Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum.
BACKGROUND
Two-component systems (TCS) play critical roles in sensing and responding to environmental cues. Azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. Despite numerous studies about its plant beneficial properties, little is known about how the bacterium senses and responds to its rhizospheric environment. The availability of complete genome sequenced from four Azospirillum strains (A. brasilense Sp245 and CBG 497, A. lipoferum 4B and Azospirillum sp. B510) offers the opportunity to conduct a comprehensive comparative analysis of the TCS gene family.


RESULTS
Azospirillum genomes harbour a very large number of genes encoding TCS, and are especially enriched in hybrid histidine kinases (HyHK) genes compared to other plant-associated bacteria of similar genome sizes. We gained further insight into HyHK structure and architecture, revealing an intriguing complexity of these systems. An unusual proportion of TCS genes were orphaned or in complex clusters, and a high proportion of predicted soluble HKs compared to other plant-associated bacteria are reported. Phylogenetic analyses of the transmitter and receiver domains of A. lipoferum 4B HyHK indicate that expansion of this family mainly arose through horizontal gene transfer but also through gene duplications all along the diversification of the Azospirillum genus. By performing a genome-wide comparison of TCS, we unraveled important 'genus-defining' and 'plant-specifying' TCS.


CONCLUSIONS
This study shed light on Azospirillum TCS which may confer important regulatory flexibility. Collectively, these findings highlight that Azospirillum genomes have broad potential for adaptation to fluctuating environments.
Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France. stephanie.borland@hotmail.fr.
Stéphanie
S
Borland
Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France. anne.oudart@gmail.com.
Anne
A
Oudart
Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France. claire.prigent-combaret@univ-lyon1.fr.
Claire
C
Prigent-Combaret
Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France. celine.brochier-armanet@univ-lyon1.fr.
Céline
C
Brochier-Armanet
Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France. florence.wisniewski@univ-lyon1.fr.
Florence
F
Wisniewski-Dyé
D016949:Azospirillum / Q000235:genetics* / Q000378:metabolism*; D005075:Biological Evolution; D030541:Databases, Genetic; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D015398:Signal Transduction