Ree N.A., Likhoshvai V.A., Khlebodarova T.M.
Membrane Potential as a Regulation Mechanism of Periplasmic Nitrite Reductase Activity: A Mathematical Model
Mathematical Biology & Bioinformatics. 2018;13(1):238-269.
doi: 10.17537/2018.13.238.
References
- Simon J. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiology Reviews. 2002;26(3):285-309. doi: 10.1111/j.1574-6976.2002.tb00616.x
- Simon J., Klotz M.G. Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. Biochim. Biophys. Acta. 2013;1827(2):114-135. doi: 10.1016/j.bbabio.2012.07.005
- Page L., Griffiths L., Cole J.A. Different physiological roles of two independent pathways for nitrite reduction to ammonia by enteric bacteria. Arch. Microbiol. 1990;154(4):349-354. doi: 10.1007/BF00276530
- Cole J. Nitrate reduction to ammonia by enteric bacteria: redundancy, or a strategy for survival during oxygen starvation? FEMS Microbiol. Lett. 1996;136(1):1-11. doi: 10.1111/j.1574-6968.1996.tb08017.x
- Abaibou H., Pommier J., Benoit S., Giordano G., Mandrand-Berthelot M.A. Expression and characterization of the Escherichia coli fdo locus and a possible physiological role for aerobic formate dehydrogenase. J. Bacteriol. 1995;177(24):7141-7149. doi: 10.1128/jb.177.24.7141-7149.1995
- Wang H., Gunsalus R.P. Coordinate regulation of the Escherichia coli formate dehydrogenase fdnGHI and fdhF genes in response to nitrate, nitrite, and formate: roles for NarL and NarP. J. Bacteriol. 2003;185(17):5076-5085. doi: 10.1128/JB.185.17.5076-5085.2003
- Wang H., Gunsalus R.P. The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. J. Bacteriol. 2000;182:5813-5822. doi: 10.1128/JB.182.20.5813-5822.2000
- Darwin A., Tormay P, Page L, Griffiths L, Cole J. Identification of the formate dehydrogenases and genetic determinants of formate-dependent nitrite reduction by Escherichia coli K12. J. Gen Microbiol. 1993;139(8):1829-1840. doi: 10.1099/00221287-139-8-1829
- Stewart V., Bledsoe P. Synthetic lac operator substitutions for studying the nitrate- and nitrite-responsive NarX-NarL and NarQ-NarP two-component regulatory systems of Escherichia coli K-12. J. Bacteriol. 2003;185:2104-2111. doi: 10.1128/JB.185.7.2104-2111.2003
- Khlebodarova T.M., Kogai V.V., Akberdin I.R., Ri N.A., Fadeev S.I., Likhoshvai V.A. Modeling of Nitrite Utilization in E. coli Cells: Flux Analysis. Mathematical Biology and Bioinformatics. 2013;8(1):276-294 (in Russ.). doi: 10.17537/2013.8.276
- Ree N.A.,Likhoshvai V.A., Khlebodarova T.M. On The Mechanisms of Nitrite Utilization by Escherichia coli Cells during Stationary Growth. Mathematical Biology and Bioinformatics. 2015;10(1):193-205 (in Russ.). doi: 10.17537/2015.10.193
- Khlebodarova T.M., Ree N.A., Likhoshvai V.A. On the control mechanisms of the nitrite level in Escherichia coli cells: the mathematical model. BMC Microbiol. 2016;16(1). Article No 7. doi: 10.1186/s12866-015-0619-x
- Hakobyan M., Sargsyan H., Bagramyan K. Proton translocation coupled to formate oxidation in anaerobically grown fermenting Escherichia coli. Biophys. Chem. 2005;115:55-61. doi: 10.1016/j.bpc.2005.01.002
- Andrews S.C., Berks B.C., McClay J., Ambler A., Quail M.A., Golby P. Guest J.R.A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate-hydrogenlyase system. Microbiology. 1997;143:3633-3647. doi: 10.1099/00221287-143-11-3633
- Wang H., Tseng C.P., Gunsalus R.P. The napF and narG nitrate reductase operons in Escherichia coli are differentially expressed in response to submicromolar concentrations of nitrate but not nitrite. J. Bacteriol. 1999;181(17):5303-5308.
- McDowall J.S., Murphy B.J., Haumann M., Palmer T., Armstrong F.A., Sargent F. Bacterial formate hydrogenlyase complex. Proc. Natl. Acad. Sci. USA. 2014;111(38):3948-3956. doi: 10.1073/pnas.1407927111
- Sargent F. The Model [NiFe]-Hydrogenases of Escherichia coli. Adv. Microb. Physiol. 2016;68:433-507. doi: 10.1016/bs.ampbs.2016.02.008
- Noguchi K., Riggins D.P., Eldahan K.C., Kitko R.D., Slonczewski J.L. Hydrogenase-3 contributes to anaerobic acid resistance of Escherichia coli. PLoS One. 2010;5(4). Article No. e10132. doi: 10.1371/journal.pone.0010132
- Rossmann R., Sawers G., Böck A. Mechanism of regulation of the formate-hydrogenlyase pathway by oxygen, nitrate, and pH: definition of the formate regulon. Mol Microbiol. 1991;5(11):2807-2814. doi: 10.1111/j.1365-2958.1991.tb01989.x
- Tseng C.P., Hansen A.K., Cotter P., Gunsalus R.P. Effect of cell growth rate on expression of the anaerobic respiratory pathway operons frdABCD, dmsABC, and narGHJI of Escherichia coli. J. Bacteriol. 1994;176(21):6599-6605. doi: 10.1128/jb.176.21.6599-6605.1994
- Pinske C., Jaroschinsky M., Linek S., Kelly C.L., Sargent F., Sawers R.G. Physiology and bioenergetics of [NiFe]-hydrogenase 2-catalyzed H2-consuming and H2-producing reactions in Escherichia coli. J. Bacteriol. 2015;197(2):296-306. doi: 10.1128/JB.02335-14
- Ballantine S.P., Boxer D.H. Isolation and characterization of a soluble active fragment of hydrogenase isoenzyme 2 from the membranes of anaerobically grown Escherichia coli. Eur. J. Biochem. 1986;156(2):277-284. doi: 10.1111/j.1432-1033.1986.tb09578.x
- Francis K., Patel P., Wendt J.C., Shanmugam K.T. Purification and characterization of two forms of hydrogenase isoenzyme 1 from Escherichia coli. J. Bacteriol. 1990;172(10):5750-5757. doi: 10.1128/jb.172.10.5750-5757.1990
- Lukey M.J., Parkin A., Roessler M.M., Murphy B.J., Harmer J., Palmer T., Sargent F., Armstrong F.A. How Escherichia coli is equipped to oxidize hydrogen under different redox conditions. J. Biol. Chem. 2010;285(6):3928-2938. doi: 10.1074/jbc.M109.067751
- Laurinavichene T.V., Tsygankov A.A. H2 consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors. FEMS Microbiol. Lett. 2001;202(1):121-124. doi: 10.1111/j.1574-6968.2001.tb10790.x
- Efremov R.G., Sazanov L.A. The coupling mechanism of respiratory complex I - a structural and evolutionary perspective. Biochim. Biophys. Acta. 2012;1817(10):1785-1795. doi: 10.1016/j.bbabio.2012.02.015
- Gwyer J.D., Richardson D.J., Butt J.N. Inhibiting Escherichia coli cytochrome c nitrite reductase: voltammetry reveals an enzyme equipped for action despite the chemical challenges it may face in vivo. Biochem. Soc. Trans. 2006;1:133-135. doi: 10.1042/BST0340133
- Pinske C., Sargent F. Exploring the directionality of Escherichia coli formate hydrogenlyase: a membrane-bound enzyme capable of fixing carbon dioxide to organic acid. Microbiologyopen. 2016;5(5):721-737. doi: 10.1002/mbo3.365
- Skibinski D.A., Golby P., Chang Y.S., Sargent F., Hoffman R., Harper R., Guest J.R., Attwood M.M., Berks B.C., Andrews S.C. Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR. J. Bacteriol. 2002;184(23):6642-6653. doi: 10.1128/JB.184.23.6642-6653.2002
- Bagramyan K., Mnatsakanyan N., Poladian A., Vassilian A., Trchounian A. The roles of hydrogenases 3 and 4, and the F0F1-ATPase, in H2 production by Escherichia coli at alkaline and acidic pH. FEBS Lett. 2002;516(1-3):172-178. doi: 10.1016/S0014-5793(02)02555-3
- Mnatsakanyan N., Bagramyan K., Trchounian A. Hydrogenase 3 but not hydrogenase 4 is major in hydrogen gas production by Escherichia coli formate hydrogenlyase at acidic pH and in the presence of external formate. Cell. Biochem. Biophys. 2004;41(3):357-366. doi: 10.1385/CBB:41:3:357
- Likhoshvai V., Ratushny A. Generalized Hill function method for modeling molecular processes. J. Bioinform. Comput. Biol. 2007:521-531. doi: 10.1142/S0219720007002837
- Sawers R.G. Formate and its role in hydrogen production in Escherichia coli. Biochem. Soc. Trans. 2005;33:42-46. doi: 10.1042/BST0330042
- Kaiser M., Sawers G. Nitrate repression of the Escherichia coli pfl operon is mediated by the dual sensors NarQ and NarX and the dual regulators NarL and NarP. J. Bacteriol. 1995;177(13):3647-3655. doi: 10.1128/jb.177.13.3647-3655.1995
- Sawers R. G. The hydrogenases and formate dehydrogenases of Escherichia coli. Antonie Van Leeuwenhoek. 1994;66:57-88. doi: 10.1007/BF00871633
- Hopper S., Babst M., Schlensog V., Fischer H.M., Hennecke H., Böck A. Regulated expression in vitro of genes coding for formate hydrogenlyase components of Escherichia coli. J. Biol. Chem. 1994;269(30):19597-19604.
- Richard D.J., Sawers G., Sargent F., McWalter L., Boxer D.H. Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe]hydrogenases 1 and 2 of Escherichia coli. Microbiology. 1999;145:2903-2912. doi: 10.1099/00221287-145-10-2903
- Kasimoglu E., Park S.J., Malek J., Tseng C.P., Gunsalus R.P. Transcriptional regulation of the proton-translocating ATPase (atpIBEFHAGDC) operon of Escherichia coli: control by cell growth rate. J. Bacteriol. 1996;178(19):5563-5567. doi: 10.1128/jb.178.19.5563-5567.1996
- Wiedenmann A., Dimroth P., von Ballmoos C. Deltapsi and DeltapH are equivalent driving forces for proton transport through isolated F(0) complexes of ATP synthases. Biochim. Biophys. Acta. 2008;1777(10):1301-1310. doi: 10.1016/j.bbabio.2008.06.008
- Bremer H., Dennis P.P. Modulation of chemical composition and other parameters of the cell at different exponential growth rates. EcoSal. Plus. 2008;3(1). doi: 10.1128/ecosal.5.2.3
- Unden G., Bongaerts J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim. Biophys. Acta. 1997;1320(3):217-234. doi: 10.1016/S0005-2728(97)00034-0
- Outten C.E., O'Halloran T.V. Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis. Science. 2001;292(5526):2488-2492. doi: 10.1126/science.1060331
- Axley M.J., Grahame D.A. Kinetics for formate dehydrogenase of Escherichia coli formate-hydrogenlyase. J. Biol. Chem. 1991;266(21):13731-13736.
- Etzold C., Deckers-Hebestreit G., Altendorf K. Turnover number of Escherichia coli F0F1 ATP synthase for ATP synthesis in membrane vesicles. Eur. J. Biochem. 1997;243(1-2):336-343. doi: 10.1111/j.1432-1033.1997.0336a.x
- Maeda T., Sanchez-Torres V., Wood T.K. Escherichia coli hydrogenase 3 is a reversible enzyme possessing hydrogen uptake and synthesis activities. Appl. Microbiol. Biotechnol. 2007;76(5):1035-1042. doi: 10.1007/s00253-007-1086-6
- Leonhartsberger S., Korsa I., Böck A. The molecular biology of formate metabolism in enterobacteria. J. Mol. Microbiol. Biotechnol. 2002;4(3):269-276.
- Wilks J.C., Slonczewski J.L. pH of the cytoplasm and periplasm of Escherichia coli: rapid measurement by green fluorescent protein fluorimetry. J. Bacteriol. 2007;189(15):5601-5607. doi: 10.1128/JB.00615-07
- Rodrigue A., Chanal A., Beck K., Müller M., Wu L.F. Co-translocation of a periplasmic enzyme complex by a hitchhiker mechanism through the bacterial tat pathway. J. Biol. Chem. 1999;274(19):13223-13228. doi: 10.1074/jbc.274.19.13223
- Pope N., Cole J. Generation of a membrane potential by one of two independent pathways for nitrite reduction by Escherichia coli. J. Gen. Microbiol. 1982;128:219-222. doi: 10.1099/00221287-128-1-219
- Daniels C., Bole D., Quay S., Oxender D. Role for membrane potential in the secretion of protein into the periplasm of Escherichia coli. Proc. Natl. Acad. Sci. USA. 1981;78:5396-5400. doi: 10.1073/pnas.78.9.5396
- Price C.E., Driessen A.J.M. Biogenesis of membrane bound respiratory complexes in Escherichia coli. Biochim. Biophys. Acta. 2010;1803(6):748-766. doi: 10.1016/j.bbamcr.2010.01.019
- Jones S.A., Chowdhury F.Z., Fabich A.J., Anderson A., Schreiner D.M., House A.L., Autieri S.M., Leatham M.P., Lins J.J., Jorgensen M., Cohen P.S., Conway T. Respiration of Escherichia coli in the mouse intestine. Infect. Immun. 2007;75(10):4891-4899. doi: 10.1128/IAI.00484-07
- Stewart V., Lu Y., Darwin A.J. Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12. J. Bacteriol. 2002;184(5):1314-1323. doi: 10.1128/JB.184.5.1314-1323.2002
- Aldridge C., Storm A., Cline K., Dabney-Smith C. The chloroplast twin arginine transport (Tat) component, Tha4, undergoes conformational changes leading to Tat protein transport. J. Biol. Chem. 2012;287(41):34752-34763. doi: 10.1074/jbc.M112.385666
- Dyall S.D., Brown M.T., Johnson P.J. Ancient invasions: from endosymbionts to organelles. Science. 2004;304(5668):253-257. doi: 10.1126/science.1094884
- Zimorski V., Ku C., Martin W.F., Gould S.B. Endosymbiotic theory for organelle origins. Curr. Opin. Microbiol. 2014:38-48. doi: 10.1016/j.mib.2014.09.008
- Sawers R.G., Jamieson D.J., Higgins C.F., Boxer D.H. Characterization and physiological roles of membrane-bound hydrogenase isoenzymes from Salmonella typhimurium. J. Bacteriol. 1986;168:398-404. doi: 10.1128/jb.168.1.398-404.1986
- Clarke T.A., Cole J.A., Richardson D.J., Hemmings A.M. The crystal structure of the pentahaem c-type cytochrome NrfB and characterization of its solutionstate interaction with the pentahaem nitrite reductase NrfA. Biochem J. 2007;406:19-30. doi: 10.1042/BJ20070321
- Graham L.L., Harris R., Villiger W., Beveridge T.J. Freeze-substitution of gramnegative eubacteria: general cell morphology and envelope profiles. J. Bacteriol. 1991;173:1623-1633. doi: 10.1128/jb.173.5.1623-1633.1991
- Talmadge K., Gilbert W. Cellular location affects protein stability in Escherichia coli. Proc. Natl. Acad. Sci. USA. 1982;79:1830-1833. doi: 10.1073/pnas.79.6.1830
- Kemp G.L., Clarke T.A., Marritt S.J., Lockwood C., Poock S.R., Hemmings A.M. Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. Biochem J. 2010;431:73-80. doi: 10.1042/BJ20100866
- Coleman K.J., Cornish-Bowden A., Cole J.A. Activation of nitrite reductase from Escherichia coli K 12 by oxidized nicotinamide-adenine dinucleotide. Biochem. J. 1978;175:495-499. doi: 10.1042/bj1750495
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