Analysis of the transcriptional response to mutations in PHB cycle genes in Sinorhizobium meliloti reveals disproportionately affected regions on pSymA containing nitrogen utilization genes

Glycogen and the polyhydroxybutyrate (PHB) polymer are produced by bacteria as a carbon store under unbalanced growth conditions. Although the genetics of the PHB cycle in Sinorhizobium meliloti are well understood, the nature of the regulation of PHB net accumulation is not defined. To gain insights into the transcriptional responses associated with carbon storage, we have investigated the global transcriptomic effects of genetic disruption of the PHB PHB synthesis and degradation, and glycogen synthesis. The transcriptomes of PHB synthesis (phbA, phbB, phbC) and degradation (bdhA, phaZ and acsA2), as well as glycogen synthesis (glgA1) mutants were analyzed under both nitrogen-limited and balanced growth conditions. A cluster of loci on pSymA was differentially expressed in the PHB cycle mutants. A FNR-like transcription factor motif was found to be the most significantly enriched motif upstream of these genes, suggesting an FNR-mediated transcriptional response. Not only do these regions contain a genomic overrepresentation of FNR family transcription factors (six in the loci), but they possess the highest genome-wide density of promoter FNR motifs. The presence of a motif upstream of a gene in these loci correlates with a significant decrease in transcript abundance. As this transcriptional response is enhanced in PHB cycle mutants and not in the glycogen synthase mutant in nitrogen-limited conditions, we hypothesize that these loci, containing mostly nitrogen utilization, denitrification, and fixation genes, are regulated in response to intracellular carbon/nitrogen balance. Our results indicate a transcriptional connection between the cells intracellular levels of carbon (mediated through the functionality of the PHB cycle), and expression of nitrogen utilization genes.