Cze vs Ger: Comparing Post-Transcriptional Regulation in Two Strains of PHA Producing Caldimonas thermodepolymerans

Cze vs Ger: Comparing Post-Transcriptional Regulation in Two Strains of PHA Producing Caldimonas thermodepolymerans

Abstract

Polyhydroxyalkanoates (PHAs) are biodegradable, biocompatible, and renewable polymers naturally produced by microorganisms as intracellular carbon and energy reserves. Thanks to their promising material properties, PHAs represent a sustainable alternative to conventional petroleum-based plastics. Caldimonas thermodepolymerans, a moderately thermophilic, non-sporulating, Gram-negative bacterium represent promising candidate for the Next Generation Industrial Biotechnology (NGIB) approach which exploits its special properties, such as thriving in extreme conditions, for sustainable production of value-added chemicals. The bacterial post-transcriptional regulation of gene expression by small RNAs (sRNAs) is a powerful mechanism how bacteria response to stress. 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 in two strains of C. thermodepolymerans DSM 15344T. The type strain was initially isolated from activated sludge in Germany, deposited in Leibniz Institute DSMZ in Germany (GER) and later in the Czech Collection of Microorganisms in Czechia (CZE). The aim was to evaluate whether variations in cultivation conditions and phenotypic characteristics of C. thermodepolymerans strains obtained from different public culture collections are associated with differential expression of sRNAs. We analysed RNA-Seq experiments in which both strains were cultured on xylose. Using state-of-the-art tools for the structural and functional annotation, we conducted a comparative analysis of sRNAs in these bacteria. Additionally, we explored expression profiles of sRNAs and performed a differential expression analysis. The focus was mainly on the PHA metabolism and related sRNAs addressing differences between these two strains.

Polyhydroxyalkanoates (PHAs) are biodegradable, biocompatible, and renewable polymers naturally produced by microorganisms as intracellular carbon and energy reserves. Thanks to their promising material properties, PHAs represent a sustainable alternative to conventional petroleum-based plastics. Caldimonas thermodepolymerans, a moderately thermophilic, non-sporulating, Gram-negative bacterium represent promising candidate for the Next Generation Industrial Biotechnology (NGIB) approach which exploits its special properties, such as thriving in extreme conditions, for sustainable production of value-added chemicals. The bacterial post-transcriptional regulation of gene expression by small RNAs (sRNAs) is a powerful mechanism how bacteria response to stress. 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 in two strains of C. thermodepolymerans DSM 15344T. The type strain was initially isolated from activated sludge in Germany, deposited in Leibniz Institute DSMZ in Germany (GER) and later in the Czech Collection of Microorganisms in Czechia (CZE). The aim was to evaluate whether variations in cultivation conditions and phenotypic characteristics of C. thermodepolymerans strains obtained from different public culture collections are associated with differential expression of sRNAs. We analysed RNA-Seq experiments in which both strains were cultured on xylose. Using state-of-the-art tools for the structural and functional annotation, we conducted a comparative analysis of sRNAs in these bacteria. Additionally, we explored expression profiles of sRNAs and performed a differential expression analysis. The focus was mainly on the PHA metabolism and related sRNAs addressing differences between these two strains.

C.thermodepolymerans;polyhydroxyalkanoates;sRNA;microorganism

C.thermodepolymerans;polyhydroxyalkanoates;sRNA;microorganism

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

01.10.2025

Lisbon, Portugal

105

105

204

https://media.sci-meet.com/www.esbp2025.org/326b420a-8f47-4973-a2a8-2d4010491cbc/BookofAbstractsESBP2025.pdf