Genome-wide Transcriptional Response during the Shift to N2-fixing Conditions in Heliobacterium modesticaldum

Abstract

Heliobacteria are the only known phototrophic Firmicute; all known members of this group appear to be capable of N2 fixation but incapable of CO2 fixation. They are anoxygenic and possess the simplest photosynthetic apparatus known. The sequence of the 3.1-Mb genome of Heliobacterium modesticaldum, a moderate thermophile within the family Heliobacteriaceae, is publicly available. The focus of this study is to understand how this organism operates at a fundamental level by examining changes in its transcriptome during a shift from ammonium-containing medium to N2-fixing conditions. RNA was purified from cells grown with pyruvate as the carbon source and ammonia or N2 as the nitrogen source. After rRNA depletion, the RNA pool was sequenced using the Ion Torrent PGM platform. We found that the nitrogenase gene cluster was only expressed under N2-fixing conditions, concomitant with increased expression of the high-affinity ammonium transporter. Most genes were down-regulated in N2-fixing conditions by a factor of at least three. A drastic down-regulation of the highly expressed genes encoding proteins involved in the cyclic electron transport chain also occurred. The photosynthetic pshA transcript also decreased more than 100-fold but subsequent photochemical analysis demonstrated no large drop in the concentration of the reaction center protein complex. This indicates that there is a role for substantial translational regulation in some genes. The transcriptomic analyses revealed a network of differentially expressed genes in H. modesticaldum. This study represents the first step in the creation of a quantitative genome-scale metabolic model establishing H. modesticaldum as a model organism for the Heliobacteriaceae family.