Comparative Analysis of Small RNAs in Two PHA-Producing Bacteria

Comparative Analysis of Small RNAs in Two PHA-Producing Bacteria

Abstrakt

The main role of small RNAs (sRNAs) in bacteria is the post-transcriptional regulation of gene expression. These non-coding regulatory elements can modulate gene transcription levels, ensuring that the abundance of gene products is appropriate for the bacterial needs at a given time, whether that means stimulation or inhibition of the translation. Their investigation promises a more precise understanding of regulatory processes and offers additional genomic elements that can be targeted by synthetic biology in order to fine-tune bacteria used in biotechnology. In this work, we compare the sRNA content of two bacteria that produce polyhydroxyalkanoates (PHAs), polymers that could serve as biodegradable and biocompatible alternatives to petrochemical plastics. The first is the thermophilic bacterium Caldimonas thermodepolymerans DSM 15344T, formerly Schlegelella thermodepolymerans [1]. The second is the purple bacterium Rhodospirillum rubrum DSM 467, whose sRNA content has already been outlined [2]. Both bacteria represent promising candidates for the Next Generation Industrial Biotechnology (NGIB) [3] approach which exploits their special properties, such as thriving in extreme conditions, for sustainable production of value-added chemicals. The data comes from RNA-Seq experiments in which both bacteria were cultured on their preferred substrates triggering PHA production. Using state-of-the-art tools for the structural and functional annotation, we conducted a comparative analysis of the non-coding regulatory elements in these bacteria. The analysis primarily focuses on the PHA metabolism and related sRNAs addressing differences between these two bacteria from distant genera.

The main role of small RNAs (sRNAs) in bacteria is the post-transcriptional regulation of gene expression. These non-coding regulatory elements can modulate gene transcription levels, ensuring that the abundance of gene products is appropriate for the bacterial needs at a given time, whether that means stimulation or inhibition of the translation. Their investigation promises a more precise understanding of regulatory processes and offers additional genomic elements that can be targeted by synthetic biology in order to fine-tune bacteria used in biotechnology. In this work, we compare the sRNA content of two bacteria that produce polyhydroxyalkanoates (PHAs), polymers that could serve as biodegradable and biocompatible alternatives to petrochemical plastics. The first is the thermophilic bacterium Caldimonas thermodepolymerans DSM 15344T, formerly Schlegelella thermodepolymerans [1]. The second is the purple bacterium Rhodospirillum rubrum DSM 467, whose sRNA content has already been outlined [2]. Both bacteria represent promising candidates for the Next Generation Industrial Biotechnology (NGIB) [3] approach which exploits their special properties, such as thriving in extreme conditions, for sustainable production of value-added chemicals. The data comes from RNA-Seq experiments in which both bacteria were cultured on their preferred substrates triggering PHA production. Using state-of-the-art tools for the structural and functional annotation, we conducted a comparative analysis of the non-coding regulatory elements in these bacteria. The analysis primarily focuses on the PHA metabolism and related sRNAs addressing differences between these two bacteria from distant genera.

RNA-Seq; PHA; sRNA; functional annotation; NGIB

RNA-Seq; PHA; sRNA; functional annotation; NGIB

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

28.11.2024

978-80-214-6298-4

Studentská odborná konference Chemie je život 2024 Sborník abstraktů

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https://www.fch.vut.cz/vav/konference/sok/vystupy/sbornik-abstraktu-2024-p276490

http://hdl.handle.net/