1. Academic Validation
  2. Transcriptome Analysis Reveals the Effect of PdhR in Plesiomonas shigelloides

Transcriptome Analysis Reveals the Effect of PdhR in Plesiomonas shigelloides

  • Int J Mol Sci. 2023 Sep 23;24(19):14473. doi: 10.3390/ijms241914473.
Junxiang Yan 1 2 3 Bin Yang 1 2 3 Xinke Xue 1 2 3 Jinghao Li 1 2 3 Yuehua Li 1 2 3 Ang Li 4 5 Peng Ding 1 2 3 Boyang Cao 1 2 3
Affiliations

Affiliations

  • 1 TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China.
  • 2 Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China.
  • 3 Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China.
  • 4 State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China.
  • 5 College of Pharmacy Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.
Abstract

The pyruvate dehydrogenase complex regulator (PdhR) was originally identified as a repressor of the pdhR-aceEF-lpd operon, which encodes the pyruvate dehydrogenase complex (PDHc) and PdhR itself. According to previous reports, PdhR plays a regulatory role in the physiological and metabolic pathways of bacteria. At present, the function of PdhR in Plesiomonas shigelloides is still poorly understood. In this study, RNA Sequencing (RNA-Seq) of the wild-type strain and the ΔpdhR mutant strains was performed for comparison to identify the PdhR-controlled pathways, revealing that PdhR regulates ~7.38% of the P. shigelloides transcriptome. We found that the deletion of pdhR resulted in the downregulation of practically all polar and lateral flagella genes in P. shigelloides; meanwhile, motility assay and transmission electron microscopy (TEM) confirmed that the ΔpdhR mutant was non-motile and lacked flagella. Moreover, the results of RNA-seq and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) showed that PdhR positively regulated the expression of the T3SS cluster, and the ΔpdhR mutant significantly reduced the ability of P. shigelloides to infect Caco-2 cells compared with the WT. Consistent with previous research, pyruvate-sensing PdhR directly binds to its promoter and inhibits pdhR-aceEF-lpd operon expression. In addition, we identified two additional downstream genes, metR and nuoA, that are directly negatively regulated by PdhR. Furthermore, we also demonstrated that ArcA was identified as being located upstream of pdhR and lpdA and directly negatively regulating their expression. Overall, we revealed the function and regulatory pathway of PdhR, which will allow for a more in-depth investigation into P. shigelloides pathogenicity as well as the complex regulatory network.

Keywords

ArcA; PdhR; Plesiomonas shigelloides; RNA-seq; T3SS; motility.

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