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Escherichia coli K-12 substr. MG1655 Pathway: putrescine biosynthesis I
Inferred from experiment

Pathway diagram: putrescine biosynthesis 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 putrescine biosynthesis I

Superclasses: BiosynthesisAmines and Polyamines BiosynthesisPutrescine Biosynthesis

General Backround

The polyamines (the most common of which are putrescine, spermidine, and spermine) are a group of positively charged organic polycations that are involved in many biological processes, including binding to nucleic acids, stabilizing membranes, and stimulating several enzymes [Tabor85, Abraham68, Frydman92, Huang90]. While it is clear that polyamines are essential for normal cell growth, we still do not fully understand their specific molecular functions in vivo [Tabor85]. putrescine and spermidine are found in all life forms, and spermine is found mostly in eukaryotes.

putrescine can be formed either directly from L-ornithine by ornithine decarboxylase (ODC) (see putrescine biosynthesis III) or indirectly from L-arginine by arginine decarboxylase (ADC) (see putrescine biosynthesis I and putrescine biosynthesis II). While the ODC pathway was considered the only mammalian pathway for polyamine biosynthesis, recently the presence of the ADC pathway in mammals has been demonstrated [Mistry02, Zhu04]. In higher plants the presence of both pathways has been known for some time [Galston90]. In bacteria, both pathways are common, and are often found side by side in the same organism [Tabor85].

There are two flavors of the ADC pathway. In both cases L-arginine is first converted to agmatine by a biosynthetic arginine decarboxylase. However, in enterobacteria and mycobacteria agmatine is converted directly to putrescine by the enzyme agmatinase (this pathway), while in higher plants, Pseudomonas spp., Aeromonas spp., and lactic bacteria, agmatine is first hydrolyzed by agmatine deiminase into N-carbamoylputrescine and ammonia, and putrescine is formed by removal of the ureido group from N-carbamoylputrescine by the enzyme N-carbamoylputrescine amidohydrolase (see pathway putrescine biosynthesis II).

About This Pathway

This pathway was studied mostly in enterobacteria, but it was also found in the mycobacteria Mycobacterium phlei and Mycobacterium smegmatis [Zeller54] and in the Gram positive bacterium Bacillus subtilis [Sekowska98]. While Escherichia coli K-12 possesses both an ODC and an ADC pathways, in Bacillus subtilis this is the only putrescine biosynthetic pathway. Remarkably, even though spermidine is only synthesized in Bacillus subtilis via putrescine, no intracellular putrescine was found in this organism [Sekowska98].

It should be mentioned that in some organisms, including Escherichia coli K-12, this pathway can also operate in a catabolic manner [Shaibe85], catalyzing the degradation of L-arginine through putrescine into succinate (see L-arginine degradation III (arginine decarboxylase/agmatinase pathway)). However, the main catabolic arginine pathway in these bacteria is the succinyltransferase pathway ( L-arginine degradation II (AST pathway)). Interestingly, unlike Escherichia coli K-12, wild-type E. coli strains are unable to use L-arginine as a carbon source, even though they can use it as a nitrogen source [Cunin86].

Escherichia coli K-12 has two forms of the enzyme arginine decarboxylase: a constitutive, biosynthetic form, encoded by the speA gene, and an inducible catabolic form, encoded by the adiA gene. When the cataolic form is not expressed, the pathway operates only in an anabolic manner, catalyzing the biosynthesis of putrescine, which is used by the bacteria either directly or as a precursor for the biosynthesis of other polyamines (see superpathway of polyamine biosynthesis I). However, when the cells are grown in an arginine-rich medium, especially if the medium is acidic and conditions are semi-anaerobic, the catabolic arginine decarboxylase is expressed, and the pathway operates in a catabolic manner, feeding putrescine via 4-aminobutanoate and succinate into the TCA cycle I (prokaryotic) [Tabor85].

Superpathways: superpathway of polyamine biosynthesis I, superpathway of arginine and polyamine biosynthesis

Variants: putrescine biosynthesis III

Created 10-Oct-2005 by Caspi R, SRI International


Abraham68: Abraham KA (1968). "Studies on DNA-dependent RNA polymerase from Escherichia coli. 1. The mechanism of polyamine induced stimulation of enzyme activity." Eur J Biochem 5(1);143-6. PMID: 4873311

Cunin86: Cunin R, Glansdorff N, Pierard A, Stalon V (1986). "Biosynthesis and metabolism of arginine in bacteria." Microbiol Rev 1986;50(3);314-52. PMID: 3534538

Frydman92: Frydman L, Rossomando PC, Frydman V, Fernandez CO, Frydman B, Samejima K (1992). "Interactions between natural polyamines and tRNA: an 15N NMR analysis." Proc Natl Acad Sci U S A 89(19);9186-90. PMID: 1409623

Galston90: Galston AW, Sawhney RK (1990). "Polyamines in plant physiology." Plant Physiol 94(2);406-10. PMID: 11537482

Huang90: Huang SC, Panagiotidis CA, Canellakis ES (1990). "Transcriptional effects of polyamines on ribosomal proteins and on polyamine-synthesizing enzymes in Escherichia coli." Proc Natl Acad Sci U S A 87(9);3464-8. PMID: 2185470

Mistry02: Mistry SK, Burwell TJ, Chambers RM, Rudolph-Owen L, Spaltmann F, Cook WJ, Morris SM (2002). "Cloning of human agmatinase. An alternate path for polyamine synthesis induced in liver by hepatitis B virus." Am J Physiol Gastrointest Liver Physiol 282(2);G375-81. PMID: 11804860

Sekowska98: Sekowska A, Bertin P, Danchin A (1998). "Characterization of polyamine synthesis pathway in Bacillus subtilis 168." Mol Microbiol 1998;29(3);851-8. PMID: 9723923

Shaibe85: Shaibe E, Metzer E, Halpern YS (1985). "Metabolic pathway for the utilization of L-arginine, L-ornithine, agmatine, and putrescine as nitrogen sources in Escherichia coli K-12." J Bacteriol 163(3);933-7. PMID: 3897201

Tabor85: Tabor CW, Tabor H (1985). "Polyamines in microorganisms." Microbiol Rev 1985;49(1);81-99. PMID: 3157043

Zeller54: Zeller EA, Van Orden LS, Vogtli W (1954). "Enzymology of mycobacteria. VII. Degradation of guanidine derivatives." J Biol Chem 209(1);429-35. PMID: 13192096

Zhu04: Zhu MY, Iyo A, Piletz JE, Regunathan S (2004). "Expression of human arginine decarboxylase, the biosynthetic enzyme for agmatine." Biochim Biophys Acta 1670(2);156-64. PMID: 14738999

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

Andrell09: Andrell J, Hicks MG, Palmer T, Carpenter EP, Iwata S, Maher MJ (2009). "Crystal structure of the acid-induced arginine decarboxylase from Escherichia coli: reversible decamer assembly controls enzyme activity." Biochemistry 48(18);3915-27. PMID: 19298070

Bitonti87: Bitonti AJ, Casara PJ, McCann PP, Bey P (1987). "Catalytic irreversible inhibition of bacterial and plant arginine decarboxylase activities by novel substrate and product analogues." Biochem J 1987;242(1);69-74. PMID: 3297044

Blethen68: Blethen SL, Boeker EA, Snell EE (1968). "Argenine decarboxylase from Escherichia coli. I. Purification and specificity for substrates and coenzyme." J Biol Chem 1968;243(8);1671-7. PMID: 4870599

Boyle84: Boyle SM, Markham GD, Hafner EW, Wright JM, Tabor H, Tabor CW (1984). "Expression of the cloned genes encoding the putrescine biosynthetic enzymes and methionine adenosyltransferase of Escherichia coli (speA, speB, speC and metK)." Gene 30(1-3);129-36. PMID: 6392022

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

Buch85: Buch JK, Boyle SM (1985). "Biosynthetic arginine decarboxylase in Escherichia coli is synthesized as a precursor and located in the cell envelope." J Bacteriol 163(2);522-7. PMID: 3894328

Carvajal04: Carvajal N, Orellana MS, Salas M, Enriquez P, Alarcon R, Uribe E, Lopez V (2004). "Kinetic studies and site-directed mutagenesis of Escherichia coli agmatinase. A role for Glu274 in binding and correct positioning of the substrate guanidinium group." Arch Biochem Biophys 430(2);185-90. PMID: 15369817

Carvajal99: Carvajal N, Lopez V, Salas M, Uribe E, Herrera P, Cerpa J (1999). "Manganese is essential for catalytic activity of Escherichia coli agmatinase." Biochem Biophys Res Commun 258(3);808-11. PMID: 10329468

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Giles07: Giles TN, Graham DE (2007). "Characterization of an acid-dependent arginine decarboxylase enzyme from Chlamydophila pneumoniae." J Bacteriol 189(20);7376-83. PMID: 17693492

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hafner77: Hafner EW, Tabor CW, Tabor H (1977). "Isolation of a metK mutant with a temperature-sensitive S-adenosylmethionine synthetase." J Bacteriol 132(3);832-40. PMID: 336609

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Moore90: Moore RC, Boyle SM (1990). "Nucleotide sequence and analysis of the speA gene encoding biosynthetic arginine decarboxylase in Escherichia coli." J Bacteriol 1990;172(8);4631-40. PMID: 2198270

Moore91: Moore RC, Boyle SM (1991). "Cyclic AMP inhibits and putrescine represses expression of the speA gene encoding biosynthetic arginine decarboxylase in Escherichia coli." J Bacteriol 1991;173(12);3615-21. PMID: 1646785

Morris66: Morris DR, Pardee AB (1966). "Multiple pathways of putrescine biosynthesis in Escherichia coli." J Biol Chem 241(13);3129-35. PMID: 5330264

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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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