Characterization of an rpoN mutant of Mesorhizobium ciceri

Characterization of a (pckA) mutant of the non-nodulating bacterium Rhizobium pusense NRCPB10 induced by transposon Tn5 mutagenesis

Phosphoenolpyruvate carboxykinase (PCK) catalyzes the decarboxylation and phosphorylation of oxaloacetate to phosphoenolpyruvate in the gluconeogenic pathway in most organisms. A pckA gene encoding PCK was cloned and sequenced from strain Rhizobium pusense NRCPB100, a spontaneous rifampicin resistant mutant of R. pusense NRCPB10^T (JCM16209^T) of a recently described new species of a non-nodulating and non-tumorigenic bacterium. The mapping of the pck gene region following Tn5 mutagenesis located the gene downstream of a transcriptional regulatory protein gene (chvI) and upstream of a conserved hypothetical protein gene. The pck of 1,611 bp was deduced to encode 536 amino acids and showed high homology to the genes of known ATP-dependent PCK enzymes. Phylogenetic analysis of the gene placed it in a cluster with pck of other known members of Rhizobiales. Amino acid sequences of the putative functional regions of the deduced enzyme were found to be conserved.

Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

BACKGROUND

The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production.

RESULTS

An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III), which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT.

CONCLUSION

The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes.