title: Coordinated Regulation of Species-Specific Hydroxycinnamic Acid Degradation and Siderophore Biosynthesis Pathways in Agrobacterium fabrum.
abstract: The rhizosphere-inhabiting species Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (HCAs), especially ferulic acid and p-coumaric acid, via the novel A. fabrum HCA degradation pathway. Gene expression profiles of A. fabrum strain C58 were investigated in the presence of HCAs, using a C58 whole-genome oligoarray. Both ferulic acid and p-coumaric acid caused variations in the expression of more than 10% of the C58 genes. Genes of the A. fabrum HCA degradation pathway, together with the genes involved in iron acquisition, were among the most highly induced in the presence of HCAs. Two operons coding for the biosynthesis of a particular siderophore, as well as genes of the A. fabrum HCA degradation pathway, have been described as being specific to the species. We demonstrate here their coordinated expression, emphasizing the interdependence between the iron concentration in the growth medium and the rate at which ferulic acid is degraded by cells. The coordinated expression of these functions may be advantageous in HCA-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. The present results confirm that there is cooperation between the A. fabrum-specific genes, defining a particular ecological niche.
  
  
  
  We previously identified seven genomic regions in Agrobacterium fabrum that were specifically present in all of the members of this species only. Here we demonstrated that two of these regions, encoding the hydroxycinnamic acid degradation pathway and the iron acquisition pathway, were regulated in a coordinated manner. The coexpression of these functions may be advantageous in hydroxycinnamic acid-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. These data support the view that bacterial genomic species emerged from a bacterial population by acquiring specific functions that allowed them to outcompete their closest relatives. In conclusion, bacterial species could be defined not only as genomic species but also as ecological species.
authors.affiliation: Université Lyon 1, CNRS UMR 5240, Microbiologie Adaptation et Pathogénie, Villeurbanne, France.|Université Lyon 1, CNRS UMR5308, INSERM U1111, ENS Lyon, CIRI, Pathogenèses des Infections à Staphylocoques, Lyon, France.
authors.forename: Jessica
authors.initials: J
authors.lastname: Baude
authors.affiliation: Université Lyon 1, CNRS UMR 5557, INRA UMR1418, Ecologie Microbienne, Villeurbanne, France.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Vial
authors.affiliation: Université Lyon 1, CNRS UMR 5240, Microbiologie Adaptation et Pathogénie, Villeurbanne, France.
authors.forename: Camille
authors.initials: C
authors.lastname: Villard
authors.affiliation: Université Lyon 1, CNRS UMR 5240, Microbiologie Adaptation et Pathogénie, Villeurbanne, France.|Université Lyon 1, CNRS UMR 5557, INRA UMR1418, Ecologie Microbienne, Villeurbanne, France.
authors.forename: Tony
authors.initials: T
authors.lastname: Campillo
authors.affiliation: Université Lyon 1, CNRS UMR 5557, INRA UMR1418, Ecologie Microbienne, Villeurbanne, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Lavire
authors.affiliation: Université Lyon 1, CNRS UMR 5557, INRA UMR1418, Ecologie Microbienne, Villeurbanne, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Nesme
authors.affiliation: Université Lyon 1, CNRS UMR 5240, Microbiologie Adaptation et Pathogénie, Villeurbanne, France florence.hommais@univ-lyon1.fr.
authors.forename: Florence
authors.initials: F
authors.lastname: Hommais
mesh_terms: D016960:Agrobacterium tumefaciens / Q000235:genetics* / Q000378:metabolism*; D001711:Biotransformation; D003373:Coumaric Acids / Q000378:metabolism*; D003470:Culture Media / Q000737:chemistry; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D007501:Iron / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D046228:Microarray Analysis; D009876:Operon; D017262:Siderophores / Q000096:biosynthesis*
chemical_list: D003373:Coumaric Acids; D003470:Culture Media; D017262:Siderophores; D007501:Iron