Transcriptomic analysis of Rhodospirillum rubrum wild-type and mutant strains

Abstract

Rhodospirillum rubrum is a versatile bacterium capable of thriving under various cultivation conditions, including both aerobic and anaerobic environments. It is also known as a promising candidate for production of biopolymers such as polyhydroxyalkanoates (PHA), which are of significant interest for biodegradable plastic production. However, comprehensive genome-wide transcriptomic studies are lacking, limiting our ability to fully explore gene regulation in R. rubrum, particularly in relation to PHA production. In our study, we present an analysis of RNA-Seq data of Rhodospirillum rubrum DSM 467T wild-type strain and ΔphaC1ΔphaC2 mutant strain [1]. Both strains were cultivated under identical conditions using either fructose or acetate as a substrate, with RNA samples collected at the same grow phases. The resulting RNA-Seq data were analyzed to uncover the main differences between the cultivation conditions and between the two strains on transcriptomic level. To achieve this, we employed differential expression analysis and gene ontology (GO) enrichment analysis to identify GO terms associated with the most significant changes in gene expression under the studied conditions. The results were visualized as show in Figure 1, where a heatmap represents the expression profiles of selected genes associated with significantly enriched GO terms, and arrows indicate statistically significant changes in the gene expression. For instance, Figure 1 compares of cultivations of R. rubrum wild-type strain on fructose and acetate, highlighting enriched GO terms such as electron transfer activity (molecular function (MF) GO term) and response to stress (biological process (BP) GO term). Our analysis provides further insights into the responses of R. rubrum wild-type and ΔphaC1ΔphaC2 mutant strains to specific substrates, enhancing our understanding of their metabolic adaptability and potential for biopolymer production.

ŠABATOVÁ, K.; JAKUBÍČKOVÁ, M.; SLANINOVÁ, E.; FLEURIOT-BLITMAN, H.; AMSTUTZ, V.; HEŘMÁNKOVÁ, K.; ZINN, M.; OBRUČA, S.; SEDLÁŘ, K.

12.09.2024

9th Meeting on Chemistry & Life