From RNA-Seq to Regulatory Small RNAs in Non- Model Bacteria for Biotechnological Applications

From RNA-Seq to Regulatory Small RNAs in Non- Model Bacteria for Biotechnological Applications

Abstrakt

Small RNAs (sRNAs) play a crucial role in the post-transcriptional regulation of bacterial gene expression, influencing bacterial phenotype and chemical tolerance by modulating transcript translation. This regulatory mechanism can be harnessed to engineer bacterial genomes, optimizing fermentation processes for the production of bio-based chemicals, such as PolyHydroxyAlkanoates (PHA), which are biodegradable, biocompatible, and renewable materials with broad industrial applications. Despite their importance, sRNAs are often under-annotated in bacterial genomes. However, RNA-Seq combined with computational analysis enables genome-wide prediction of sRNAs and provides insights into bacterial regulatory networks under various conditions. In this study, we present a computational approach that integrates state-of-the-art tools to structurally annotate sRNAs in the genomes of non-model bacteria and predict their target sequences for regulatory function. Our recent results revealed the prediction of hundreds of regulatory sRNAs from intergenic regions in the genome of C. thermodepolymerans DSM 15344T, a moderately thermophilic non-model bacterium producing PHA. By analysing loci information and expression profile correlations, we identified regulatory relationships between sRNAs and genes involved in PHA metabolism, proposing these sequences as potential PHA-regulating sRNAs. Understanding the role of sRNAs in non-model bacteria and linking this knowledge to specific metabolic pathways is critical, as it remains poorly understood and may offer new strategies for optimizing the bioproduction of value-added chemicals.

Small RNAs (sRNAs) play a crucial role in the post-transcriptional regulation of bacterial gene expression, influencing bacterial phenotype and chemical tolerance by modulating transcript translation. This regulatory mechanism can be harnessed to engineer bacterial genomes, optimizing fermentation processes for the production of bio-based chemicals, such as PolyHydroxyAlkanoates (PHA), which are biodegradable, biocompatible, and renewable materials with broad industrial applications. Despite their importance, sRNAs are often under-annotated in bacterial genomes. However, RNA-Seq combined with computational analysis enables genome-wide prediction of sRNAs and provides insights into bacterial regulatory networks under various conditions. In this study, we present a computational approach that integrates state-of-the-art tools to structurally annotate sRNAs in the genomes of non-model bacteria and predict their target sequences for regulatory function. Our recent results revealed the prediction of hundreds of regulatory sRNAs from intergenic regions in the genome of C. thermodepolymerans DSM 15344T, a moderately thermophilic non-model bacterium producing PHA. By analysing loci information and expression profile correlations, we identified regulatory relationships between sRNAs and genes involved in PHA metabolism, proposing these sequences as potential PHA-regulating sRNAs. Understanding the role of sRNAs in non-model bacteria and linking this knowledge to specific metabolic pathways is critical, as it remains poorly understood and may offer new strategies for optimizing the bioproduction of value-added chemicals.

small RNA;gene expression;polyhydroxyalkanoates;RNA-Seq

small RNA;gene expression;polyhydroxyalkanoates;RNA-Seq

HEŘMÁNKOVÁ, K.; SEDLÁŘ, K.; ŠLOSÁROVÁ, K.; OBRUČA, S.

20.07.2025

Liverpool, UK

Book of Abstracts ISMB/ECCB 2025

912

913

1187

https://www.iscb.org/images/stories/ismbeccb2025/document.AbstractsBook.ISMBECCB.2025.pdf