The overall long-term goals of this project are to understand the functions of the bacterial enhancer-binding protein NtrC (nitrogen- regulatory protein C) in activating transcription by the sigma 54- holoenzyme from its distant enhancer sites by DNA loop formation and must hydrolyze ATP to allow the polymerase to isomerize from closed to open complexes at a promoter. The requirement for ATP hydrolysis is thermodynamic as well as kinetic and therefore there must be a mechanism to couple the energy available to a change in conformation of polymerse-promoter complexes. To hydrolyze ATP, NtrC must be phosphorylated on an aspartic acid residue in its amino-terminal domain. This domain acts positively on the central, catalytic domain of the protein and can be thought of as the 'switch' that controls the 'motor'.
The specific aims with respect to NtrC function are: a) to study the effect of phosphorylation on communication between the N- terminal and central domains of NtrC; b) to establish an assay(s) for cyclic conformational changes in NtrC upon ATP hydrolysis; c) to establish an assay(s) for contact between NtrC and sigma 54 holoenzyme; c) to expand our collection of NtrCrepressor proteins, those that fail uniquely in positive control but not phosphorylation or DNA-binding, and test all such proteins for subfunctions of the central domain; 5) to continue structural studies of NtrC.
Specific aims with respect to metabolism are: a) to determine whether a ratio of glutamine/2-oxoglutarate controls the rate of glnA transcription in vivo; b) to determine whether the glutamine pool is depleted in nitrogen- limited B. Subtilis as it is in enteric bacteria, 3) to further characteriz the consequences of K= glutamate depletion in glnE mutant strains to determine whether there are compensatory increases in polyamines and whether turgor is grossly aberrant; 4) to determine whether protein- DNA interactions are altered in mutant strains with low K= glutamate, particularly whether protein-DNA affinity is usually high. The proposed studies will contribute to an understanding of transcriptional enhancers and enhancer-binding proteins generally, these being critical to the normal metabolism and development of humans and other eukaryotes. Further, they will contribute to understanding of nitrogen regulation, osmoregulation, and mechanisms for integrating these two major metabolic regulatory circuits.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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Study Section
Microbial Physiology and Genetics Subcommittee 2 (MBC)
Program Officer
Tompkins, Laurie
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University of California Berkeley
Other Basic Sciences
Schools of Earth Sciences/Natur
United States
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Hall, Jason A; Yan, Dalai (2013) The molecular basis of K+ exclusion by the Escherichia coli ammonium channel AmtB. J Biol Chem 288:14080-6
Vo, Jason; Inwood, William; Hayes, John M et al. (2013) Mechanism for nitrogen isotope fractionation during ammonium assimilation by Escherichia coli K12. Proc Natl Acad Sci U S A 110:8696-701
Hall, Jason A; Kustu, Sydney (2011) The pivotal twin histidines and aromatic triad of the Escherichia coli ammonium channel AmtB can be replaced. Proc Natl Acad Sci U S A 108:13270-4
Kim, Kwang-Seo; Pelton, Jeffrey G; Inwood, William B et al. (2010) The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. J Bacteriol 192:4089-102
Inwood, William B; Hall, Jason A; Kim, Kwang-Seo et al. (2009) Epistatic effects of the protease/chaperone HflB on some damaged forms of the Escherichia coli ammonium channel AmtB. Genetics 183:1327-40
Inwood, William B; Hall, Jason A; Kim, Kwang-Seo et al. (2009) Genetic evidence for an essential oscillation of transmembrane-spanning segment 5 in the Escherichia coli ammonium channel AmtB. Genetics 183:1341-55
Inwood, William; Yoshihara, Corinne; Zalpuri, Reena et al. (2008) The ultrastructure of a Chlamydomonas reinhardtii mutant strain lacking phytoene synthase resembles that of a colorless alga. Mol Plant 1:925-37
Yoshihara, Corinne; Inoue, Kentaro; Schichnes, Denise et al. (2008) An Rh1-GFP fusion protein is in the cytoplasmic membrane of a white mutant strain of Chlamydomonas reinhardtii. Mol Plant 1:1007-20
Fong, Rebecca N; Kim, Kwang-Seo; Yoshihara, Corinne et al. (2007) The W148L substitution in the Escherichia coli ammonium channel AmtB increases flux and indicates that the substrate is an ion. Proc Natl Acad Sci U S A 104:18706-11
Yan, Dalai (2007) Protection of the glutamate pool concentration in enteric bacteria. Proc Natl Acad Sci U S A 104:9475-80

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