title: RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots.
abstract: Herbaspirillum seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize plants, wheat seedlings growing hydroponically in Hoagland's medium were inoculated with H. seropedicae and incubated for 3 days. Total mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of root attached and planktonic bacteria revealed extensive metabolic adaptations to the epiphytic life style. These adaptations include expression of specific adhesins and cell wall re-modeling to attach to the root. Additionally, the metabolism was adapted to the microxic environment and nitrogen-fixation genes were expressed. Polyhydroxybutyrate (PHB) synthesis was activated, and PHB granules were stored as observed by microscopy. Genes related to plant growth promotion, such as auxin production were expressed. Many ABC transporter genes were regulated in the bacteria attached to the roots. The results provide new insights into the adaptation of H. seropedicae to the interaction with the plant.
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: V C S
authors.initials: VC
authors.lastname: Pankievicz
authors.affiliation: Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, Londrina, PR, Brazil.
authors.forename: D
authors.initials: D
authors.lastname: Camilios-Neto
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: P
authors.initials: P
authors.lastname: Bonato
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: E
authors.initials: E
authors.lastname: Balsanelli
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: M Z
authors.initials: MZ
authors.lastname: Tadra-Sfeir
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: H
authors.initials: H
authors.lastname: Faoro
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: L S
authors.initials: LS
authors.lastname: Chubatsu
authors.affiliation: Department of Cellular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: L
authors.initials: L
authors.lastname: Donatti
authors.affiliation: Bioinformatics Unit, Clinical Research Coordination, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.|Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.
authors.forename: G
authors.initials: G
authors.lastname: Wajnberg
authors.affiliation: Bioinformatics Unit, Clinical Research Coordination, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.|Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.
authors.forename: F
authors.initials: F
authors.lastname: Passetti
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: R A
authors.initials: RA
authors.lastname: Monteiro
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
authors.forename: F O
authors.initials: FO
authors.lastname: Pedrosa
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil. souzaem@ufpr.br.
authors.forename: E M
authors.initials: EM
authors.lastname: Souza
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002630:Chemotactic Factors / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D042803:Herbaspirillum / Q000166:cytology* / Q000235:genetics* / Q000502:physiology; D007210:Indoleacetic Acids / Q000378:metabolism; D009586:Nitrogen Fixation / Q000235:genetics; D010937:Plant Growth Regulators / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000382:microbiology*; D058441:Rhizosphere; D036226:Seedlings / Q000382:microbiology; D017423:Sequence Analysis, RNA; D012988:Soil Microbiology; D059467:Transcriptome; D014908:Triticum / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D002630:Chemotactic Factors; D007210:Indoleacetic Acids; D010937:Plant Growth Regulators
keywords: Biological nitrogen fixation; H. seropedicae; PGPB-plant growth promoting bacteria; RNA-seq profiling; Rhizosphere