1
|
González-Tobón J, Diaz A, Helmann TC, Karp MA, Daughtrey M, Stodghill PV, Filiatrault MJ. Genomic insights into a Pseudomonas amygdali isolate from Hibiscus rosa-sinensis. Genomics 2023; 115:110600. [PMID: 36889367 DOI: 10.1016/j.ygeno.2023.110600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/31/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023]
Abstract
The taxonomy of Pseudomonas has been extensively studied, yet the determination of species is currently difficult because of recent taxonomic changes and the lack of complete genomic sequence data. We isolated a bacterium causing a leaf spot disease on hibiscus (Hibiscus rosa-sinensis). Whole genome sequencing revealed similarity to Pseudomonas amygdali pv. tabaci and pv. lachrymans. The genome of this isolate (referred to as P. amygdali 35-1) shared 4987 genes with P. amygdali pv. hibisci, but possessed 204 unique genes and contained gene clusters encoding putative secondary metabolites and copper resistance determinants. We predicted this isolate's type III secretion effector (T3SE) repertoire and identified 64 putative T3SEs, some of which are present in other P. amygdali pv hibisci strains. Assays showed that the isolate was resistant to copper at a concentration of 1.6 mM. This study provides an improved understanding of the genomic relatedness and diversity of the P. amygdali species.
Collapse
Affiliation(s)
- Juliana González-Tobón
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Allison Diaz
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Tyler C Helmann
- United States Department of Agriculture - Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Mary Ann Karp
- United States Department of Agriculture - Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Margery Daughtrey
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Paul V Stodghill
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; United States Department of Agriculture - Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Melanie J Filiatrault
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; United States Department of Agriculture - Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
| |
Collapse
|
2
|
Añorga M, Urriza M, Ramos C, Murillo J. Multiple relaxases contribute to the horizontal transfer of the virulence plasmids from the tumorigenic bacterium Pseudomonas syringae pv. savastanoi NCPPB 3335. Front Microbiol 2022; 13:1076710. [PMID: 36578579 PMCID: PMC9791958 DOI: 10.3389/fmicb.2022.1076710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas syringae pv. savastanoi NCPPB 3335 is the causal agent of olive knot disease and contains three virulence plasmids: pPsv48A (pA), 80 kb; pPsv48B (pB), 45 kb, and pPsv48C (pC), 42 kb. Here we show that pB contains a complete MPFT (previously type IVA secretion system) and a functional origin of conjugational transfer adjacent to a relaxase of the MOBP family; pC also contains a functional oriT-MOBP array, whereas pA contains an incomplete MPFI (previously type IVB secretion system), but not a recognizable oriT. Plasmid transfer occurred on solid and in liquid media, and on leaf surfaces of a non-host plant (Phaseolus vulgaris) with high (pB) or moderate frequency (pC); pA was transferred only occasionally after cointegration with pB. We found three plasmid-borne and three chromosomal relaxase genes, although the chromosomal relaxases did not contribute to plasmid dissemination. The MOBP relaxase genes of pB and pC were functionally interchangeable, although with differing efficiencies. We also identified a functional MOBQ mobilization region in pC, which could only mobilize this plasmid. Plasmid pB could be efficiently transferred to strains of six phylogroups of P. syringae sensu lato, whereas pC could only be mobilized to two strains of phylogroup 3 (genomospecies 2). In two of the recipient strains, pB was stably maintained after 21 subcultures in liquid medium. The carriage of several relaxases by the native plasmids of P. syringae impacts their transfer frequency and, by providing functional diversity and redundancy, adds robustness to the conjugation system.
Collapse
Affiliation(s)
- Maite Añorga
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain
| | - Miriam Urriza
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain
| | - Cayo Ramos
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain,Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Jesús Murillo
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain,*Correspondence: Jesús Murillo
| |
Collapse
|
3
|
Jia J, Copes WE, Phillips K, Lu SE. Complete Genome Sequence Resource for Pseudomonas amygdali pv. loropetali Strain AAC Causing Bacterial Gall of Loropetalum chinense. Plant Dis 2022; 106:2502-2505. [PMID: 35881929 DOI: 10.1094/pdis-04-22-0919-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Jiayuan Jia
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mail Stop 9655, Mississippi State, MS 39762
| | - Warren E Copes
- United States Department of Agriculture-Agricultural Research Service, Thad Cochran Southern Horticultural Research Laboratory, Poplarville, MS 39740
| | - Kate Phillips
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mail Stop 9655, Mississippi State, MS 39762
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mail Stop 9655, Mississippi State, MS 39762
| |
Collapse
|
4
|
Jung H, Kim HS, Han G, Park J, Seo YS. Comparative Analyses of Four Complete Genomes in Pseudomonas amygdali Revealed Differential Adaptation to Hostile Environments and Secretion Systems. Plant Pathol J 2022; 38:167-174. [PMID: 35385921 PMCID: PMC9343901 DOI: 10.5423/ppj.nt.11.2021.0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Pseudomonas amygdali is a hemibiotrophic phytopathogen that causes disease in woody and herbaceous plants. Complete genomes of four P. amygdali pathovars were comparatively analyzed to decipher the impact of genomic diversity on host colonization. The pan-genome indicated that 3,928 core genes are conserved among pathovars, while 504-1,009 are unique to specific pathovars. The unique genome contained many mobile elements and exhibited a functional distribution different from the core genome. Genes involved in O-antigen biosynthesis and antimicrobial peptide resistance were significantly enriched for adaptation to hostile environments. While the type III secretion system was distributed in the core genome, unique genomes revealed a different organization of secretion systems as follows: type I in pv. tabaci, type II in pv. japonicus, type IV in pv. morsprunorum, and type VI in pv. lachrymans. These findings provide genetic insight into the dynamic interactions of the bacteria with plant hosts.
Collapse
Affiliation(s)
- Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Hong-Seop Kim
- Korea Seed & Variety Service, Pyeongchang 25343, Korea
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| |
Collapse
|
5
|
Guardado-Valdivia L, Chacón-López A, Murillo J, Poveda J, Hernández-Flores JL, Xoca-Orozco L, Aguilera S. The Pbo Cluster from Pseudomonas syringae pv. Phaseolicola NPS3121 Is Thermoregulated and Required for Phaseolotoxin Biosynthesis. Toxins (Basel) 2021; 13:toxins13090628. [PMID: 34564632 PMCID: PMC8473136 DOI: 10.3390/toxins13090628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
The bean (Phaseolus vulgaris) pathogen Pseudomonas syringae pv. phaseolicola NPS3121 synthesizes phaseolotoxin in a thermoregulated way, with optimum production at 18 °C. Gene PSPPH_4550 was previously shown to be thermoregulated and required for phaseolotoxin biosynthesis. Here, we established that PSPPH_4550 is part of a cluster of 16 genes, the Pbo cluster, included in a genomic island with a limited distribution in P. syringae and unrelated to the possession of the phaseolotoxin biosynthesis cluster. We identified typical non-ribosomal peptide synthetase, and polyketide synthetase domains in several of the pbo deduced products. RT-PCR and the analysis of polar mutants showed that the Pbo cluster is organized in four transcriptional units, including one monocistronic and three polycistronic. Operons pboA and pboO are both essential for phaseolotoxin biosynthesis, while pboK and pboJ only influence the amount of toxin produced. The three polycistronic units were transcribed at high levels at 18 °C but not at 28 °C, whereas gene pboJ was constitutively expressed. Together, our data suggest that the Pbo cluster synthesizes secondary metabolite(s), which could participate in the regulation of phaseolotoxin biosynthesis.
Collapse
Affiliation(s)
- Lizeth Guardado-Valdivia
- Laboratorio Integral de Investigación en Alimentos, Departamento de Química y Bioquímica, Tecnológico Nacional de México, Instituto Tecnológico de Tepic, 63175 Nayarit, Mexico; (L.G.-V.); (A.C.-L.)
| | - Alejandra Chacón-López
- Laboratorio Integral de Investigación en Alimentos, Departamento de Química y Bioquímica, Tecnológico Nacional de México, Instituto Tecnológico de Tepic, 63175 Nayarit, Mexico; (L.G.-V.); (A.C.-L.)
| | - Jesús Murillo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Avda. de Pamplona 123, 31192 Mutilva Baja, Spain; (J.M.); (J.P.)
| | - Jorge Poveda
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Avda. de Pamplona 123, 31192 Mutilva Baja, Spain; (J.M.); (J.P.)
| | - José Luis Hernández-Flores
- Centro de Investigación y Estudios Avanzados del IPN, Departamento de Ingeniería Genética, Irapuato, 36821 Guanajuato, Mexico;
| | - Luis Xoca-Orozco
- Departamento de Ingeniería Bioquímica, Instituto Tecnológico Superior de Purísima del Rincón, Purísima del Rincón, 36413 Guanajuato, Mexico;
| | - Selene Aguilera
- Laboratorio Integral de Investigación en Alimentos, Departamento de Química y Bioquímica, Tecnológico Nacional de México, Instituto Tecnológico de Tepic, 63175 Nayarit, Mexico; (L.G.-V.); (A.C.-L.)
- Correspondence:
| |
Collapse
|
6
|
Caballo-Ponce E, Pintado A, Moreno-Pérez A, Murillo J, Smalla K, Ramos C. Pseudomonas savastanoi pv. mandevillae pv. nov., a Clonal Pathogen Causing an Emerging, Devastating Disease of the Ornamental Plant Mandevilla spp. Phytopathology 2021; 111:1277-1288. [PMID: 33428471 DOI: 10.1094/phyto-11-20-0526-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Commercial production of the ornamental plant dipladenia (Mandevilla spp.) is threatened by dipladenia leaf and stem spot disease, caused by the bacterium Pseudomonas savastanoi. P. savastanoi includes four pathovars of woody hosts differentiated by a characteristic host range in olive, oleander, ash, and broom plants. However, isolates from dipladenia have not been ascribed to any particular lineage or P. savastanoi pathovar. Here we report that isolates from dipladenia represent a distinct, clonal lineage. First, dipladenia isolates display very similar plasmid profiles, including a plasmid encoding the iaaM gene for biosynthesis of indole-3-acetic acid. Second, multilocus sequence analysis and core genome single-nucleotide polymorphisms phylogenies showed a monophyletic origin for dipladenia isolates, which cluster with isolates from oleander (pathovar nerii) in a distinct clade well separated from other P. savastanoi strains. Metabolic profiling and cross-pathogenicity tests in olive, oleander, ash, broom, and dipladenia clearly distinguished dipladenia isolates from the four P. savastanoi pathovars. Comparative genomics of the draft genome sequence of the dipladenia strain Ph3 with the other four pathovars showed that Ph3 encodes very few strain-specific genes and a similar set of virulence genes to pv. nerii, including its repertoire of type III secretion system effectors. However, hierarchical clustering based on the catalog of effectors and their allelic variants clearly separated Ph3 from pv. nerii strains. Based on their distinctive pathogenicity profile, we propose a de novo pathovar for P. savastanoi isolates from dipladenia, P. savastanoi pv. mandevillae pv. nov., for which strain Ph3 (CFBP 8832PT) has been designated as the pathotype strain.
Collapse
Affiliation(s)
- Eloy Caballo-Ponce
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Campus Teatinos s/n, E-29010 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, 29010 Málaga, Spain
| | - Adrián Pintado
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Campus Teatinos s/n, E-29010 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, 29010 Málaga, Spain
| | - Alba Moreno-Pérez
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Campus Teatinos s/n, E-29010 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, 29010 Málaga, Spain
| | - Jesús Murillo
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra, E-31192 Mutilva Baja, Spain
| | - Kornelia Smalla
- Julius Kühn-Institute Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, D-38104 Braunschweig, Germany
| | - Cayo Ramos
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Campus Teatinos s/n, E-29010 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, 29010 Málaga, Spain
| |
Collapse
|