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Open Access Research article

Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli

Tom Groot Kormelink1235, Eric Koenders5, Yanick Hagemeijer5, Lex Overmars245, Roland J Siezen1245, Willem M de Vos23 and Christof Francke1245*

Author Affiliations

1 Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA, Delft, The Netherlands

2 TI Food and Nutrition, P.O. Box 557, 6700 AN, Wageningen, The Netherlands

3 Laboratory of Microbiology, Wageningen University & Research Centre, Dreijenplein 10, 6700 HB, Wageningen, The Netherlands

4 Netherlands Bioinformatics Centre, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands

5 Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands

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BMC Genomics 2012, 13:191  doi:10.1186/1471-2164-13-191

Published: 18 May 2012

Abstract

Background

The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine synthetase, glutaminase, glutamate dehydrogenase and glutamine alpha-ketoglutarate aminotransferase. In low-GC Gram-positive bacteria the transcriptional control over the levels of the related enzymes is mediated by four regulators: GlnR, TnrA, GltC and CodY. We have analyzed the genomes of all species belonging to the taxonomic families Bacillaceae, Listeriaceae, Staphylococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae to determine the diversity in central nitrogen metabolism and reconstructed the regulation by GlnR.

Results

Although we observed a substantial difference in the extent of central nitrogen metabolism in the various species, the basic GlnR regulon was remarkably constant and appeared not affected by the presence or absence of the other three main regulators. We found a conserved regulatory association of GlnR with glutamine synthetase (glnRA operon), and the transport of ammonium (amtB-glnK) and glutamine/glutamate (i.e. via glnQHMP, glnPHQ, gltT, alsT). In addition less-conserved associations were found with, for instance, glutamate dehydrogenase in Streptococcaceae, purine catabolism and the reduction of nitrite in Bacillaceae, and aspartate/asparagine deamination in Lactobacillaceae.

Conclusions

Our analyses imply GlnR-mediated regulation in constraining the import of ammonia/amino-containing compounds and the production of intracellular ammonia under conditions of high nitrogen availability. Such a role fits with the intrinsic need for tight control of ammonia levels to limit futile cycling.