and P. stewartii subsp. indologenes). Critical onion pathogenicity determinants for P. ananatis were recently described, but whether those determinants are common among other onion-pathogenic Pantoea species remains unknown. In this work, we report onion pathogenicity determinants in P. stewartii subsp. indologenes and P. allii. We identified two distinct secondary metabolite biosynthetic gene clusters present separately in different strains of onion-pathogenic P. stewartii subsp. indologenes. One cluster is similar to the previously described HiVir phosphonate biosynthetic cluster identified in P. ananatis and another is a novel putative phosphonate biosynthetic gene cluster, which we named Halophos. The Halophos gene cluster was also identified in P. allii strains. Both clusters are predicted to be phosphonate biosynthetic clusters based on the presence of a characteristic phosphoenolpyruvate phosphomutase (pepM) gene. The deletion of the pepM gene from either HiVir or Halophos clusters in P. stewartii subsp. indologenes caused loss of necrosis on onion leaves and red onion scales and resulted in significantly lower bacterial populations compared with the corresponding wild-type and complemented strains. Seven (halB to halH) of 11 genes (halA to halK) in the Halophos gene cluster are required for onion necrosis phenotypes. The onion nonpathogenic strain PNA15-2 (P. stewartii subsp. indologenes) gained the capacity to cause foliar necrosis on onion via exogenous expression of a minimal seven-gene Halophos cluster (genes halB to halH). Furthermore, cell-free culture filtrates of PNA14-12 expressing the intact Halophos gene cluster caused necrosis on onion leaves consistent with the presence of a secreted toxin. Based on the similarity of proteins to those with experimentally determined functions, we are able to predict most of the steps in Halophos biosynthesis. Together, these observations indicate that production of the toxin phosphonate seems sufficient to account for virulence of a variety of different Pantoea strains, although strains differ in possessing a single but distinct phosphonate biosynthetic cluster. Overall, this is the first report of onion pathogenicity determinants in P. stewartii subsp. indologenes and P. allii. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mei Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, P. R. China
- Department of Plant Pathology, University of Georgia, Tifton GA USA
| | - Gi Yoon Shin
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Shaun Stice
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Jonathon Luke Bown
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL
| | - Teresa Coutinho
- The Genomics Research Institute, University of Pretoria, Hatfield, South Africa
| | - William W. Metcalf
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL
| | - Ron Gitaitis
- Department of Plant Pathology, University of Georgia, Tifton GA USA
| | - Brian Kvitko
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton GA USA
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Myers BK, Shin GY, Agarwal G, Stice SP, Gitaitis RD, Kvitko BH, Dutta B. Genome-wide association and dissociation studies in Pantoea ananatis reveal potential virulence factors affecting Allium porrum and Allium fistulosum × Allium cepa hybrid. Front Microbiol 2023; 13:1094155. [PMID: 36817114 PMCID: PMC9933511 DOI: 10.3389/fmicb.2022.1094155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/30/2022] [Indexed: 02/05/2023] Open
Abstract
Pantoea ananatis is a member of a Pantoea species complex that causes center rot of bulb onions (A. cepa) and also infects other Allium crops like leeks (Allium porrum), chives (Allium schoenoprasum), bunching onion or Welsh onion (Allium fistulosum), and garlic (Allium sativum). This pathogen relies on a chromosomal phosphonate biosynthetic gene cluster (HiVir) and a plasmid-borne thiosulfinate tolerance cluster (alt) for onion pathogenicity and virulence, respectively. However, pathogenicity and virulence factors associated with other Allium species remain unknown. We used phenotype-dependent genome-wide association (GWAS) and phenotype-independent gene-pair coincidence (GPC) analyses on a panel of diverse 92 P. ananatis strains, which were inoculated on A. porrum and A. fistulosum × A. cepa under greenhouse conditions. Phenotypic assays showed that, in general, these strains were more aggressive on A. fistulosum × A. cepa as opposed to A. porrum. Of the 92 strains, only six showed highly aggressive foliar lesions on A. porrum compared to A. fistulosum × A. cepa. Conversely, nine strains showed highly aggressive foliar lesions on A. fistulosum × A. cepa compared to A. porrum. These results indicate that there are underlying genetic components in P. ananatis that may drive pathogenicity in these two Allium spp. Based on GWAS for foliar pathogenicity, 835 genes were associated with P. ananatis' pathogenicity on A. fistulosum × A. cepa whereas 243 genes were associated with bacterial pathogenicity on A. porrum. The Hivir as well as the alt gene clusters were identified among these genes. Besides the 'HiVir' and the alt gene clusters that are known to contribute to pathogenicity and virulence from previous studies, genes annotated with functions related to stress responses, a potential toxin-antitoxin system, flagellar-motility, quorum sensing, and a previously described phosphonoglycan biosynthesis (pgb) cluster were identified. The GPC analysis resulted in the identification of 165 individual genes sorted into 39 significant gene-pair association components and 255 genes sorted into 50 significant gene-pair dissociation components. Within the coincident gene clusters, several genes that occurred on the GWAS outputs were associated with each other but dissociated with genes that did not appear in their respective GWAS output. To focus on candidate genes that could explain the difference in virulence between hosts, a comparative genomics analysis was performed on five P. ananatis strains that were differentially pathogenic on A. porrum or A. fistulosum × A. cepa. Here, we found a putative type III secretion system, and several other genes that occurred on both GWAS outputs of both Allium hosts. Further, we also demonstrated utilizing mutational analysis that the pepM gene in the HiVir cluster is important than the pepM gene in the pgb cluster for P. ananatis pathogenicity in A. fistulosum × A. cepa and A. porrum. Overall, our results support that P. ananatis may utilize a common set of genes or gene clusters to induce symptoms on A. fistulosum × A. cepa foliar tissue as well as A. cepa but implicates additional genes for infection on A. porrum.
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Affiliation(s)
- Brendon K. Myers
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Gi Yoon Shin
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Gaurav Agarwal
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Shaun P. Stice
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Ronald D. Gitaitis
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States,*Correspondence: Bhabesh Dutta, ✉
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Zhao M, Tyson C, Gitaitis R, Kvitko B, Dutta B. Rouxiella badensis, a new bacterial pathogen of onion causing bulb rot. Front Microbiol 2022; 13:1054813. [DOI: 10.3389/fmicb.2022.1054813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Onion bulb rot can be caused by multiple plant pathogens including bacterial pathogens. During our routine survey of commercial onion farms in 2014, 2020, and 2021, seven putative Rouxiella spp. strains were isolated from symptomatic onion samples in Georgia, United States. Upon fulfilling Koch’s postulates on onion, a genome analysis was conducted. Whole-genome indices (ANI and dDDH) showed that the strains belonged to Rouxiella badensis. Although the seven R. badensis strains were not pathogenic on onion foliage, the strains were able to cause bulb rot and could also produce necrotic lesions in a red onion scale assay. R. badensis populations increased significantly and to a level comparable to P. ananatis PNA 97-1R in a red onion scale infection assay. The core-genome analysis grouped all onion R. badensis strains from Georgia together, and distinct from R. badensis strains isolated from other sources and locations. Based on the genome analysis of strains (from the current study and available genomes in the repository), type I, III (Ssa-Esc and Inv-Mxi-Spa types), and V secretion systems are present in R. badensis genomes, while type II, IV, and VI secretion systems are absent. However, various secondary metabolite gene clusters were identified from R. badensis genomes, and a thiol/redox-associated enzyme gene cluster similar to the Pantoea alt cluster mediating thiosulfinate tolerance was also present in onion strains of R. badensis. This is the first report of R. badensis as a plant pathogen.
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Choi O, Kang B, Lee Y, Kim S, Kwon JH, Lee JT, Kim J. Bacterial Disease Complex Including Bleached Spot, Soft Rot, and Blight on Onion Seedlings Caused by Complex Infections. PLANT DISEASE 2021; 105:3925-3931. [PMID: 34152204 DOI: 10.1094/pdis-03-21-0484-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In 2018, a bacterial disease complex composed of bleached spots and soft rot-blight on onion seedlings was observed in nursery beds in Changnyeong, a major onion-producing county in South Korea. Four bacteria isolated from the diseased lesions were identified: Pseudomonas viridiflava, Acidovorax avenae subsp. avenae, Pantoea ananatis, and Xanthomonas axonopodis, respectively. We referred to the four strains as a "bacterial disease complex" because they were isolated from the same sample with multiple symptoms. We examined the synergistic activity among the four strains to understand their relationships and roles. We monitored in vivo bacterial population density and disease progression after artificially inoculating the bacteria on onion seedlings at a temperature of 22 or 28°C. The disease pattern progressed sooner at 28 than at 22°C (by an average of 4 to 6 days). The rate of disease progression induced by inoculation of P. ananatis alone was consistent with that induced by coinoculation of P. ananatis with the other strains, regardless of the temperature (22 or 28°C). The in vivo growth of P. ananatis on onion seedlings was not different after inoculation alone versus together with the other strains. The rate of disease progression induced by P. viridiflava was similar when inoculated alone and when inoculated with other tree strains at 28°C, but disease progression induced by inoculation alone was slower at 22°C. The in vivo growth of P. viridiflava or X. axonopodis on onion seedlings decreased rapidly or gradually, respectively, when inoculated with the other strains. Coinfection with the other three strains had repression effects on the growth of P. viridiflava, a slight effect on X. axonopodis, and no effect on P. or A. avenae subsp. avenae in vivo. These results indicate that the strains coexist or interact antagonistically, rather than synergistically, depending on the conditions. These results were consistent with the results of the in vitro growth inhibition assay, in which P. viridiflava growth was inhibited by X. axonopodis or P. ananatis. These results also confirmed that X. axonopodis is present on bleached spots and P. viridiflava on soft rot-blight lesions, and that P. viridiflava and P. ananatis cause soft rot-blight but do not coexist. A. avenae subsp. avenae is a minor causative pathogen of bleached spots on onion seedlings, but it is not significantly affected by temperature and has no antagonistic or synergistic interactions with X. axonopodis.
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Affiliation(s)
- Okhee Choi
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Byeongsam Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yeyeong Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Seunghoe Kim
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jin-Hyeuk Kwon
- Onion Research Institute, Gyeongsangnam-do Agricultural Research and Extension Services, Changnyeong-Gun 50319, Republic of Korea
| | - Jong-Tae Lee
- Onion Research Institute, Gyeongsangnam-do Agricultural Research and Extension Services, Changnyeong-Gun 50319, Republic of Korea
| | - Jinwoo Kim
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
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7
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Asselin JAE, Bonasera JM, Helmann TC, Beer SV, Stodghill PV. Complete Genome Sequence Resources for the Onion Pathogen, Pantoea ananatis OC5a. PHYTOPATHOLOGY 2021; 111:1885-1888. [PMID: 33724871 DOI: 10.1094/phyto-09-20-0416-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here, we report on the genomic sequence and annotation for Pantoea ananatis OC5a, a strain that was isolated from an onion bulb grown in New York and that is pathogenic to onion, causing center rot of onion. OC5a is the first P. ananatis strain pathogenic to onion from New York to be completely assembled and sequenced. Having been assembled using long PacBio reads and high-fidelity Illumina reads, this genome is closed, complete, and of high quality.
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Affiliation(s)
- Jo Ann E Asselin
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY
| | - Jean M Bonasera
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY
| | - Tyler C Helmann
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY
| | - Steven V Beer
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY
| | - Paul V Stodghill
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY
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Agarwal G, Choudhary D, Stice SP, Myers BK, Gitaitis RD, Venter SN, Kvitko BH, Dutta B. Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion. Front Microbiol 2021; 12:684756. [PMID: 34489883 PMCID: PMC8417944 DOI: 10.3389/fmicb.2021.684756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the 'alt' gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.
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Affiliation(s)
- Gaurav Agarwal
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Divya Choudhary
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Shaun P Stice
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Brendon K Myers
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Ronald D Gitaitis
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
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Koirala S, Zhao M, Agarwal G, Gitaitis R, Stice S, Kvitko B, Dutta B. Identification of Two Novel Pathovars of Pantoea stewartii subsp. indologenes Affecting Allium sp. and Millets. PHYTOPATHOLOGY 2021; 111:1509-1519. [PMID: 33599528 DOI: 10.1094/phyto-11-20-0508-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pantoea stewartii subsp. indologenes is a causative agent of leafspot of foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onion. We phenotypically and genotypically characterized 17 P. stewartii subsp. indologenes strains from onion and other sources (pearl millet, foxtail millet, guar pulse, verbena, and corn). Based on the host range evaluation, we propose two pathovars: P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. P. stewartii subsp. indologenes pv. cepacicola pv. nov. causes symptoms on Allium spp. (leek, onion, chive, and Japanese bunching onion) and on foxtail millet, pearl millet, and oat. However, P. stewartii subsp. indologenes pv. setariae pv. nov. can only infect the members of Poaceae family (foxtail millet, pearl millet, and oat). We also propose that the type strain of P. stewartii subsp. indologenes (LMG 2632T) should be designated as a pathotype strain of P. stewartii subsp. indologenes pv. setariae and recommend that the strain PNA 14-12 be designated as the pathotype strain of P. stewartii subsp. indologenes pv. cepacicola. The digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and multilocus sequence analysis study showed that the two pathovars are genotypically closely related. Our study also showed that P. stewartii subsp. indologenes pathovars and P. stewartii subsp. stewartii share high genotypic relatedness and cannot be differentiated by dDDH and ANI values. Although the newly proposed pathovars are not clearly distinguishable by their fatty acid and methyl esterase profiles and substrate use patterns, a fatty acid (unknown with retention time: 10.9525) and a few metabolites (3-methyl glucose, Na butyrate, and fusidic acid) can be potentially used to distinguish them. We also report the distribution of previously known pathogenicity (HiVir, hrcC) and virulence (alt) factors of Pantoea spp. in the new pathovars. The impact of these new pathovars in the center rot pathosystem of onion is yet to be determined.
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Affiliation(s)
- Santosh Koirala
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - Mei Zhao
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - Gaurav Agarwal
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - Ron Gitaitis
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - Shaun Stice
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Brian Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
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Agarwal G, Gitaitis RD, Dutta B. Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer. Microorganisms 2021; 9:1761. [PMID: 34442840 PMCID: PMC8399035 DOI: 10.3390/microorganisms9081761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/16/2022] Open
Abstract
Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.
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Affiliation(s)
- Gaurav Agarwal
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793, USA;
| | | | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793, USA;
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11
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Predatory and biocontrol potency of Bdellovibrio bacteriovorus toward phytopathogenic strains of Pantoea sp. and Xanthomonas campestris in the presence of exo-biopolymers: in vitro and in vivo assessments. Int Microbiol 2021; 24:399-413. [PMID: 33956240 DOI: 10.1007/s10123-021-00177-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/09/2021] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
Bdellovibrios are predatory bacteria that invade other live Gram-negative bacterial cells for growth and reproduction. They have recently been considered as potential living antibiotics and biocontrol agents. In this study, the predatory activity and biocontrol potency of Bdellovibrio bacteriovorus strain SOIR-1 against Pantoea sp. strain BCCS and Xanthomonas campestris, two exo-biopolymer-producing phytopathogens, was evaluated. Plaque formation assays and lysis analysis in the broth co-cultures were used for the in vitro evaluation of bacteriolytic activity of strain SOIR-1. The in vivo biocontrol potential of strain SOIR-1 was evaluated by pathogenicity tests on the onion bulbs and potato tuber slices. The phytopathogens were also recovered from the infected plant tissues and confirmed using biochemical tests and PCR-based 16S rRNA gene sequence analysis. Typical bdellovibrios plaques were developed on the lawn cultures of Pantoea sp. BCCS and X. campestris. The killing rate of strain SOIR-1 toward Pantoea sp. BCCS and X. campestris was 84.3% and 76.3%, respectively. Exo-biopolymers attenuated the predation efficiency of strain SOIR-1 up to 10.2-18.2% (Pantoea sp. BCCS) and 12.2-17.3% (X. campestris). The strain SOIR-1 significantly reduced rotting symptoms in the onion bulbs caused by Pantoea sp. BCCS (69.0%) and potato tuber slices caused by X. campestris (73.1%). Although more field assessments are necessary, strain SOIR-1 has the preliminary potential as a biocontrol agent against phytopathogenic Pantoea sp. BCCS and X. campestris, especially in postharvest storage. Due to the particular physicochemical properties of evaluated exo-biopolymers, they can be used in the designing encapsulation systems for delivery of bdellovibrios.
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Stice SP, Shin GY, De Armas S, Koirala S, Galván GA, Siri MI, Severns PM, Coutinho T, Dutta B, Kvitko BH. The Distribution of Onion Virulence Gene Clusters Among Pantoea spp. FRONTIERS IN PLANT SCIENCE 2021; 12:643787. [PMID: 33777079 PMCID: PMC7988079 DOI: 10.3389/fpls.2021.643787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/18/2021] [Indexed: 05/31/2023]
Abstract
Pantoea ananatis is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and alt, associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of pantaphos, (2-hydroxy[phosphono-methyl)maleate), a phosphonate phytotoxin. The alt gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other Pantoea species suggests that these gene clusters are present outside of P. ananatis. To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and alt. Two hundred fifty-two strains of Pantoea spp. were phenotyped using the red onion scale necrosis (RSN) assay and were genotyped using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 Pantoea species, 41 isolation sources, and 23 countries, collected from 1946-2019, was tested. There is a significant association between the alt PCR assay and Pantoea strains recovered from symptomatic onion (P < 0.001). There is also a significant association of a positive HiVir PCR and RSN assay among P. ananatis strains but not among Pantoea spp., congeners. This may indicate a divergent HiVir cluster or different pathogenicity and virulence mechanisms. Last, we describe natural alt positive [RSN+/HiVir+/alt +] P. ananatis strains, which cause extensive bulb necrosis in a neck-to-bulb infection assay compared to alt negative [RSN+/HiVir+/alt -] P. ananatis strains. A combination of assays that include PCR of virulence genes [HiVir and alt] and an RSN assay can potentially aid in identification of onion-bulb-rotting pathogenic P. ananatis strains.
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Affiliation(s)
- Shaun P. Stice
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
| | - Gi Yoon Shin
- Centre for Microbial Ecology and Genomics, Forestry and Agriculture Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Stefanie De Armas
- Área de Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Santosh Koirala
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
| | - Guillermo A. Galván
- Departamento de Producción Vegetal, Centro Regional Sur (CRS), Facultad de Agronomía, Universidad de la República, Canelones, Uruguay
| | - María Inés Siri
- Área de Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Paul M. Severns
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
| | - Teresa Coutinho
- Centre for Microbial Ecology and Genomics, Forestry and Agriculture Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
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A Phosphonate Natural Product Made by Pantoea ananatis is Necessary and Sufficient for the Hallmark Lesions of Onion Center Rot. mBio 2021; 12:mBio.03402-20. [PMID: 33531390 PMCID: PMC7858074 DOI: 10.1128/mbio.03402-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pantoea ananatis is the primary cause of onion center rot. Genetic data suggest that a phosphonic acid natural product is required for pathogenesis; however, the nature of the molecule is unknown. Here, we show that P. ananatis produces at least three phosphonates, two of which were purified and structurally characterized. The first, designated pantaphos, was shown to be 2-(hydroxy[phosphono]methyl)maleate; the second, a probable biosynthetic precursor, was shown to be 2-(phosphonomethyl)maleate. Purified pantaphos is both necessary and sufficient for the hallmark lesions of onion center rot. Moreover, when tested against mustard seedlings, the phytotoxic activity of pantaphos was comparable to the widely used herbicides glyphosate and phosphinothricin. Pantaphos was also active against a variety of human cell lines but was significantly more toxic to glioblastoma cells. Pantaphos showed little activity when tested against a variety of bacteria and fungi.IMPORTANCE Pantoea ananatis is a significant plant pathogen that targets a number of important crops, a problem that is compounded by the absence of effective treatments to prevent its spread. Our identification of pantaphos as the key virulence factor in onion center rot suggests a variety of approaches that could be employed to address this significant plant disease. Moreover, the general phytotoxicity of the molecule suggests that it could be developed into an effective herbicide to counter the alarming rise in herbicide-resistant weeds.
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Kini K, Lefeuvre P, Poulin L, Silué D, Koebnik R. Genome Resources of Three West African Strains of Pantoea ananatis Causing Bacterial Blight and Grain Discoloration of Rice. PHYTOPATHOLOGY 2020; 110:1500-1502. [PMID: 32338197 DOI: 10.1094/phyto-03-20-0091-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Members of the genus Pantoea have been reported as pathogens for many economically important crops, including rice. Little is known about their host-pathogen interactions at the molecular level and the lack of comprehensive genome data impedes targeted breeding strategies toward resistant rice cultivars. Here, we describe the structural and functional annotation of the draft genome sequences of three rice-pathogenic Pantoea ananatis strains, ARC272, ARC310, and ARC311, which were isolated in Burkina Faso, Togo, and Benin, respectively. The genome sequences of these strains will help in developing molecular diagnostic tools and provide new insight into common traits that may enable P. ananatis to infect rice.
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Affiliation(s)
- Kossi Kini
- AfricaRice, Plant Pathology, Africa Rice Center, B.P. 2031, Cotonou, Benin
- IRD, Cirad, Université de Montpellier, IPME, 34394 Montpellier, France
| | | | - Lucie Poulin
- IRD, Cirad, Université de Montpellier, IPME, 34394 Montpellier, France
| | - Drissa Silué
- AfricaRice, Plant Pathology, Africa Rice Center, B.P. 2031, Cotonou, Benin
| | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, 34394 Montpellier, France
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Thiosulfinate Tolerance Is a Virulence Strategy of an Atypical Bacterial Pathogen of Onion. Curr Biol 2020; 30:3130-3140.e6. [PMID: 32619480 DOI: 10.1016/j.cub.2020.05.092] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/07/2020] [Accepted: 05/29/2020] [Indexed: 01/01/2023]
Abstract
Unlike most characterized bacterial plant pathogens, the broad-host-range plant pathogen Pantoea ananatis lacks both the virulence-associated type III and type II secretion systems. In the absence of these typical pathogenicity factors, P. ananatis induces necrotic symptoms and extensive cell death in onion tissue dependent on the HiVir proposed secondary metabolite synthesis gene cluster. Onion (Allium. cepa L), garlic (A. sativum L.), and other members of the Allium genus produce volatile antimicrobial thiosulfinates upon cellular damage. However, the roles of endogenous thiosulfinate production in host-bacterial pathogen interactions have not been described. We found a strong correlation between the genetic requirements for P. ananatis to colonize necrotized onion tissue and its capacity for tolerance to the thiosulfinate "allicin" based on the presence of an eleven-gene, plasmid-borne, virulence cluster of sulfur redox genes. We have designated them "alt" genes for allicin tolerance. We show that allicin and onion thiosulfinates restrict bacterial growth with similar kinetics. The alt gene cluster is sufficient to confer allicin tolerance and protects the glutathione pool during allicin treatment. Independent alt genes make partial phenotypic contributions indicating that they function as a collective cohort to manage thiol stress. Our work implicates endogenous onion thiosulfinates produced during cellular damage as major mediators of interactions with bacteria. The P. ananatis-onion pathosystem can be modeled as a chemical arms race of pathogen attack, host chemical counterattack, and pathogen defense.
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Shin GY, Schachterle JK, Shyntum DY, Moleleki LN, Coutinho TA, Sundin GW. Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis. Front Microbiol 2019; 10:2075. [PMID: 31572315 PMCID: PMC6749038 DOI: 10.3389/fmicb.2019.02075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022] Open
Abstract
To successfully infect plant hosts, the collective regulation of virulence factors in a bacterial pathogen is crucial. Hfq is an RNA chaperone protein that facilitates the small RNA (sRNA) regulation of global gene expression at the post-transcriptional level. In this study, the functional role of Hfq in a broad host range phytopathogen Pantoea ananatis was determined. Inactivation of the hfq gene in P. ananatis LMG 2665T resulted in the loss of pathogenicity and motility. In addition, there was a significant reduction of quorum sensing signal molecule acyl-homoserine lactone (AHL) production and biofilm formation. Differential sRNA expression analysis between the hfq mutant and wild-type strains of P. ananatis revealed 276 sRNAs affected in their abundance by the loss of hfq at low (OD600 = 0.2) and high cell (OD600 = 0.6) densities. Further analysis identified 25 Hfq-dependent sRNAs, all showing a predicted Rho-independent terminator of transcription and mapping within intergenic regions of the P. ananatis genome. These included known sRNAs such as ArcZ, FnrS, GlmZ, RprA, RyeB, RyhB, RyhB2, Spot42, and SsrA, and 16 novel P. ananatis sRNAs. The current study demonstrated that Hfq is an important component of the collective regulation of virulence factors and sets a foundation for understanding Hfq-sRNA mediated regulation in the phytopathogen P. ananatis.
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Affiliation(s)
- Gi Yoon Shin
- Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Jeffrey K Schachterle
- Department of Plant, Soil and Microbial Sciences, College of Agriculture & Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Divine Y Shyntum
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lucy N Moleleki
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Teresa A Coutinho
- Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - George W Sundin
- Department of Plant, Soil and Microbial Sciences, College of Agriculture & Natural Resources, Michigan State University, East Lansing, MI, United States
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