Publication
An endoribonuclease of the YicC-like family delays sporulation via sRNA degradation in Clostridioides difficile
| dc.contributor.author | Martins, Diogo | |
| dc.contributor.author | Salgueiro, Bruno | |
| dc.contributor.author | Sobral, Daniel | |
| dc.contributor.author | Gragera, Marcos | |
| dc.contributor.author | Hensel, Zach | |
| dc.contributor.author | Henriques, Adriano O. | |
| dc.contributor.author | Romão, Célia V. | |
| dc.contributor.author | Serrano, Mónica | |
| dc.date.accessioned | 2025-12-03T16:37:47Z | |
| dc.date.available | 2025-12-03T16:37:47Z | |
| dc.date.issued | 2025-07-08 | |
| dc.description.abstract | Clostridioides difficile CD25890 is a YicC-like endoribonuclease involved in regulating sporulation initiation, a process critical for the host-host transmission of this anaerobic pathogen. Using comparative transcriptomics we identified a small RNA, SQ528, that accumulates at higher levels in a CD25890 deletion mutant and we show that purified CD25890 cleaves SQ528 in a metal-dependent manner. Moreover, the overexpression of SQ528 increases sporulation under certain nutritional conditions phenocopying a CD25890 deletion mutant. CD25890 is an hexamer in solution and in vivo. An N-terminal domain, which self-interacts as assessed by size exclusion chromatography and a two hybrid assay, is essential for oligomerization of CD25890. A C-terminal domain harbours residues H230, E254, and E258, conserved among orthologues, important for catalysis. AlphaFold2 modelling and cryo-EM suggest an elongated barrel-like structure with an internal cavity lined with basic residues that may aid in RNA binding. We show that CD25890 forms a complex with polynucleotide phosphorylase which combines the endoribonuclease activity of the first with the exonucleolytic activity of the latter and leads to the complete degradation of SQ528. This study identifies a native substrate for the YicC-family of ribonucleases and advances our understanding of the role of CD25890 in sporulation initiation in C. difficile. | eng |
| dc.description.sponsorship | This project was supported by award PTDC/BIA-MIC/29293/2017 to M.S. and has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 857203 to C.V.R. This study was financially supported by the Portuguese Fundação para a Ciência e Tecnologia (FCT), Projects MOSTMICRO-ITQB with references UIDB/04612/2020, and LS4FUTURE Associated Laboratory (LA/P/0087/2020). D.M. is the recipient of a PhD fellowship (PD/BD/143148/2019) within the scope of the PhD program INTERFACE funded by FCT. B.A.S. is the recipient of the FCT PhD4COVID grant SFRH/BD/08066/2020. This work benefited from access to the Instruct Image Processing Centre, an Instruct-ERIC centre. Financial support was provided by “Instruct-ERIC (PID 19564 and 20782)”. The microscopy data were acquired at BIC, ITQB-NOVA, Oeiras, Portugal with equipment funded by FCT, project PPBI-POCI-01-0145-FEDER-022122. Mass spectrometry data were generated by the Mass Spectrometry Unit (UniMS), ITQB/iBET, Oeiras, Portugal. | |
| dc.identifier.citation | Nucleic Acids Res. 2025 Jul 8;53(13):gkaf644. doi: 10.1093/nar/gkaf644 | |
| dc.identifier.doi | 10.1093/nar/gkaf644 | |
| dc.identifier.eissn | 1362-4962 | |
| dc.identifier.issn | 0305-1048 | |
| dc.identifier.pmid | 40650975 | |
| dc.identifier.uri | http://hdl.handle.net/10400.18/10635 | |
| dc.language.iso | eng | |
| dc.peerreviewed | yes | |
| dc.publisher | Oxford University Press | |
| dc.relation | UIDB/04612/2020 | |
| dc.relation | PTDC/BIA-MIC/29293/2017 | |
| dc.relation | 857203 | |
| dc.relation | LA/P/0087/2020 | |
| dc.relation | SFRH/BD/08066/2020 | |
| dc.relation.hasversion | https://academic.oup.com/nar/article/53/13/gkaf644/8198043 | |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc/4.0/ | |
| dc.subject | Clostridioides Difficile | |
| dc.subject | Endoribonucleases | |
| dc.subject | Bacterial Proteins | |
| dc.subject | Gene Expression Regulation | |
| dc.subject | Bacterial | |
| dc.subject | RNA | |
| dc.subject | Genetics | |
| dc.subject | Genómica Funcional e Estrutural | |
| dc.title | An endoribonuclease of the YicC-like family delays sporulation via sRNA degradation in Clostridioides difficile | eng |
| dc.type | journal article | |
| dcterms.references | https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/53/13/10.1093_nar_gkaf644/1/gkaf644_supplemental_file.pdf?Expires=1767091748&Signature=MfwHpTWpWBmSTC~i~7z0RXfDx6mLZxUfPsJ9QHn-of3ue76Eg7C5lRRs1gzxT9wDt9nDm6xRP6oN0SVEJ0upTjA9VaJfnq-5cPX2gMTRXUJOPU41b0MSqJCoQ6Z9P8Ck2R-SlizOp9ExVZn0cnX5x3d0jdH2VEFprrnBy~ifl8CZ6BXGXwvvyoxg294hJOzbt~JA-fKqsk6odtiWnhf2gqRuA98fWpMaOBDYy0qfYN4lT5h3TZE2XfxzE-LFubvnXY37TVtsPnw4k0uBZMdKCqGtLPvS8DdZYGFPhYnEr9VJ9DkwGlpCipQipOFP07xVdOqqEEbbahK0ZOfnoJcorg__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA | |
| dspace.entity.type | Publication | |
| oaire.citation.issue | 13 | |
| oaire.citation.startPage | gkaf644 | |
| oaire.citation.title | Nucleic Acids Research | |
| oaire.citation.volume | 53 | |
| oaire.version | http://purl.org/coar/version/c_970fb48d4fbd8a85 |