Transcriptomic Insight in the Control of Legume Root Secondary Infection by the Sinorhizobium meliloti Transcriptional Regulator Clr

Abstract

The cAMP-dependent transcriptional regulator Clr of <i>Sinorhizobium meliloti</i> regulates the overall number of infection events on <i>Medicago</i> roots by a so-far unknown mechanism requiring <i>smc02178</i>, a Clr-target gene of unknown function. In order to shed light on the mode of action of Clr on infection and potentially reveal additional biological functions for Clr, we inventoried genomic Clr target genes by transcriptome profiling. We have found that Clr positively controls the synthesis of cAMP-dependent succinoglycan as well as the expression of genes involved in the synthesis of a so-far unknown polysaccharide compound. In addition, Clr activated expression of 24 genes of unknown function in addition to <i>smc02178</i>. Genes negatively controlled by Clr were mainly involved in swimming motility and chemotaxis. Functional characterization of two novel Clr-activated genes of unknown function, <i>smb20495</i> and <i>smc02177</i>, showed that their expression was activated by the same plant signal as <i>smc02178 ex planta</i>. <i>In planta</i>, however, symbiotic expression of <i>smc02177</i> proved independent of clr. Both <i>smc02177</i> and <i>smb20495</i> genes were strictly required for the control of secondary infection on <i>M. sativa</i>. None of the three <i>smc02177, smc02178</i> and <i>smb20495</i> genes were needed for plant signal perception. Altogether this work provides a refined view of the cAMP-dependent Clr regulon of <i>S. meliloti</i>. We specifically discuss the possible roles of <i>smc02177, smc02178, smb20495</i> genes and other Clr-controlled genes in the control of secondary infection of <i>Medicago</i> roots.