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

Photosynthetic microorganisms are often exposed to fluctuating light intensities in their ecological niches. <i>Rhodobacter alklitolerans</i> 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 <i>R. alklitolerans</i> 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 (<i>pufH</i>, <i>pufM</i>, and <i>pufL</i>) and light-harvesting complex transcripts (<i>pufA</i> and <i>pufB</i>, <i>pucA</i> and <i>pucB</i>) were upregulated one- to two fold more in npH with increasing light intensity conditions. However, bacteriochlorophyll (BChl) <i>a</i> and carotenoid biosynthesis genes were significantly upregulated in hpH. We also found higher expression of cell division transcripts in npH conditions (<i>murG</i>, <i>ftsZ</i>, <i>ftsQ</i>, and <i>ftsA</i> 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 <i>R. alklitolerans</i> strain JA916^T.IMPORTANCEThe study provides detailed information about the differential transcriptomic and metabolic response of the photosynthetic bacterium <i>R. alkalitolerans</i> strain JA916^T in alkaline and neutral pH conditions. The study puts emphasis on the core photosynthetic transcripts and how their expression level is lower in hpH compared to npH, especially when it is grown in high light. The study also reasons out the relatively higher expression of bacteriochlorophyll <i>a</i> and carotenoid biosynthesis pathway transcripts in hpH, emphasizing the more photoprotection in hpH growth conditions. Furthermore, it also explores the role of metabolites in the study under high light and pH conditions, such as L-proline, putrescine, phenylalanine, etc., and their intricate metabolic networks through correlation matrix and interaction networks. The high-light and alkali stress markers identified in our study from the photosynthetic bacterium <i>R. alkalitolerans</i> strain JA916T can be used to develop stress-tolerant strains.