Comparative genomics of the PGPR isolate Methylobacterium sp. 2A

Autores
Gitman, Iván Federico Berco; Grossi, Cecilia Eugenia María; Ulloa, Rita Maria
Año de publicación
2020
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
Methylobacterium sp. 2A is a plant growth-promoting rhizobacteria (PGPR) that was isolated from roots of potato plants and enhanced growth in potato and Arabidopsis plants under high salt conditions. Whole genome sequencing revealed metabolic pathways associated with its plant growth promoter capacity. A comparative genomic analysis was performed through the pangenomic approach between Methylobacterium sp. 2A and four closest relatives of the genus: M. phyllostachyos BL47, M. organophilum DSM 760, M. radiotolerans JCM 2831, and M. pseudosasicola BL36. A core-genome of 3,584 genes was identified, while 724 genes were exclusive of this isolate. The genomic island (GI) prediction of Methylobacterium sp. 2A and related species was performed by IslandViewer using integrated methods. Although weak, a correlation between GC content and percentage of exclusive genes in GIs was inferred in all species. In the Methylobacterium sp. 2A assembly, 26 genomic islands were predicted with a total of 473 protein-coding genes, representing 8.6 % of the entire genome. The prediction showed that the largest GI has a length of 68.6 Kbp and the smallest 4.3 kbp. Also, a comparison of these organisms was carried out by the functional annotation of COGs and the assignment of them to one of the 26 functional categories. COG analysis showed that COG0784 and COG0840 containing CheY chemotaxis proteins and methyl-accepting chemotaxis proteins (MCPs) are the most abundant ones in the analyzed pangenome. MCPs are chemoreceptors that sense a vast set of environmental signals enabling soil bacteria to establish plant-microbe interactions. Both, MCPs and CheY are involved in signal transduction mechanisms that modulate cell motility. The MCP signaling domain is highly conserved because it maintains multiple protein-protein interactions within the chemoreceptor-kinase complex, while MCP sensory domains are quite variable in sequence. Preliminary phylogenetic analysis of the 55 Methylobacterium sp. 2A MCPs suggests that these proteins are grouped in at least four big clusters. ScanProsite analysis revealed the presence of one or two transducing domains, HAMP, PAS and/or PAC domains in the different analyzed protein sequences. The comparative genomic analysis presented in this work revealed the relationship between Methylobacterium sp. 2A with related members of the genus, providing valuable information on its genetic and evolutionary diversity.
Fil: Gitman, Iván Federico Berco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Grossi, Cecilia Eugenia María. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Ulloa, Rita Maria. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology
CABA
Argentina
Sociedad Argentina de Investigación en Bioquímica y biología Molecular
Sociedad Argentina de Microbiología General
Materia
Methylobacterium sp. 2A
Genomics
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/202019

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network_name_str CONICET Digital (CONICET)
spelling Comparative genomics of the PGPR isolate Methylobacterium sp. 2AGitman, Iván Federico BercoGrossi, Cecilia Eugenia MaríaUlloa, Rita MariaMethylobacterium sp. 2AGenomicshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Methylobacterium sp. 2A is a plant growth-promoting rhizobacteria (PGPR) that was isolated from roots of potato plants and enhanced growth in potato and Arabidopsis plants under high salt conditions. Whole genome sequencing revealed metabolic pathways associated with its plant growth promoter capacity. A comparative genomic analysis was performed through the pangenomic approach between Methylobacterium sp. 2A and four closest relatives of the genus: M. phyllostachyos BL47, M. organophilum DSM 760, M. radiotolerans JCM 2831, and M. pseudosasicola BL36. A core-genome of 3,584 genes was identified, while 724 genes were exclusive of this isolate. The genomic island (GI) prediction of Methylobacterium sp. 2A and related species was performed by IslandViewer using integrated methods. Although weak, a correlation between GC content and percentage of exclusive genes in GIs was inferred in all species. In the Methylobacterium sp. 2A assembly, 26 genomic islands were predicted with a total of 473 protein-coding genes, representing 8.6 % of the entire genome. The prediction showed that the largest GI has a length of 68.6 Kbp and the smallest 4.3 kbp. Also, a comparison of these organisms was carried out by the functional annotation of COGs and the assignment of them to one of the 26 functional categories. COG analysis showed that COG0784 and COG0840 containing CheY chemotaxis proteins and methyl-accepting chemotaxis proteins (MCPs) are the most abundant ones in the analyzed pangenome. MCPs are chemoreceptors that sense a vast set of environmental signals enabling soil bacteria to establish plant-microbe interactions. Both, MCPs and CheY are involved in signal transduction mechanisms that modulate cell motility. The MCP signaling domain is highly conserved because it maintains multiple protein-protein interactions within the chemoreceptor-kinase complex, while MCP sensory domains are quite variable in sequence. Preliminary phylogenetic analysis of the 55 Methylobacterium sp. 2A MCPs suggests that these proteins are grouped in at least four big clusters. ScanProsite analysis revealed the presence of one or two transducing domains, HAMP, PAS and/or PAC domains in the different analyzed protein sequences. The comparative genomic analysis presented in this work revealed the relationship between Methylobacterium sp. 2A with related members of the genus, providing valuable information on its genetic and evolutionary diversity.Fil: Gitman, Iván Federico Berco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Grossi, Cecilia Eugenia María. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Ulloa, Rita Maria. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaLVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General MicrobiologyCABAArgentinaSociedad Argentina de Investigación en Bioquímica y biología MolecularSociedad Argentina de Microbiología GeneralTech Science Press2020info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectReuniónJournalhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/202019Comparative genomics of the PGPR isolate Methylobacterium sp. 2A; LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology; CABA; Argentina; 2020; 1-10327-95451667-5746CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://saib.org.ar/archivos/biocell-45.pdfinfo:eu-repo/semantics/altIdentifier/url/https://samige.org.ar//wp-content/uploads/2022/10/Libro-de-resumenes-2020-Biocell.pdfNacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:48:03Zoai:ri.conicet.gov.ar:11336/202019instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:48:03.303CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Comparative genomics of the PGPR isolate Methylobacterium sp. 2A
title Comparative genomics of the PGPR isolate Methylobacterium sp. 2A
spellingShingle Comparative genomics of the PGPR isolate Methylobacterium sp. 2A
Gitman, Iván Federico Berco
Methylobacterium sp. 2A
Genomics
title_short Comparative genomics of the PGPR isolate Methylobacterium sp. 2A
title_full Comparative genomics of the PGPR isolate Methylobacterium sp. 2A
title_fullStr Comparative genomics of the PGPR isolate Methylobacterium sp. 2A
title_full_unstemmed Comparative genomics of the PGPR isolate Methylobacterium sp. 2A
title_sort Comparative genomics of the PGPR isolate Methylobacterium sp. 2A
dc.creator.none.fl_str_mv Gitman, Iván Federico Berco
Grossi, Cecilia Eugenia María
Ulloa, Rita Maria
author Gitman, Iván Federico Berco
author_facet Gitman, Iván Federico Berco
Grossi, Cecilia Eugenia María
Ulloa, Rita Maria
author_role author
author2 Grossi, Cecilia Eugenia María
Ulloa, Rita Maria
author2_role author
author
dc.subject.none.fl_str_mv Methylobacterium sp. 2A
Genomics
topic Methylobacterium sp. 2A
Genomics
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Methylobacterium sp. 2A is a plant growth-promoting rhizobacteria (PGPR) that was isolated from roots of potato plants and enhanced growth in potato and Arabidopsis plants under high salt conditions. Whole genome sequencing revealed metabolic pathways associated with its plant growth promoter capacity. A comparative genomic analysis was performed through the pangenomic approach between Methylobacterium sp. 2A and four closest relatives of the genus: M. phyllostachyos BL47, M. organophilum DSM 760, M. radiotolerans JCM 2831, and M. pseudosasicola BL36. A core-genome of 3,584 genes was identified, while 724 genes were exclusive of this isolate. The genomic island (GI) prediction of Methylobacterium sp. 2A and related species was performed by IslandViewer using integrated methods. Although weak, a correlation between GC content and percentage of exclusive genes in GIs was inferred in all species. In the Methylobacterium sp. 2A assembly, 26 genomic islands were predicted with a total of 473 protein-coding genes, representing 8.6 % of the entire genome. The prediction showed that the largest GI has a length of 68.6 Kbp and the smallest 4.3 kbp. Also, a comparison of these organisms was carried out by the functional annotation of COGs and the assignment of them to one of the 26 functional categories. COG analysis showed that COG0784 and COG0840 containing CheY chemotaxis proteins and methyl-accepting chemotaxis proteins (MCPs) are the most abundant ones in the analyzed pangenome. MCPs are chemoreceptors that sense a vast set of environmental signals enabling soil bacteria to establish plant-microbe interactions. Both, MCPs and CheY are involved in signal transduction mechanisms that modulate cell motility. The MCP signaling domain is highly conserved because it maintains multiple protein-protein interactions within the chemoreceptor-kinase complex, while MCP sensory domains are quite variable in sequence. Preliminary phylogenetic analysis of the 55 Methylobacterium sp. 2A MCPs suggests that these proteins are grouped in at least four big clusters. ScanProsite analysis revealed the presence of one or two transducing domains, HAMP, PAS and/or PAC domains in the different analyzed protein sequences. The comparative genomic analysis presented in this work revealed the relationship between Methylobacterium sp. 2A with related members of the genus, providing valuable information on its genetic and evolutionary diversity.
Fil: Gitman, Iván Federico Berco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Grossi, Cecilia Eugenia María. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Ulloa, Rita Maria. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology
CABA
Argentina
Sociedad Argentina de Investigación en Bioquímica y biología Molecular
Sociedad Argentina de Microbiología General
description Methylobacterium sp. 2A is a plant growth-promoting rhizobacteria (PGPR) that was isolated from roots of potato plants and enhanced growth in potato and Arabidopsis plants under high salt conditions. Whole genome sequencing revealed metabolic pathways associated with its plant growth promoter capacity. A comparative genomic analysis was performed through the pangenomic approach between Methylobacterium sp. 2A and four closest relatives of the genus: M. phyllostachyos BL47, M. organophilum DSM 760, M. radiotolerans JCM 2831, and M. pseudosasicola BL36. A core-genome of 3,584 genes was identified, while 724 genes were exclusive of this isolate. The genomic island (GI) prediction of Methylobacterium sp. 2A and related species was performed by IslandViewer using integrated methods. Although weak, a correlation between GC content and percentage of exclusive genes in GIs was inferred in all species. In the Methylobacterium sp. 2A assembly, 26 genomic islands were predicted with a total of 473 protein-coding genes, representing 8.6 % of the entire genome. The prediction showed that the largest GI has a length of 68.6 Kbp and the smallest 4.3 kbp. Also, a comparison of these organisms was carried out by the functional annotation of COGs and the assignment of them to one of the 26 functional categories. COG analysis showed that COG0784 and COG0840 containing CheY chemotaxis proteins and methyl-accepting chemotaxis proteins (MCPs) are the most abundant ones in the analyzed pangenome. MCPs are chemoreceptors that sense a vast set of environmental signals enabling soil bacteria to establish plant-microbe interactions. Both, MCPs and CheY are involved in signal transduction mechanisms that modulate cell motility. The MCP signaling domain is highly conserved because it maintains multiple protein-protein interactions within the chemoreceptor-kinase complex, while MCP sensory domains are quite variable in sequence. Preliminary phylogenetic analysis of the 55 Methylobacterium sp. 2A MCPs suggests that these proteins are grouped in at least four big clusters. ScanProsite analysis revealed the presence of one or two transducing domains, HAMP, PAS and/or PAC domains in the different analyzed protein sequences. The comparative genomic analysis presented in this work revealed the relationship between Methylobacterium sp. 2A with related members of the genus, providing valuable information on its genetic and evolutionary diversity.
publishDate 2020
dc.date.none.fl_str_mv 2020
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http://purl.org/coar/resource_type/c_5794
info:ar-repo/semantics/documentoDeConferencia
status_str publishedVersion
format conferenceObject
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/202019
Comparative genomics of the PGPR isolate Methylobacterium sp. 2A; LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology; CABA; Argentina; 2020; 1-1
0327-9545
1667-5746
CONICET Digital
CONICET
url http://hdl.handle.net/11336/202019
identifier_str_mv Comparative genomics of the PGPR isolate Methylobacterium sp. 2A; LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology; CABA; Argentina; 2020; 1-1
0327-9545
1667-5746
CONICET Digital
CONICET
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