Small RNA Analysis in Caldimonas thermodepolymerans Provides Insight into Non-Coding Regulatory Mechanisms

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Caldimonas thermodepolymerans DSM 15344T is a non-model thermophilic bacterium producing polyhydroxyalkanoates (PHA), biodegradable and biocompatible alternatives to petrochemical plastics. The synthesis of these polymers in bacteria is known, in most cases, to occur under stress conditions such as stress caused by nutrient limitation. Similarly, small RNAs (sRNAs) are closely linked to stress conditions. These regulatory molecules are known to be involved in post-transcriptional regulatory processes. They are predominantly induced in response to stress and further interact with mRNA molecules to impact their translation into functional units. Such common characteristic suggests a possible regulation of the PHA synthesis pathway by sRNAs and thus extends the potential of bacteria for biotechnological applications. Even though many sRNAs have been found and reported, yet there is still lack of sRNA annotations. Here we present results from downstream analysis of RNA-Seq data from xylose cultivation up to 72h covering 8 time points, each in 3 biological replicates. Following sRNA inference, we performed differential expression analysis and co-expression analysis using state-of-the-art tools. These results provide deeper insight into regulatory mechanism of C. thermodepolymerans with the introduction of candidate sRNAs and their expression profiles, further used for the guilt-by-association functional annotation.

Caldimonas; RNA-Seq

HEŘMÁNKOVÁ, K.; KOUŘILOVÁ, X.; BUCHTÍKOVÁ, I.; OBRUČA, S.; SEDLÁŘ, K.

15. 4. 2024

978-80-88214-48-9

11th International Conference on Chemical Technology Book of Abstracts

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