Integration of transcriptomics and metabolomics for understanding the global responses to neutral pH and high pH under high light in photosynthetic bacterium Rhodobacter alkalitolerans strain JA916 ^T

Abstract

Photosynthetic microorganisms are often exposed to fluctuating light intensities in their ecological niches. Rhodobacter alklitolerans is a versatile photosynthetic bacterium able to grow in alkaline conditions. Comprehensive analysis of transcriptomic and metabolomic data reveals preferential gene expression and metabolic regulation of R. alklitolerans strain JA916^T to alkaline pH (hpH) to neutral pH (npH) growth conditions under high light intensities. The transcriptome analysis provided that the majority of the transcripts related to photosystems were found to increase their expression in both npH and hpH under high-light conditions compared to low light conditions. Interestingly, reaction center transcripts (pufH, pufM, and pufL) and light-harvesting complex transcripts (pufA and pufB, pucA and pucB) were upregulated one- to two fold more in npH with increasing light intensity conditions. However, bacteriochlorophyll (BChl) a and carotenoid biosynthesis genes were significantly upregulated in hpH. We also found higher expression of cell division transcripts in npH conditions (murG, ftsZ, ftsQ, and ftsA with 1- to 1.5-fold) than in hpH. Furthermore, the metabolome analysis showed a higher correlation among the physiologically important metabolites such as putrescine, phenylalanine, phytol, L-lysine, L-proline, β-alanine, citric acid, L—5 oxoproline, and Pentanedioic acid. These were found to be part of several important metabolic pathways, including porphyrin metabolism, responsible for BChl metabolism, amino acid metabolism, and the tricarboxylic acid (TCA) cycle, playing a crucial role in energy production, in osmotic balance, and maintaining redox balance caused by high light. The real-time PCR analysis revealed that TCA cycle pathway genes also showed higher expression levels in npH than in hpH conditions under high light. Overall, the current study identifies candidate genes, metabolites, and alkaline-dependent high-light stress defense mechanisms that could potentially enhance alkali and high-light resilience in R. alklitolerans strain JA916^T.