Abstract
Mycobacterium abscessus causes severe disease in patients with cystic fibrosis. Little is known in M. abscessus about the roles of small regulatory RNAs (sRNA) in gene regulation. We show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough strain, increased pro-inflammatory signaling and virulence in multiple infection models, and increased resistance to antibiotics. Examination of clinical isolate cohorts identified isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of mutations found in clinical isolates. Over 200 genes were differentially expressed in the deletion mutant. Strains with the clinical B11 mutations showed expression trends similar to the deletion mutant, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with B11 functioning as a negative regulator that represses translation via base-pairing to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences. Intriguingly, genes upregulated in the absence of B11 included components of the ESX-4 secretion system, critical for M. abscessus virulence. Many of these genes had B11-complementary sequences at their RBSs, which we show is sufficient to mediate repression by B11 through direct binding. Altogether, our data show that B11 acts as a direct negative regulator and mediates (likely indirect) positive regulation with pleiotropic effects on gene expression and clinically important phenotypes in M. abscessus. The presence of hypomorphic B11 mutations in clinical strains is consistent with the idea that lower B11 activity may be advantageous for M. abscessus in some clinical contexts. This is the first report on an sRNA role in M. abscessus.
| Originalsprog | Engelsk |
|---|---|
| Artikelnummer | e1011575 |
| Tidsskrift | PLoS Pathogens |
| Vol/bind | 19 |
| Antal sider | 32 |
| ISSN | 1553-7366 |
| DOI | |
| Status | Udgivet - 2023 |
| Udgivet eksternt | Ja |
Bibliografisk note
Funding Information:This work was supported in part by NIH NIAID R21 AI156415-01A1 to S.S.S., by NIH NIAID R21 AI156415-01A1 to D.B., by NSF CAREER award 1652756 to S.S.S., by NIH N AID 1 P01 AI143575-01A1 to S.S.S., and by the ISF individual grant (608/22) to D.B. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank members of the Shell and Barkan labs, M. Chiacchiaretta (IRCCS San Raffaele Scientific Institute) and F. Cugnata (Vita-Salute San Raffaele University, Milano, Italy) for technical assistance and helpful discussions. We thank Christina Stallings for critical reading of the manuscript, Margaret Fitzgibbon (St. James Hospital, Dublin) for providing information on the Irish cohort of M. abscessus, and Efrat Rorman (Israeli Ministry of Health) for providing some of the clinical isolates in the Israeli cohort. Dr. Dana Ment, Volcani Institute for Agricultural research, Israel, kindly provided G. mellonella larvae for many of the experiments. Proteomic analysis was performed at the Smolar Centre for Proteomics, Technion, Haifa, Israel.
Funding Information:
Funding:ThisworkwassupportedinpartbyNIH NIAIDR21AI156415-01A1toS.S.S.,byNIHNIAID R21AI156415-01A1toD.B.,byNSFCAREER award1652756toS.S.S.,byNIHNAID1P01 AI143575-01A1toS.S.S.,andbytheISFindividual grant(608/22)toD.B.Thefundershadnorolein
Publisher Copyright:
© 2023 Bar-Oz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.