Dataset Information

Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses.

ABSTRACT: The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species.

SUBMITTER: Pedrosa FO

PROVIDER: S-EPMC3093359 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

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Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses.

Pedrosa Fábio O FO Monteiro Rose Adele RA Wassem Roseli R Cruz Leonardo M LM Ayub Ricardo A RA Colauto Nelson B NB Fernandez Maria Aparecida MA Fungaro Maria Helena P MH Grisard Edmundo C EC Hungria Mariangela M Madeira Humberto M F HM Nodari Rubens O RO Osaku Clarice A CA Petzl-Erler Maria Luiza ML Terenzi Hernán H Vieira Luiz G E LG Steffens Maria Berenice R MB Weiss Vinicius A VA Pereira Luiz F P LF Almeida Marina I M MI Alves Lysangela R LR Marin Anelis A Araujo Luiza Maria LM Balsanelli Eduardo E Baura Valter A VA Chubatsu Leda S LS Faoro Helisson H Favetti Augusto A Friedermann Geraldo G Glienke Chirlei C Karp Susan S Kava-Cordeiro Vanessa V Raittz Roberto T RT Ramos Humberto J O HJ Ribeiro Enilze Maria S F EM Rigo Liu Un LU Rocha Saul N SN Schwab Stefan S Silva Anilda G AG Souza Eliel M EM Tadra-Sfeir Michelle Z MZ Torres Rodrigo A RA Dabul Audrei N G AN Soares Maria Albertina M MA Gasques Luciano S LS Gimenes Ciela C T CC Valle Juliana S JS Ciferri Ricardo R RR Correa Luiz C LC Murace Norma K NK Pamphile João A JA Patussi Eliana Valéria EV Prioli Alberto J AJ Prioli Sonia Maria A SM Rocha Carmem Lúcia M S C CL Arantes Olívia Márcia N OM Furlaneto Márcia Cristina MC Godoy Leandro P LP Oliveira Carlos E C CE Satori Daniele D Vilas-Boas Laurival A LA Watanabe Maria Angélica E MA Dambros Bibiana Paula BP Guerra Miguel P MP Mathioni Sandra Marisa SM Santos Karine Louise KL Steindel Mario M Vernal Javier J Barcellos Fernando G FG Campo Rubens J RJ Chueire Ligia Maria O LM Nicolás Marisa Fabiana MF Pereira-Ferrari Lilian L Silva José L da Conceição JL Gioppo Nereida M R NM Margarido Vladimir P VP Menck-Soares Maria Amélia MA Pinto Fabiana Gisele S FG Simão Rita de Cássia G Rde C Takahashi Elizabete K EK Yates Marshall G MG Souza Emanuel M EM

PLoS genetics 20110512 5

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. ...[more]

PMID: 21589895

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Project description:The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle.A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.

Dataset Information

Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses.

Publications

Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses.

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