Genome-wide changes in Rhodospirillum rubrum DSM 467T induced by knock-out of phaZ2 depolymerase

Genome-wide changes in Rhodospirillum rubrum DSM 467T induced by knock-out of phaZ2 depolymerase

Abstrakt

Rhodospirillum rubrum is a metabolically versatile, Gram-negative bacterium capable of thriving in diverse environments through aerobic respiration, anaerobic fermentation, and photosynthesis. Besides its significance in carbon and nitrogen cycling, R. rubrum is notable for its ability to synthesize and degrade polyhydroxyalkanoates (PHAs), which serve as intracellular carbon and energy reserves. PHA accumulation and mobilization are central to the organism’s survival strategy, with PHA degradation mediated by depolymerases such as PhaZ1 and PhaZ2. While PhaZ1 is thought to be periplasmic, PhaZ2 is an intracellular depolymerase that degrades native PHB granules [1, 2]. In this study, we engineered a knock-out mutant of R. rubrum DSM 467T lacking the main depolymerase gene phaZ2 and performed whole-genome sequencing using Oxford Nanopore technology. Comparative genomic analysis with the published wild-type reference genome enabled us to confirm the targeted deletion and assess genome-wide structural variations. In addition, direct detection of DNA methylation patterns revealed broad epigenetic changes associated with the loss of the PhaZ2 depolymerase. By integrating RNA-Seq data from the wild-type strain [3], we identified correlations between specific methylation patterns and gene expression. Our results demonstrate that knock-out of the intracellular depolymerase in R. rubrum DSM 467T induces widespread genomic and epigenetic changes, affecting not only PHA catabolism but also the regulation of metabolic pathways and stress responses. This study highlights the interconnection of genetic, epigenetic, and transcriptional regulation in the adaptation of R. rubrum to environmental and metabolic challenges.

Rhodospirillum rubrum is a metabolically versatile, Gram-negative bacterium capable of thriving in diverse environments through aerobic respiration, anaerobic fermentation, and photosynthesis. Besides its significance in carbon and nitrogen cycling, R. rubrum is notable for its ability to synthesize and degrade polyhydroxyalkanoates (PHAs), which serve as intracellular carbon and energy reserves. PHA accumulation and mobilization are central to the organism’s survival strategy, with PHA degradation mediated by depolymerases such as PhaZ1 and PhaZ2. While PhaZ1 is thought to be periplasmic, PhaZ2 is an intracellular depolymerase that degrades native PHB granules [1, 2]. In this study, we engineered a knock-out mutant of R. rubrum DSM 467T lacking the main depolymerase gene phaZ2 and performed whole-genome sequencing using Oxford Nanopore technology. Comparative genomic analysis with the published wild-type reference genome enabled us to confirm the targeted deletion and assess genome-wide structural variations. In addition, direct detection of DNA methylation patterns revealed broad epigenetic changes associated with the loss of the PhaZ2 depolymerase. By integrating RNA-Seq data from the wild-type strain [3], we identified correlations between specific methylation patterns and gene expression. Our results demonstrate that knock-out of the intracellular depolymerase in R. rubrum DSM 467T induces widespread genomic and epigenetic changes, affecting not only PHA catabolism but also the regulation of metabolic pathways and stress responses. This study highlights the interconnection of genetic, epigenetic, and transcriptional regulation in the adaptation of R. rubrum to environmental and metabolic challenges.

ŠABATOVÁ, K.; UMAIR, M.; CENTNEROVÁ, R.; FLEURIOT-BLITMAN, H.; BEZDÍČEK, M.; OBRUČA, S.; SEDLÁČEK, P.; SEDLÁŘ, K.

01.10.2025

12th European Symposium on Biopolymers

106

106

1