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Escherichia coli K-12 substr. MG1655 Pathway: L-lysine degradation I
Inferred from experiment

Pathway diagram: L-lysine degradation I

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Schematic showing all replicons, marked with selected genes

Genetic Regulation Schematic

Genetic regulation schematic for L-lysine degradation I

Superclasses: Degradation/Utilization/AssimilationAmino Acids DegradationProteinogenic Amino Acids DegradationL-lysine Degradation

Under conditions of anaerobiosis and phosphate starvation (believed to reflect conditions in the gut), E. coli converts glucose to weak organic acids which, though they are excreted, can reenter the cell and cause bactericidal acid stress even at only moderately acidic pH. Acid resistance system 4 (AR4) is the lysine-dependent acid resistance system which allows for the survival of E. coli under these conditions when lysine is available. AR4 couples the transport activity of a lysine:cadaverine antiporter, CadB, with lysine decarboxylase, CadA. CadB functions by exchanging external lysine for internal cadaverine. Lysine is imported into the cell through CadB. Within the cell lysine is decarboxylated by CadA to cadaverine, releasing CO2 and replacing it with a proton. Cadaverine is then exported through CadB. This effectively consumes protons within the cytoplasm, raising the pH. The glutamate-dependent acid resistance system (AR2) is also able to provide acid resistance to E. coli growing under conditions of anaerobiosis and phosphate starvation, but to a slightly lesser degree than AR4 possibly due to the different pH optimums of their respective decarboxylase enzymes. [Moreau07] AR2 is more efficient than AR3 or AR4 as a mediator of acid resistance at low pH. [Foster04]

Citations: [Neidhardt96 ]


Foster04: Foster JW (2004). "Escherichia coli acid resistance: tales of an amateur acidophile." Nat Rev Microbiol 2(11);898-907. PMID: 15494746

Moreau07: Moreau PL (2007). "The lysine decarboxylase CadA protects Escherichia coli starved of phosphate against fermentation acids." J Bacteriol 189(6);2249-61. PMID: 17209032

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Auger89: Auger EA, Redding KE, Plumb T, Childs LC, Meng SY, Bennett GN (1989). "Construction of lac fusions to the inducible arginine- and lysine decarboxylase genes of Escherichia coli K12." Mol Microbiol 3(5);609-20. PMID: 2527331

Beretskene80: Beretskene SIa, Bruzgulis PA, Ragavichus AB (1980). "[Conditions of the synthesis of lysine decarboxylase by Escherichia coli MRE 600]." Prikl Biokhim Mikrobiol 16(3);351-5. PMID: 7001435

Boeker83: Boeker EA, Fischer EH (1983). "Lysine decarboxylase (Escherichia coli B)." Methods Enzymol 94;180-4. PMID: 6353151

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chattopadhyay09: Chattopadhyay MK, Tabor CW, Tabor H (2009). "Polyamines are not required for aerobic growth of Escherichia coli: preparation of a strain with deletions in all of the genes for polyamine biosynthesis." J Bacteriol 191(17);5549-52. PMID: 19542271

Day01: Day WA, Fernandez RE, Maurelli AT (2001). "Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp." Infect Immun 69(12);7471-80. PMID: 11705922

Dell94: Dell CL, Neely MN, Olson ER (1994). "Altered pH and lysine signalling mutants of cadC, a gene encoding a membrane-bound transcriptional activator of the Escherichia coli cadBA operon." Mol Microbiol 14(1);7-16. PMID: 7830562

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

El10: El Bakkouri M, Gutsche I, Kanjee U, Zhao B, Yu M, Goret G, Schoehn G, Burmeister WP, Houry WA (2010). "Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity." Proc Natl Acad Sci U S A 107(52);22499-504. PMID: 21148420

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Goldemberg80: Goldemberg SH (1980). "Lysine decarboxylase mutants of Escherichia coli: evidence for two enzyme forms." J Bacteriol 141(3);1428-31. PMID: 6767710

Kamio83: Kamio Y, Terawaki Y (1983). "Purification and properties of Selenomonas ruminantium lysine decarboxylase." J Bacteriol 153(2);658-64. PMID: 6401702

Kanjee11: Kanjee U, Gutsche I, Ramachandran S, Houry WA (2011). "The Enzymatic Activities of the Escherichia coli Basic Aliphatic Amino Acid Decarboxylases Exhibit a pH Zone of Inhibition." Biochemistry 50(43);9388-98. PMID: 21957966

Kanjee11a: Kanjee U, Gutsche I, Alexopoulos E, Zhao B, El Bakkouri M, Thibault G, Liu K, Ramachandran S, Snider J, Pai EF, Houry WA (2011). "Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase." EMBO J 30(5);931-44. PMID: 21278708

Kikuchi97a: Kikuchi Y, Kojima H, Tanaka T, Takatsuka Y, Kamio Y (1997). "Characterization of a second lysine decarboxylase isolated from Escherichia coli." J Bacteriol 1997;179(14);4486-92. PMID: 9226257

Kikuchi98: Kikuchi Y, Kurahashi O, Nagano T, Kamio Y (1998). "RpoS-dependent expression of the second lysine decarboxylase gene in Escherichia coli." Biosci Biotechnol Biochem 62(6);1267-70. PMID: 9692215

Kuper05: Kuper C, Jung K (2005). "CadC-mediated activation of the cadBA promoter in Escherichia coli." J Mol Microbiol Biotechnol 10(1);26-39. PMID: 16491024

Lemonnier98: Lemonnier M, Lane D (1998). "Expression of the second lysine decarboxylase gene of Escherichia coli." Microbiology 1998;144 ( Pt 3);751-60. PMID: 9534244

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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