Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase

Abstract

Summary Exhaustion of nutritional resources stimulates bacterial populations to adapt their growth behaviour. General mechanisms are known to facilitate this adaptation by sensing the environmental change and coordinating gene expression. However, the existence of such mechanisms among the Alphaproteobacteria remains unclear. This study focusses on global changes in transcript levels during growth under carbon‐limiting conditions in a model Alphaproteobacterium, Rhodobacter sphaeroides, a metabolically diverse organism capable of multiple modes of growth including aerobic and anaerobic respiration, anaerobic anoxygenic photosynthesis and fermentation. We identified genes that showed changed transcript levels independently of oxygen levels during the adaptation to stationary phase. We selected a subset of these genes and subjected them to mutational analysis, including genes predicted to be involved in manganese uptake, polyhydroxybutyrate production and quorum sensing and an alternative sigma factor. Although these genes have not been previously associated with the adaptation to stationary phase, we found that all were important to varying degrees. We conclude that while R. sphaeroides appears to lack a rpoS‐like master regulator of stationary phase adaptation, this adaptation is nonetheless enabled through the impact of multiple genes, each responding to environmental conditions and contributing to the adaptation to stationary phase.

The Quorum Sensing Auto-Inducer 2 (AI-2) Stimulates Nitrogen Fixation and Favors Ethanol Production over Biomass Accumulation in Zymomonas mobilis

“…However, specific AI-2-related responses can be found in the expression of genes involved in the composition of cellular membranes and elements associated with various processes, such as bacterial motility, DNA repair, inorganic nutrient metabolism, and carbohydrate degradation. Interestingly, similar scenarios have also been observed during the QS response in additional bacterial species [26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45].…”

A major checkpoint for protein expression in Rhodobacter sphaeroides during heat stress response occurs at the level of translation

“…Expression activity of the highly active 16S promoter fused to the RBS of cerI was previously found to correlate well with growth (McIntosh et al, 2019), similarly to the expression of the rRNA genes during growth of E. coli (Maeda et al, 2015).…”

“…Other genes of COG‐K with increased transcript levels include two component regulators and transcription factors of different protein families such as the uncharacterized sigma factors RSP_0415 and RSP_3095 (and its anti‐sigma factor RSP_3094). RSP_3095 was recently found to be important for its own expression activation in cultures entering the stationary phase upon carbon limitation and to mildly slow growth during the exponential phase upon over expression (McIntosh et al ., 2019). Hence, it is likely that RSP_3095 supports the adaptation to a variety of stress conditions via the adjustment of transcription.…”

Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions

“…DNA fragments harbouring the putative promoter sequences of every UTR-derived sRNA were amplified and fused to the mVenus gene using plasmid pPHU231 as described by Charoenpanich et al [71] and McIntosh et al [72]. Restriction enzyme cleavage sites (HindIII/XbaI) were incorporated via the primer sequences as well as a strong ribosome binding site (AGGGGAGAAG).…”