|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 [Li12].
In a strain selected for increased isobutanol tolerance, a tnaA mutation contributes significantly to the tolerance phenotype [Atsumi10]. 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 [Stewart85, Stewart86] that is facilitated by the TnaC leader peptide [Stewart86a, Gollnick90]. 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 [Li12]
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
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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
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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
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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
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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
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Stewart85: 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
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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
Gong02: 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
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