Comparative genomic analysis of Salmonella type Ⅲsecreted candidate gene yiiG / 基础医学与临床

ABSTRACT

Objective To study the distribution and evolution of yiiG, a Salmonella gene encoding a candidate type secretedsubstrate .Methods Salmonella genomes were comprehensively screened for yiiG distribution with se-quence alignment strategies .The evolutionary history of yiiG was traced .Comparative genomic analysis was per-formed to study the evolutionary mechanisms of yiiG gene acquisition , loss and duplication .RNA-seq data were combined to analyzing the correlation between yiiG and other virulence factors .A variety of bioinformatic tools were used for discovering the possible type Ⅲsecretion signals .Results yiiG distributed in S.enterica subsp.enterica but variable in other subspecies of S.enterica.No yiiG was found in S.bongori.Besides Salmonella, only a part of Shigella and E.coli strains were detected with yiiG homologs .The genomic locus of yiiG and its adjacency showed conservation among all Salmonella, E.coli and Shigella strains.In most of the serovars of S.enterica subsp.enteri-ca, there was a head-to-head tandem whole yiiG repeat sequence upstream the yiiG gene, which was renamed as yiiGRrc.RNA-seq analysis showed that yiiG gene expression level was highly correlated with T 3SS-related genes . Bioinformatic prediction also indicated the T 3SS effector signals in YiiG N-terminus.Conclusions yiiG represented an ancient genomic locus , which will be a hot spot where rearrangement events frequently happened .The function of yiiG could potentially be related with Salmonella virulence.Finally, a new protein-encoding gene (yiiGRrc) was newly identified that was closely related with yiiG, providing the target for further understanding the composition , function and function variation of yiiG gene family .