title: RNA-seq analysis of the Rhizobium tropici CIAT 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt.
abstract: BACKGROUND
  Rhizobium tropici strain CIAT 899 establishes effective symbioses with several legume species, including Phaseolus vulgaris and Leucaena leucocephala. This bacterium synthesizes a large variety of nodulation factors in response to nod-gene inducing flavonoids and, surprisingly, also under salt stress conditions. The aim of this study was to identify differentially expressed genes in the presence of both inducer molecules, and analyze the promoter regions located upstream of these genes.
  
  
  RESULTS
  Results obtained by RNA-seq analyses of CIAT 899 induced with apigenin, a nod gene-inducing flavonoid for this strain, or salt allowed the identification of 19 and 790 differentially expressed genes, respectively. Fifteen of these genes were up-regulated in both conditions and were involved in the synthesis of both Nod factors and indole-3-acetic acid. Transcription of these genes was presumably activated through binding of at least one of the five NodD proteins present in this strain to specific nod box promoter sequences when the bacterium was induced by both apigenin and salt. Finally, under saline conditions, many other transcriptional responses were detected, including an increase in the transcription of genes involved in trehalose catabolism, chemotaxis and protein secretion, as well as ribosomal genes, and a decrease in the transcription of genes involved in transmembrane transport.
  
  
  CONCLUSIONS
  To our knowledge this is the first time that a transcriptomic study shows that salt stress induces the expression of nodulation genes in the absence of flavonoids. Thus, in the presence of both nodulation inducer molecules, apigenin and salt, R. tropici CIAT 899 up-regulated the same set of symbiotic genes. It could be possible that the increases in the transcription levels of several genes related to nodulation under saline conditions could represent a strategy to establish symbiosis under abiotic stressing conditions.
authors.affiliation: Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012, Sevilla, Spain. fperezm@us.es.
authors.forename: Francisco
authors.initials: F
authors.lastname: Pérez-Montaño
authors.affiliation: Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012, Sevilla, Spain. pdelcerro@us.es.
authors.forename: Pablo
authors.initials: P
authors.lastname: Del Cerro
authors.affiliation: Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012, Sevilla, Spain. ijimgue@us.es.
authors.forename: Irene
authors.initials: I
authors.lastname: Jiménez-Guerrero
authors.affiliation: Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012, Sevilla, Spain. jlopez@us.es.
authors.forename: Francisco Javier
authors.initials: FJ
authors.lastname: López-Baena
authors.affiliation: Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012, Sevilla, Spain. cubo@us.es.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Cubo
authors.affiliation: Embrapa Soja, Londrina, Paraná, Brazil. mariangela.hungria@embrapa.br.
authors.forename: Mariangela
authors.initials: M
authors.lastname: Hungria
authors.affiliation: Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012, Sevilla, Spain. megiasg@us.es.
authors.forename: Manuel
authors.initials: M
authors.lastname: Megías
authors.affiliation: Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012, Sevilla, Spain. fjom@us.es.
authors.forename: Francisco Javier
authors.initials: FJ
authors.lastname: Ollero
mesh_terms: D047310:Apigenin / Q000737:chemistry*; D001483:Base Sequence; D015964:Gene Expression Regulation, Bacterial; D007210:Indoleacetic Acids / Q000378:metabolism; D009876:Operon; D055170:Plant Root Nodulation / Q000235:genetics; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000235:genetics; D042162:Rhizobium tropici / Q000235:genetics* / Q000502:physiology; D017423:Sequence Analysis, RNA; D012965:Sodium Chloride / Q000737:chemistry*; D013312:Stress, Physiological; D013559:Symbiosis / Q000235:genetics*; D059467:Transcriptome
chemical_list: D007210:Indoleacetic Acids; D012329:RNA, Bacterial; D012965:Sodium Chloride; C030737:indoleacetic acid; D047310:Apigenin