PHA-Related Regulatory Small RNAs in Caldimonas Thermodepolymerans

abstract

English

Small RNAs represent a group of post-transcriptional regulatory elements, a part of the machinery regulating gene expression in bacteria. These non-coding regulatory elements are not translated into proteins, and therefore can act as rapid responses to stress. The sRNA molecule is after transcription able to bind an mRNA target, and by multiple mechanisms determine whether to discard the mRNA or not. With this principle, levels of mRNAs in cells are influenced in response to changing environments and the needs of bacteria. Caldimonas thermodepolymerans DSM 15344T is a moderately thermophilic bacterium, a promising candidate for application in biotechnology. This bacterium is primarily known for the production of polyhydroxyalkanoate (PHA) granules, a source material for bioplastics. C. thermodepolymerans also represents a candidate for the Next generation industrial biotechnology (NGIB) approach that aims for sustainable production using bacteria. The NGIB tries to reduce the biotechnological production costs by finding bacterial candidates that are able for efficient production without the need for expensive conditions for batch production. To further investigate the capacity of C. thermodepolymerans metabolism, we used the transcriptomic data measured with RNA-Seq to infer sRNAs and conduct downstream analyses. The drawback of the sRNAs analyses is the lack of their structural annotations in bacterial genomes and thus they need to be first predicted. One option represents the prediction of sRNAs from RNA-Seq data as the transcription from intergenic regions. As well as the structural annotation, the functional annotation of sRNAs is missing. Therefore, to find putative small RNAs that relate to PHA metabolism, we conducted a co-expression analysis to infer the functionality of sRNAs with a ‘guilt by association’ approach. These sRNAs that have similar expression profiles to those genes known to be involved in PHA metabolism were further investigated. The candidate sRNAs were predicted from RNA-Seq samples measured from the cultivation of bacterium with xylose. Three biological replicates were measured in 8 time points to cover 72 hours. With the help of state-of-the-art tools, further analyses lead to the structural and functional annotation of sRNAs. Using a ‘guilt by association’ approach, those sRNAs that were assigned to genes involved in PHA metabolism were further investigated. These results provide deeper insight into the sRNAs regulatory mechanism of C. thermodepolymerans DSM 15344T. Overall, results contribute to the assessment of bacterial utilization in industrial applications by providing further knowledge of bacterial capacity.

RNA-Seq; Caldimonas; small RNAs

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

12. 9. 2024

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