Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in Rhodobacter sphaeroides 2.4.1

Department of Microbiology and Molecular Genetics, University of Texas, Health Science Center, Houston, Texas, and Department of Biotechnology, University of Tokyo, Tokyo, Japan

^* To whom correspondence should be addressed. Email: samuel.kaplan{at}uth.tmc.edu.

	Abstract

Rhodobacter sphaeroides 2.4.1 is a facultative photosynthetic anaerobe that grows by anoxygenic photosynthesis under anaerobic-light conditions. Changes in energy generation pathways under photosynthetic and aerobic respiratory conditions are primarily controlled by oxygen tensions. In this study, we performed time-series microarray analyses to investigate transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration. Major changes in gene expression profiles occurred in the initial 15 min after the shift from anaerobic-light to aerobic-dark conditions, with changes continuing to occur up to four hours post-shift. Those genes whose expression levels changed significantly during the time-series were grouped into three major classes by clustering analysis. Class I contains genes, such as the aa₃ cytochrome oxidase, whose expression levels increased after the shift. Class II contains genes, such as the photosynthetic apparatus and Calvin cycle enzymes, whose expression levels decreased after the shift. Class III contains genes whose expression levels temporarily increased during the time-series. Many genes for metabolism and transport of carbohydrates or lipids were significantly induced early during the transition, suggesting that those endogenous compounds were initially utilized as carbon sources. Oxidation of those compounds might also be required for maintenance of redox homeostasis after exposure to oxygen. Genes for repair of protein and sulfur groups and uptake of ferric iron were temporarily upregulated soon after the shift, suggesting they were involved in a response to oxidative stress. The flagellar biosynthesis genes were expressed in a hierarchical manner at 1560 min after the shift. Numerous transporters were induced at various time points, suggesting that the cellular composition went through significant changes during the transition from anaerobic photosynthesis to aerobic respiration. Analyses of these data make it clear that numerous regulatory activities come into play during the transition from one homeostatic state to another.