Cyclic Diguanylate Regulates Virulence Factor Genes via Multiple Riboswitches in Clostridium difficile

Abstract

In Clostridium difficile, the signaling molecule c-di-GMP regulates multiple processes affecting its ability to cause disease, including swimming and surface motility, biofilm formation, toxin production, and intestinal colonization. In this study, we used RNA-seq to define the transcriptional regulon of c-di-GMP in C. difficile. Many new targets of c-di-GMP regulation were identified, including multiple putative colonization factors. Transcriptional analyses revealed a prominent role for riboswitches in c-di-GMP signaling. Only a subset of the 16 previously predicted c-di-GMP riboswitches were functional in vivo and displayed potential variability in their response kinetics to c-di-GMP. This work underscores the importance of studying c-di-GMP riboswitches in a relevant biological context and highlights the role of the riboswitches in controlling gene expression in C. difficile.

Type I toxin-antitoxin systems contribute to mobile genetic elements maintenance inClostridioides difficileand can be used as a counter-selectable marker for chromosomal manipulation

“…Sixteen predicted c-di-GMP sensing riboswitches are encoded in the C. difficile 630 genome and the regulatory function of five of them has been investigated so far. Interestingly, cdi1_4 and cdi1_5 riboswitches were recently reported to be insensitive to an elevation of the c-di-GMP levels, and only transcript reads corresponding to the riboswitch sequences themselves (the short form) were detected, and no read-through seemed to occur 30 . In contrast, our RACE-PCR and Northern-blot analysis indicated the presence of a transcript downstream from these riboswitches.…”

Phase variation of a signal transduction system controlsClostridioides difficilecolony morphology, motility, and virulence

“…A c-di-GMP binding riboswitch (Cdi-2-2) lies 5’ of cmrRST and the invertible sequence and positively regulates expression of the operon (Figure 3A) (39, 41). Additionally, rough and smooth colony morphotypes exhibited inverse swimming and surface motility phenotypes, which is characteristic of c-di-GMP regulation (36, 43).…”

“…As in many bacteria, the intracellular signaling molecule c-di-GMP regulates the transition between community-associated and planktonic, motile lifestyles of C. difficile (33, 35–38). This regulation occurs in part through direct control of gene expression by c-di-GMP via riboswitches (39–42). For example, a c-di-GMP riboswitch lies in the 5’ leader sequence of the flgB operon and causes transcription termination when c-di-GMP is bound, thus inhibiting swimming motility (39, 40, 43).…”

“…This regulation occurs in part through direct control of gene expression by c-di-GMP via riboswitches (39–42). For example, a c-di-GMP riboswitch lies in the 5’ leader sequence of the flgB operon and causes transcription termination when c-di-GMP is bound, thus inhibiting swimming motility (39, 40, 43). Because flagellum and toxin gene expression is linked through SigD, c-di-GMP also inhibits toxin production (34, 43).…”

Insights into the ligand-free structure of cyclic diguanosine monophosphate I riboswitch of Vibrio cholerae using molecular dynamics simulation

“…The cyclic-di-GMP I is a secondary messenger involved in the mechanisms such as virulence, mobility, quorum sensing and biofilm formation. McKee et al (2018) showed that the c-di-GMP regulates virulence factor genes via riboswitches in C. difficile. In a recent study, Tamayo (2019) reported the role of c-di-GMP riboswitches in controlling bacterial pathogenesis mechanisms.…”