Whole-genome transcriptional profiling of Bradyrhizobium japonicum during chemoautotrophic growth

Abstract

Bradyrhizobium japonicum is a facultative chemoautotroph capable of utilizing hydrogen gas as an electron donor in a respiratory chain terminated by oxygen to provide energy for cellular processes and carbon dioxide assimilation via a reductive pentose phosphate pathway. A transcriptomic analysis of B. japonicum cultured chemoautotrophically identified 1,485 transcripts, representing 17.5% of the genome, as differentially expressed when compared to heterotrophic cultures. Genetic determinants required for hydrogen utilization and carbon fixation, including the uptake hydrogenase system and components of the Calvin-Benson-Bassham cycle, were strongly induced in chemoautotrophically cultured cells. A putative isocitrate lyase (aceA; blr2455) was among the most strongly upregulated genes, suggesting a role for the glyoxylate cycle during chemoautotrophic growth. Addition of arabinose to chemoautotrophic cultures of B. japonicum did not significantly alter transcript profiles. Furthermore, a subset of nitrogen fixation genes was moderately induced during chemoautotrophic growth. In order to specifically address the role of isocitrate lyase and nitrogenase in chemoautotrophic growth, we cultured aceA, nifD, and nifH mutants under chemoautotrophic conditions. Growth of each mutant was similar to that of the wild type, indicating that the glyoxylate bypass and nitrogenase activity are not essential components of chemoautotrophy in B. japonicum.

FIG. 1.

Functional classification of differentially expressed genes with transcript changes greater than 1.5-fold. (A) Chemoautotrophy and heterotrophy comparison. (B) Arabinose-supplemented chemoautotrophy and heterotrophy comparison. In both panels, black bars represent the chemoautotrophic condition and gray bars represent the heterotrophic condition. Functional classifications were derived from B. japonicum genome annotations available via Rhizobase (http://bacteria.kazusa.or.jp/rhizobase/) and the JCVI Comprehensive Microbial Resource (http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi).

FIG. 2.

Comparison of log-transformed qRT-PCR data and microarray data of eight representative genes selected from Tables S1 to S4 in the supplemental material.