|Gene:||tnaA||Accession Numbers: EG11005 (EcoCyc), b3708, ECK3701|
Synonyms: ind, tnaR
Subunit composition of
tryptophanase / L-cysteine desulfhydrase = [TnaA]4
tryptophanase = TnaA
Tryptophanase or tryptophan indole-lyase (TnaA) is an extremely well-studied pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the cleavage of L-tryptophan to indole, pyruvate and NH4+. Together with the tryptophan transporter TnaC, it enables utilization of L-tryptophan as sole source of nitrogen or carbon for growth. In recent years, it has become clear that one of the reaction products, indole, plays a significant role as an extracellular [Wang01, Martino03, KuczynskaWisnik10, KuczynskaWisnik10a, Chu12] and intracellular [Gaimster14] signal, even acting as a cell cycle regulator [Field12]. Indole production by TnaA depends directly on the amount of exogenous tryptophan, and the enzyme does not appear to degrade internal anabolic tryptophan [Li13a].
Tryptophanase is a major contributor towards the cellular L-cysteine desulfhydrase (CD) activity [Awano03, Awano05]. In vitro, tryptophanase also catalyzes α,β elimination, β replacement, and α hydrogen exchange reactions with a variety of L-amino acids [Watanabe77].
Molecular and biochemical properties of tryptophanase have been studied in depth by several groups; only a small number of papers can be cited here, with preference given to work performed on the K-12 enzyme. Tryptophanase consists of four identical subunits [London72], each of which contains one molecule of pyridoxal phosphate (PLP) [HogbergRaibaud75]. The dissociated dimeric form of the enzyme appears to be inactive [Raibaud76, Raibaud77]. Crystal structures of wild-type and mutant TnaA apoenzyme have been solved [Ku06, Tsesin07, Kogan09]. The tetramer contains four bound K+ ions [Ku06].
PLP forms an aldimine bond with Lys270 of the enzyme [Kagamiyama72]; binding of PLP induces a conformational change [HogbergRaibaud75, Raibaud76a]. The enzyme requires K+ for its activity and for tight PLP binding [HogbergRaibaud75, Tokushige89, Erez98]. Analysis of site-directed mutants, e.g. in [Kawata90, Erez98, Phillips02], has identified a number of residues that are required for interaction with PLP, orienting the substrate-PLP intermediates in the optimal conformation for catalysis, and are important for overall enzyme activity and substrate specificity. The enzyme may react by a rare SE2-type mechanism. Some of this work is reviewed in [Phillips03].
Different benzimidazole analogs of the indolenine intermediate/transition state are either substrates or inhibitors of tryptophanase [Harris13]. L-bishomotryptophan is a potent and selective competitive inhibitor of the enzyme [Do14].
Tryptophanase localizes to a single focus at one of the cell poles, mainly during the logarithmic growth phase. The Min system is involved in localization of the protein [Li12c].
In a strain selected for increased isobutanol tolerance, a tnaA mutation contributes significantly to the tolerance phenotype [Atsumi10a]. A tnaA mutant has decreased viability during long-term stationary phase [Gaimster14].
Regulation of expression of tryptophanase has been of interest for a long time and was shown to be induced by L-tryptophan and regulated by catabolite repression [Evans41, Evans42, Dawson43, Bilezikian67, Botsford71, Immken72, Ramirez72, Piovant75, Botsford75, Ward76, Yudkin77, Deeley82, Isaacs94]. Regulation by L-tryptophan is exerted via antitermination in the leader region [Stewart85a, Stewart86] that is facilitated by the TnaC leader peptide [Stewart86a, Gollnick90a]. For a description of the attenuation mechanism, please see tnaCAB and a recent review, [Yanofsky07]. tnaA mRNA levels are significantly downregulated in E. coli cells inoculated on lettuce leaves [Fink12].
TnaA protein levels are significantly increased by growth at high external pH [Blankenhorn99, Stancik02] and growth on glycerol [MartinezGomez12]. Increased TnaA expression via TorRS is involved in survival of alkaline stress conditions due to TMAO respiration [Bordi03]. Increased tnaA expression at the onset of stationary phase is dependent on σS [Lacour04] and Crl [Lelong07, Dong08]. Expression of the toxin YafQ reduces TnaA levels, possibly by cleavage of the tnaA mRNA at the in-frame YafQ cleavage cites [Hu14]. Addition of glucose and other carbohydrates inhibits TnaA function, suggesting an additional level of carbohydrate-dependent post-translational regulation [Li14].
Tryptophanase is the regulatory target of the small RNA Rcd, which ensures stable maintenance of the ColE1 plasmid. Upregulation of tryptophanase activity increases indole production; indole then appears to act as an intracellular signaling molecule to induce a cell division delay [Chant07].
Locations: cytosol, membrane
|Map Position: [3,886,753 -> 3,888,168] (83.77 centisomes)||Length: 1416 bp / 471 aa|
Molecular Weight of Polypeptide: 52.773 kD (from nucleotide sequence), 52.0 kD (experimental) [Deeley81 ]
Molecular Weight of Multimer: 223.0 kD (experimental) [London72]
Unification Links: ASAP:ABE-0012133 , CGSC:101 , DIP:DIP-31878N , EchoBASE:EB0998 , EcoGene:EG11005 , EcoliWiki:b3708 , Entrez-gene:948221 , Mint:MINT-1267429 , ModBase:P0A853 , OU-Microarray:b3708 , PortEco:tnaA , PR:PRO_000024075 , Pride:P0A853 , Protein Model Portal:P0A853 , RefSeq:NP_418164 , RegulonDB:EG11005 , SMR:P0A853 , String:511145.b3708 , Swiss-Model:P0A853 , UniProt:P0A853
Relationship Links: InterPro:IN-FAMILY:IPR001597 , InterPro:IN-FAMILY:IPR011166 , InterPro:IN-FAMILY:IPR013440 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015422 , InterPro:IN-FAMILY:IPR015424 , InterPro:IN-FAMILY:IPR018176 , PDB:Structure:2C44 , PDB:Structure:2OQX , PDB:Structure:2V0Y , PDB:Structure:2V1P , Pfam:IN-FAMILY:PF01212 , Prosite:IN-FAMILY:PS00853
|Biological Process:||GO:0006569 - tryptophan catabolic process
[UniProtGOA11, GOA06, Ng63]
GO:0006520 - cellular amino acid metabolic process [GOA01]
GO:0006568 - tryptophan metabolic process [GOA01]
GO:0009072 - aromatic amino acid family metabolic process [GOA01]
|Molecular Function:||GO:0005515 - protein binding
GO:0009034 - tryptophanase activity [GOA06, GOA01a, GOA01, Raibaud73, Burns62, Gartner65]
GO:0030170 - pyridoxal phosphate binding [GOA01, Raibaud73]
GO:0030955 - potassium ion binding [Ku06]
GO:0042802 - identical protein binding [Rajagopala14, Lasserre06, London72]
GO:0080146 - L-cysteine desulfhydrase activity [Awano03]
GO:0003824 - catalytic activity [GOA01]
GO:0016829 - lyase activity [UniProtGOA11, GOA01]
GO:0016830 - carbon-carbon lyase activity [GOA01]
|Cellular Component:||GO:0005829 - cytosol
GO:0016020 - membrane [Lasserre06]
GO:0060187 - cell pole [Li12c]
GO:0005737 - cytoplasm [UniProtGOA11a, UniProtGOA11]
|MultiFun Terms:||metabolism → carbon utilization → amino acids|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB enriched||Yes||37||Aerobic||6.95||Yes [Gerdes03, Comment 1]|
|LB Lennox||Yes||37||Aerobic||7||Yes [Baba06, Comment 2]|
|M9 medium with 1% glycerol||Yes||37||Aerobic||7.2||0.35||Yes [Joyce06, Comment 3]|
|MOPS medium with 0.4% glucose||Yes||37||Aerobic||7.2||0.22||Yes [Baba06, Comment 2] |
Yes [Feist07, Comment 4]
Enzymatic reaction of: tryptophanase
Synonyms: L-tryptophan indole-lyase (deaminating), Trpase
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.
The reaction is physiologically favored in the direction shown.
Alternative Substrates [Comment 5]:
In Pathways: tryptophan degradation II (via pyruvate)
The catalytic properties of the tryptophanase from E. coli B have been studied earlier; e.g. [Morino67, Watanabe72, Watanabe77] and many subsequent publications, mainly from the Snell and Tokushige laboratories. It was later shown that the amino acid sequence of the K-12 and B enzymes is identical [Tokushige89]. At high concentrations of pyruvate and ammonia, the reaction is reversible in vitro [Watanabe72]; however, the physiological relevance of the reverse reaction is unclear.
Enzymatic reaction of: L-cysteine desulfhydrase
Synonyms: cysteine desulfhydrase, L-cysteine hydrogen sulfide-lyase (deaminating)
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.
The reaction is physiologically favored in the direction shown.
In Pathways: L-cysteine degradation II
|Sequence-Conflict||137 -> 140|
|Sequence-Conflict||379 -> 380|
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3708 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11005; confirmed by SwissProt match.
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Awano03: Awano N, Wada M, Kohdoh A, Oikawa T, Takagi H, Nakamori S (2003). "Effect of cysteine desulfhydrase gene disruption on L-cysteine overproduction in Escherichia coli." Appl Microbiol Biotechnol 62(2-3);239-43. PMID: 12883870
Awano05: Awano N, Wada M, Mori H, Nakamori S, Takagi H (2005). "Identification and functional analysis of Escherichia coli cysteine desulfhydrases." Appl Environ Microbiol 71(7);4149-52. PMID: 16000837
Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554
Blankenhorn99: Blankenhorn D, Phillips J, Slonczewski JL (1999). "Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis." J Bacteriol 181(7);2209-16. PMID: 10094700
Bordi03: Bordi C, Theraulaz L, Mejean V, Jourlin-Castelli C (2003). "Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli." Mol Microbiol 48(1);211-23. PMID: 12657056
Chu12: Chu W, Zere TR, Weber MM, Wood TK, Whiteley M, Hidalgo-Romano B, Valenzuela E, McLean RJ (2012). "Indole production promotes Escherichia coli mixed-culture growth with Pseudomonas aeruginosa by inhibiting quorum signaling." Appl Environ Microbiol 78(2);411-9. PMID: 22101045
Dawson43: Dawson J, Happold FC (1943). "The tryptophanase-tryptophan reaction: 6. Carbohydrate-amino acid relationships concerned in the inhibition of indole production by glucose in cultures of Escherichia coli." Biochem J 37(3);389-92. PMID: 16747655
Erez98: Erez T, Phillips RS, Parola AH (1998). "Pyridoxal phosphate binding to wild type, W330F, and C298S mutants of Escherichia coli apotryptophanase: unraveling the cold inactivation." FEBS Lett 433(3);279-82. PMID: 9744811
Evans41: Evans WC, Richard W, Handley C, Happold FC (1941). "The tryptophanase-indole reaction: Some observations on the production of tryptophanase by Esch. coli; in particular the effect of the presence of glucose and amino acids on the formation of tryptophanase." Biochem J 35(1-2);207-12. PMID: 16747382
Evans42: Evans WC, Handley WC, Happold FC (1942). "The 'tryptophanase-tryptophan reaction: Possible mechanisms for the inhibition of indole production by glucose in cultures of B. coli." Biochem J 36(3-4);311-8. PMID: 16747528
Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909
Fink12: Fink RC, Black EP, Hou Z, Sugawara M, Sadowsky MJ, Diez-Gonzalez F (2012). "Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves." Appl Environ Microbiol 78(6);1752-64. PMID: 22247152
Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938
Gish93: Gish K, Yanofsky C (1993). "Inhibition of expression of the tryptophanase operon in Escherichia coli by extrachromosomal copies of the tna leader region." J Bacteriol 1993;175(11);3380-7. PMID: 8501042
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Harris13: Harris AP, Phillips RS (2013). "Benzimidazole analogs of (L)-tryptophan are substrates and inhibitors of tryptophan indole lyase from Escherichia coli." FEBS J 280(8);1807-17. PMID: 23438036
HogbergRaibaud75: Hogberg-Raibaud A, Raibaud O, Goldberg ME (1975). "Kinetic and equilibrium studies on the activation of Escherichia coli K12 tryptophanase by pyridoxal 5'-phosphate and monovalent cations." J Biol Chem 250(9);3352-8. PMID: 1091651
Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394
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Kawata90: Kawata Y, Tsujimoto N, Tani S, Mizobata T, Tokushige M (1990). "Role of tryptophan 248 in the active site of tryptophanase from Escherichia coli." Biochem Biophys Res Commun 173(2);756-62. PMID: 2260981
Kogan09: Kogan A, Gdalevsky GY, Cohen-Luria R, Goldgur Y, Phillips RS, Parola AH, Almog O (2009). "Conformational changes and loose packing promote E. coli Tryptophanase cold lability." BMC Struct Biol 9;65. PMID: 19814824
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KuczynskaWisnik10a: Kuczynska-Wisnik D, Matuszewska E, Furmanek-Blaszk B, Leszczynska D, Grudowska A, Szczepaniak P, Laskowska E (2010). "Antibiotics promoting oxidative stress inhibit formation of Escherichia coli biofilm via indole signalling." Res Microbiol 161(10);847-53. PMID: 20868745
Lacour04: Lacour S, Landini P (2004). "SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences." J Bacteriol 186(21);7186-95. PMID: 15489429
Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726
London74: London J, Skrzynia C, Goldberg ME (1974). "Renaturation of Escherichia coli tryptophanase after exposure to 8 M urea. Evidence for the existence of nucleation centers." Eur J Biochem 47(2);409-15. PMID: 4607014
MartinezGomez12: Martinez-Gomez K, Flores N, Castaneda HM, Martinez-Batallar G, Hernandez-Chavez G, Ramirez OT, Gosset G, Encarnacion S, Bolivar F (2012). "New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol." Microb Cell Fact 11;46. PMID: 22513097
Martino03: Martino PD, Fursy R, Bret L, Sundararaju B, Phillips RS (2003). "Indole can act as an extracellular signal to regulate biofilm formation of Escherichia coli and other indole-producing bacteria." Can J Microbiol 49(7);443-9. PMID: 14569285
Phillips02: Phillips RS, Johnson N, Kamath AV (2002). "Formation in vitro of hybrid dimers of H463F and Y74F mutant Escherichia coli tryptophan indole-lyase rescues activity with L-tryptophan." Biochemistry 41(12);4012-9. PMID: 11900544
Phillips12: Phillips RS, Kalu U, Hay S (2012). "Evidence of preorganization in quinonoid intermediate formation from L-Trp in H463F mutant Escherichia coli tryptophan indole-lyase from effects of pressure and pH." Biochemistry 51(33);6527-33. PMID: 22852771
Piovant75: Piovant M, Lazdunski C (1975). "Different cyclic adenosine 3',5'-monophosphate requirements for induction of beta-galactosidase and tryptophanase. Effect of osmotic pressure on intracellular cyclic adenosine 3,5-monophosphate concentrations." Biochemistry 14(9);1821-5. PMID: 164897
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Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554
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Stewart85a: Stewart V, Yanofsky C (1985). "Evidence for transcription antitermination control of tryptophanase operon expression in Escherichia coli K-12." J Bacteriol 1985;164(2);731-40. PMID: 3902796
Stewart86: Stewart V, Landick R, Yanofsky C (1986). "Rho-dependent transcription termination in the tryptophanase operon leader region of Escherichia coli K-12." J Bacteriol 166(1);217-23. PMID: 2420781
Taylor78: Taylor HV, Yudkin MD (1978). "Synthesis of tryptophanase in Escherichia coli: isolation and characterization of a structural-gene mutant and two regulatory mutants." Mol Gen Genet 165(1);95-102. PMID: 362170
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CruzVera08: Cruz-Vera LR, Yanofsky C (2008). "Conserved residues Asp16 and Pro24 of TnaC-tRNAPro participate in tryptophan induction of Tna operon expression." J Bacteriol 190(14);4791-7. PMID: 18424524
Gish95: Gish K, Yanofsky C (1995). "Evidence suggesting cis action by the TnaC leader peptide in regulating transcription attenuation in the tryptophanase operon of Escherichia coli." J Bacteriol 177(24);7245-54. PMID: 8522534
Gong01: Gong F, Yanofsky C (2001). "Reproducing tna operon regulation in vitro in an S-30 system. Tryptophan induction inhibits cleavage of TnaC peptidyl-tRNA." J Biol Chem 276(3);1974-83. PMID: 11050101
Gong01a: Gong F, Ito K, Nakamura Y, Yanofsky C (2001). "The mechanism of tryptophan induction of tryptophanase operon expression: tryptophan inhibits release factor-mediated cleavage of TnaC-peptidyl-tRNA(Pro)." Proc Natl Acad Sci U S A 98(16);8997-9001. PMID: 11470925
Gong02a: Gong F, Yanofsky C (2002). "Analysis of tryptophanase operon expression in vitro: accumulation of TnaC-peptidyl-tRNA in a release factor 2-depleted S-30 extract prevents Rho factor action, simulating induction." J Biol Chem 277(19);17095-100. PMID: 11880383
Gong07: Gong M, Cruz-Vera LR, Yanofsky C (2007). "Ribosome recycling factor and release factor 3 action promotes TnaC-peptidyl-tRNA Dropoff and relieves ribosome stalling during tryptophan induction of tna operon expression in Escherichia coli." J Bacteriol 189(8);3147-55. PMID: 17293419
Konan00: Konan KV, Yanofsky C (2000). "Rho-dependent transcription termination in the tna operon of Escherichia coli: roles of the boxA sequence and the rut site." J Bacteriol 182(14);3981-8. PMID: 10869076
Yanofsky95: Yanofsky C, Horn V (1995). "Bicyclomycin sensitivity and resistance affect Rho factor-mediated transcription termination in the tna operon of Escherichia coli." J Bacteriol 177(15);4451-6. PMID: 7543478
Yanofsky96: Yanofsky C, Horn V, Nakamura Y (1996). "Loss of overproduction of polypeptide release factor 3 influences expression of the tryptophanase operon of Escherichia coli." J Bacteriol 178(13);3755-62. PMID: 8682777
Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470
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