Gene expression analysis reveals distinct PHB depolymerization mechanisms and broader involvement of the PHB cycle in Rhodospirillum rubrum growing on acetate and fructose

TL;DR

This study shows that PHB cycle genes in Rhodospirillum rubrum are expressed even when PHB is not formed, suggesting broader roles for the PHB cycle beyond storage and degradation.

Contribution

The study reveals distinct gene expression patterns of PHB cycle genes on different carbon sources and suggests regulatory roles of PHB beyond its known functions.

Findings

PHB cycle genes are expressed during growth on fructose despite no PHB accumulation.

phaZ1 is mainly expressed on acetate, while phaZ2 and apdA are upregulated on fructose.

PHB cycle genes remain expressed in a mutant strain lacking PHB polymerization.

Abstract

Rhodospirillum rubrum owns a dynamic poly(3-hydroxybutyrate) (PHB) cycle: During growth PHB is accumulated and subsequently degraded under carbon starvation. Interestingly, this cycle is typically found for acetate grown R. rubrum but not for fructose grown cells, where no PHB accumulation has been observed. This study aimed to determine whether expression of PHB cycle genes correlates with the phases of PHB accumulation and degradation on acetate in comparison to absence of PHB synthesis during growth on fructose and ΔphaC1ΔphaC2 mutant unable to polymerize PHB on acetate.

Surprisingly, transcriptomic analyses of the wild-type strain demonstrated that PHB cycle genes were not only expressed during growth on acetate but also for growth on fructose, regardless of PHB content. Substrate-specific expression patterns were identified: The PHB depolymerase gene phaZ1 was predominantly expressed on acetate, while phaZ2 and the depolymerase regulator apdA were upregulated on fructose. Interestingly, phaC3 and phaZ3 showed distinct expression patterns compared with other PHB cycle genes, particularly in mutant strains. Despite the absence of PHB granules in the ΔphaC1ΔphaC2 strain, several PHB cycle genes remained expressed, and volatile fatty acid assimilation pathways were transcriptionally impacted.

These findings highlight the complexity of the PHB cycle and suggest that PHB participates in other physiological processes, such as substrate assimilation, potentially via regulatory actions of PHB granule bound regulator PhaR.

The online version contains supplementary material available at 10.1186/s12934-026-02946-7.

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