Probing RNA structural landscapes across Candida yeast genomes
Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions i...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-02-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1362067/full |
| _version_ | 1797295027449233408 |
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| author | Uciel Chorostecki Uciel Chorostecki Uciel Chorostecki Ester Saus Ester Saus Toni Gabaldón Toni Gabaldón Toni Gabaldón Toni Gabaldón |
| author_facet | Uciel Chorostecki Uciel Chorostecki Uciel Chorostecki Ester Saus Ester Saus Toni Gabaldón Toni Gabaldón Toni Gabaldón Toni Gabaldón |
| author_sort | Uciel Chorostecki |
| collection | DOAJ |
| description | Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of the Candida genus, which are the leading cause of hospital-acquired fungal infections. Our work addresses the gap between RNA structure and their biology by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four major Candida pathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5′ untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species. Additionally, we provide the first experimental characterization of lncRNA structures in Candida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs across Candida species, humans, and Arabidopsis thaliana, suggesting a conserved role for these structures. In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function in Candida pathogens, with implications for gene expression regulation and potential therapeutic strategies against Candida infections. |
| first_indexed | 2024-03-07T21:40:37Z |
| format | Article |
| id | doaj.art-9bcd863a7ce04e3999b42dded348f1a7 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-07T21:40:37Z |
| publishDate | 2024-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-9bcd863a7ce04e3999b42dded348f1a72024-02-26T10:09:50ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2024-02-011510.3389/fmicb.2024.13620671362067Probing RNA structural landscapes across Candida yeast genomesUciel Chorostecki0Uciel Chorostecki1Uciel Chorostecki2Ester Saus3Ester Saus4Toni Gabaldón5Toni Gabaldón6Toni Gabaldón7Toni Gabaldón8Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, SpainBarcelona Supercomputing Centre (BSC-CNS), Barcelona, SpainInstitute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, SpainBarcelona Supercomputing Centre (BSC-CNS), Barcelona, SpainInstitute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, SpainBarcelona Supercomputing Centre (BSC-CNS), Barcelona, SpainInstitute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, SpainICREA, Barcelona, SpainCentro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, SpainUnderstanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of the Candida genus, which are the leading cause of hospital-acquired fungal infections. Our work addresses the gap between RNA structure and their biology by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four major Candida pathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5′ untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species. Additionally, we provide the first experimental characterization of lncRNA structures in Candida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs across Candida species, humans, and Arabidopsis thaliana, suggesting a conserved role for these structures. In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function in Candida pathogens, with implications for gene expression regulation and potential therapeutic strategies against Candida infections.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1362067/fullsecondary structurelncRNACandidafungievolution |
| spellingShingle | Uciel Chorostecki Uciel Chorostecki Uciel Chorostecki Ester Saus Ester Saus Toni Gabaldón Toni Gabaldón Toni Gabaldón Toni Gabaldón Probing RNA structural landscapes across Candida yeast genomes Frontiers in Microbiology secondary structure lncRNA Candida fungi evolution |
| title | Probing RNA structural landscapes across Candida yeast genomes |
| title_full | Probing RNA structural landscapes across Candida yeast genomes |
| title_fullStr | Probing RNA structural landscapes across Candida yeast genomes |
| title_full_unstemmed | Probing RNA structural landscapes across Candida yeast genomes |
| title_short | Probing RNA structural landscapes across Candida yeast genomes |
| title_sort | probing rna structural landscapes across candida yeast genomes |
| topic | secondary structure lncRNA Candida fungi evolution |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1362067/full |
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