A model for the proteolytic regulation of LpxC in the lipopolysaccharide pathway of Escherichia coli

Computational Biology and Chemistry

Volumn 47, Issue , 2013, Pages 1-7

  Emiola, Akintunde ^a   Falcarin, Paolo ^a   Tocher, Joanne ^a   George, John ^a  

^a UNIVERSITY OF EAST LONDON   (United Kingdom)

Author keywords

FtsH cleavage; Lipid A; Metabolic pathway; Simulation

Indexed keywords

FTSH CLEAVAGE; GRAM-NEGATIVE BACTERIA; HUMAN IMMUNE SYSTEMS; LIPID A; METABOLIC PATHWAYS; SIMULATION; SIMULATION PARAMETERS; STRUCTURAL COMPONENT;

CELL PROLIFERATION; CHEMICAL ACTIVATION; ENZYMES; EQUILIBRIUM CONSTANTS; ESCHERICHIA COLI;

SYNTHESIS (CHEMICAL);

AMIDASE; LIPID A; LIPOPOLYSACCHARIDE; UDP 3 O ACYL N ACETYLGLUCOSAMINE DEACETYLASE; UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE;

ARTICLE; BIOLOGICAL MODEL; BIOSYNTHESIS; ESCHERICHIA COLI; FTSH CLEAVAGE; METABOLISM; PROTEIN DEGRADATION; SIMULATION;

FTSH CLEAVAGE; LIPID A; METABOLIC PATHWAY; SIMULATION;

AMIDOHYDROLASES; ESCHERICHIA COLI; LIPID A; LIPOPOLYSACCHARIDES; MODELS, BIOLOGICAL; PROTEOLYSIS;

EID: 84880067946     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2013.06.001     Document Type: Article

References (43)

1. Y. Akiyama Quality control of cytoplasmic membrane proteins in Escherichia coli J. Biochem. 146 2009 449 454
2. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter Molecular Biology of the Cell fourth ed. 2002 Garland Science New York
3. M.S. Anderson, C.E. Bulawa, and C.R. Raetz The biosynthesis of gram-negative endotoxin. Formation of lipid A precursors from UDP-GlcNAc in extracts of Escherichia coli J. Biol. Chem. 260 1985 15536 15541 (Pubitemid 16170091)
4. M.S. Anderson, H.G. Bull, S.M. Galloway, T.M. Kelly, S. Mohan, K. Radika, and C.R. Raetz UDP-N-acetylglucosamine acyltransferase of Escherichia coli. The first step of endotoxin biosynthesis is thermodynamically unfavourable J. Biol. Chem. 268 1993 19858 19865 (Pubitemid 23270781)
5. M.S. Anderson, and C.R. Raetz Biosynthesis of lipid A precursors in Escherichia coli. A cytoplasmic acyltransferase that converts UDP-N-acetylglucosamine to UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine J Biol. Chem. 262 1987 5159 5169
6. A.W. Barb, and P. Zhou Mechanism and inhibition of LpxC: an essential zinc-dependent deacetylase of bacterial lipid A synthesis Curr. Pharm. Biotechnol. 9 2008 9 15 (Pubitemid 351266965)
7. B. Beall, and J. Lutkenhaus Sequence analysis, transcriptional organization, and insertional mutagenesis of the envA gene of Escherichia coli J. Bacteriol. 169 1987 5408 5415 (Pubitemid 18017834)
8. C.J. Belunis, and C.R. Raetz Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-d-manno-octulosonic acid transferase from Escherichia coli J. Biol. Chem. 267 1992 9988 9997
9. J.A. Bernstein, A.B. Khodursky, P.L.S. Lin-Chao, and S.N. Cohen Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays Proc. Natl. Acad. Sci. U.S.A. 99 2002 9697 9702 (Pubitemid 34831110)
10. S. Cayley, B.A. Lewis, H.J. Guttman, and M.T. Record Jr. Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo J. Mol. Biol. 222 1991 281 300 (Pubitemid 121004007)
11. C.Y. Chen, N. Ezzeddine, and A.B. Shyu Messenger RNA half-life measurements in mammalian cells Methods Enzymol. 448 2008 335 357
12. J. Coleman, and C.R.H. Raetz First committed step of lipid A biosynthesis in Escherichia coli: sequence of the lpxA gene J. Bacteriol. 170 1988 1268 1274 (Pubitemid 18079066)
13. C. Creuzenet, M. Belanger, W.W. Wakarchuk, and J.S. Lam Expression, purification, and biochemical characterization of WbpP, a new UDP-GlcNAc C4 epimerase from Pseudomonas aeruginosa serotype O6 J Biol. Chem. 275 2000 19060 19067 (Pubitemid 30422873)
14. T.A. Garrett, J.L. Kadrmas, and C.R. Raetz Identification of the gene encoding the Escherichia coli lipid A 4′-kinase. Facile phosphorylation of endotoxin analogs with recombinant LpxK J. Biol. Chem. 272 1997 21855 21864 (Pubitemid 27382802)
15. I. Golding, J. Paulsson, S.M. Zawilski, and E.C. Cox Real-time kinetics of gene activity in individual bacteria Cell 123 2005 1025 1036 (Pubitemid 41785418)
16. D.G. Hardie AMP-activated protein kinase: an energy sensor that regulates all aspects of cell function Genes Dev. 25 2011 1895 1908
17. M. Hernick, H.A. Gennadios, D.A. Whittington, K.M. Rusche, D.W. Christianson, and C.A. Fierke UDP-3-O-((R)-3-hydroxymyristoyl)-N- acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism J. Biol. Chem. 280 2005 16969 16978 (Pubitemid 41389158)
18. P.A. Hoen, M. Hirsch, E.J. de Meijer, R.X. de Menezes, G.J. van Ommen, and J.T. den Dunnen mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance Nucleic Acids Res. 39 2011 556 566
19. S.A. Hyland, S.S. Eveland, and M.S. Anderson The lipid A biosynthesis pathway. Pseudomonas aeruginosa: a metalloamidase of UDP-3-O-acyl-GlcNAc deacetylase from cloning J. Bacteriol. 179 1997 2029 2037 (Pubitemid 27123088)
20. Y. Ishihama, T. Schmidt, J. Rappsilber, M. Mann, F.U. Hart, M.J. Kerner, and D. Frishman Protein abundance profiling of the Escherichia coli cytosol BMC Genomics 9 2008 10.1186/1471-2164-9-102 (Pubitemid 351517450)
21. C. Katz, and E.Z. Ron Dual role of FtsH in regulating lipopolysaccharide biosynthesis in Escherichia coli J. Bacteriol. 190 2008 7117 7122
22. S. Langklotz, M. Schäkermann, and F. Narberhaus Control of lipopolysaccharide biosynthesis by FtsH-mediated proteolysis of LpxC is conserved in enterobacteria but not in all gram-negative bacteria J. Bacteriol. 193 2011 1090 1097
23. J.E. Lunn, M. Droux, J. Martin, and R. Douce Localization of ATP Sulfurylase and O-acetylserine(thiol)lyase in spinach leaves Plant Physiol. 94 1990 1345 1352 (Pubitemid 120015701)
24. G.A. Mackie RNase E: at the interface of bacterial RNA processing and decay Nat. Rev. Microbiol. 11 2013 45 57
25. H.H. McAdams, and A. Arkin Stochastic mechanisms in gene expression Proc. Natl. Acad. Sci. U.S.A. 94 1997 814 819 (Pubitemid 27074404)
26. P. Mendes, S. Hoops, S. Sahle, R. Gauges, J. Dada, and U. Kummer Computational modelling of biochemical networks using COPASI Methods Mol. Biol. 500 2009 17 59
27. N. Mitarai, K. Sneppen, and S. Pedersen Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization J. Mol. Biol. 382 2008 236 245
28. T. Ogura, K. Inoue, T. Tatsuta, T. Suzaki, K. Karata, K. Young, L.H. Su, C.A. Fierke, J.E. Jackman, C.R. Raetz, J. Coleman, T. Tomoyasu, and H. Matsuzawa Balanced biosynthesis of major membrane components through regulated degradation of the committed enzyme of lipid A biosynthesis by the AAA protease FtsH (HflB) in Escherichia coli Mol. Microbiol. 31 1999 833 844 (Pubitemid 29057286)
29. L.D. Plank, and J.D. Harvey Generation Time Statistics of Escherichia coli B measured by synchronous culture techniques J. Gen. Microbiol. 115 1979 69 77 (Pubitemid 10200254)
30. I.R. Poxton Antibodies to Lipopolysaccharide J. Immunol. Methods 186 1995 1 15
31. C.R. Raetz, and C. Whitfield Lipopolysaccharide endotoxins Annu. Rev. Biochem. 71 2002 635 700 (Pubitemid 34800232)
32. C.R. Raetz, C.M. Reynolds, M.S. Trent, and R.E. Bishop Lipid A modification systems in gram-negative bacteria Annu. Rev. Biochem. 76 2007 295 329
33. C.R. Raetz, Z. Guan, B.O. Ingram, D.A. Six, F. Song, X. Wang, and J. Zhao Discovery of new biosynthetic pathways: the lipid A story J. Lipid Res. 50 2009 S103 S108
34. E. Roberts, A. Magis, J.O. Ortiz, W. Baumeister, and Z. Luthey-Schulten Noise contributions in an inducible genetic switch: a whole-cell simulation study PLoS Comput. Biol. 7 2011 10.1371/journal.pcbi.1002010
35. M. Schäkermann, S. Langklotz, and F. Narberhaus FtsH-mediated coordination of lipopolysaccharide biosynthesis in Escherichia coli correlates with the growth rate and the alarmone (p)ppGpp J. Bacteriol. 2013 10.1128/JB.02134-12
36. V. Shahrezaei, and P.S. Swain Analytical distributions for stochastic gene expression Proc. Natl. Acad. Sci. U.S.A. 105 2008 17256 17261
37. Y. Shih, and G.M. Whitesides Large-scale ATP-requiring enzymatic phosphorylation of creatine can be driven by enzymatic ATP regeneration J. Org. Chem. 42 1977 4165 4166
38. P.G. Sorensen, J. Lutkenhaus, K. Young, S.S. Eveland, M.S. Anderson, and C.R. Raetz Regulation of UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase in Escherichia coli. The second enzymatic step of lipid a biosynthesis J. Biol. Chem. 271 1996 25898 25905
39. S. Sundararaj, A. Guo, B. Habibi-Nazhad, M. Rouani, P. Stothard, M. Ellison, and D.S. Wishart The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli Nucleic Acids Res. 32 2004 D293 D295
40. B.D. Ventura, and V. Sourjik Self-organized partitioning of dynamically localized proteins in bacterial cell division Mol. Syst. Biol. 7 2011 10.1038/msb.2010.111
41. S.L. Walker, J.A. Redman, and M. Elimelech Role of cell surface lipopolysaccharides in Escherichia coli K12 adhesion and transport Langmuir 20 2004 7736 7746
42. T.J.O. Wyckoff, and C.R.H. Raetz The active site of Escherichia coli UDP-N-acetylglucosamine acyltransferase. Chemical modification and site-directed mutagenesis J. Biol. Chem. 274 1999 27047 27055
43. K. Young, L.L. Silver, D. Bramhill, P. Cameron, S.S. Eveland, C.R. Raetz, S.A. Hyland, and M.S. Anderson The envA permeability/cell division gene of Escherichia coli encodes the second enzyme of lipid A biosynthesis. UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase J. Biol. Chem. 270 1995 30384 30391