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Escherichia coli K-12 substr. MG1655 Enzyme: tryptophanase / L-cysteine desulfhydrase



Gene: tnaA Accession Numbers: EG11005 (EcoCyc), b3708, ECK3701

Synonyms: ind, tnaR

Regulation Summary Diagram: ?

Subunit composition of tryptophanase / L-cysteine desulfhydrase = [TnaA]4
         tryptophanase = TnaA

Summary:
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 [Wang01c, Martino03, KuczynskaWisnik10a, KuczynskaWisnik10, 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 [Li13c].

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 [Raibaud76a, 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, Raibaud76]. 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 [Phillips03a].

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 [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 [Li14a].

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].

Reviews: [Phillips03a, Chattoraj07, Yanofsky07]

Citations: [Wood47, Taylor78]

Gene Citations: [Gish93, Edwards82]

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]

pI: 6.2

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

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006569 - tryptophan catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Ng63]
GO:0006520 - cellular amino acid metabolic process Inferred by computational analysis [GOA01]
GO:0006568 - tryptophan metabolic process Inferred by computational analysis [GOA01]
GO:0009072 - aromatic amino acid family metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Zheng11]
GO:0009034 - tryptophanase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Raibaud73, Burns62, Gartner65]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA01, Raibaud73]
GO:0030955 - potassium ion binding Inferred from experiment [Ku06]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Lasserre06, London72]
GO:0080146 - L-cysteine desulfhydrase activity Inferred from experiment [Awano03]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016830 - carbon-carbon lyase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0060187 - cell pole Inferred from experiment [Li12c]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: metabolism carbon utilization amino acids

Essentiality data for tnaA knockouts: ?

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]

Credits:
Last-Curated ? 03-Sep-2014 by Keseler I , SRI International


Enzymatic reaction of: tryptophanase

Synonyms: L-tryptophan indole-lyase (deaminating), Trpase

L-tryptophan <=> indole + 2-aminoprop-2-enoate + H+

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)

Summary:
The enzyme binds one molecule of PLP per subunit; the Km for PLP is 0.42 µM [HogbergRaibaud75]. It requires K+ for its activity and for tight PLP binding [HogbergRaibaud75, Tokushige89].

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.

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [HogbergRaibaud75, Wood47a, Deeley81]

Activators (Unknown Mechanism): K+ [Tokushige89, HogbergRaibaud75, Comment 6] , ammonium [Tokushige89, HogbergRaibaud75, Comment 6]

Inhibitors (Unknown Mechanism): Na+ [HogbergRaibaud75, Comment 7]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
indole
19.0
[Watanabe72]
L-tryptophan
120.0
[Kawata90]
L-tryptophan
6.8
[Phillips89]


Enzymatic reaction of: L-cysteine desulfhydrase

Synonyms: cysteine desulfhydrase, L-cysteine hydrogen sulfide-lyase (deaminating)

L-cysteine <=> 2-aminoprop-2-enoate + hydrogen sulfide + H+

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 Features

Feature Class Location Citations Comment
Acetylation-Modification 5
[Zhang09b, UniProt11]
UniProt: N6-acetyllysine.
Acetylation-Modification 115
[Zhang09b, UniProt11]
UniProt: N6-acetyllysine.
Sequence-Conflict 137 -> 140
[Deeley81, UniProt10]
Alternate sequence: DTTQ → TTQG; UniProt: (in Ref. 1; no nucleotide entry);
Acetylation-Modification 156
[Zhang09b, UniProt11]
UniProt: N6-acetyllysine.
Acetylation-Modification 239
[Yu08]
 
N6-pyridoxal-phosphate-Lys-Modification 270
[UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine.
Mutagenesis-Variant 294
[Phillips89, UniProt11]
Alternate sequence: C → S; UniProt: Identical to wild-type.
Mutagenesis-Variant 298
[Phillips89, UniProt11]
Alternate sequence: C → S; UniProt: Alters activity.
Sequence-Conflict 379 -> 380
[Tokushige89, Deeley81, UniProt10]
Alternate sequence: QA → TG; UniProt: (in Ref. 1; AAA24676 and 2; CAA34096);
Acetylation-Modification 450
[Zhang09b, UniProt11]
UniProt: N6-acetyllysine.
Acetylation-Modification 459
[Yu08]
 


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
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.


References

Atsumi10a: Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC (2010). "Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli." Mol Syst Biol 6;449. PMID: 21179021

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

Bilezikian67: Bilezikian JP, Kaempfer RO, Magasanik B (1967). "Mechanism of tryptophanase induction in Escherichia coli." J Mol Biol 27(3);495-506. PMID: 4860581

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

Botsford71: Botsford JL, DeMoss RD (1971). "Catabolite repression of tryptophanase in Escherichia coli." J Bacteriol 105(1);303-12. PMID: 4322348

Botsford75: Botsford JL (1975). "Metabolism of cyclic adenosine 3',5'-monophosphate and induction of tryptophanase in Escherichia coli." J Bacteriol 124(1);380-90. PMID: 170248

Burns62: Burns RO, Demoss RD (1962). "Properties of tryptophanase from Escherichia coli." Biochim Biophys Acta 65;233-44. PMID: 14017164

Chant07: Chant EL, Summers DK (2007). "Indole signalling contributes to the stable maintenance of Escherichia coli multicopy plasmids." Mol Microbiol 63(1);35-43. PMID: 17163976

Chattoraj07: Chattoraj DK (2007). "Tryptophanase in sRNA control of the Escherichia coli cell cycle." Mol Microbiol 63(1);1-3. PMID: 17163965

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

Deeley81: Deeley MC, Yanofsky C (1981). "Nucleotide sequence of the structural gene for tryptophanase of Escherichia coli K-12." J Bacteriol 1981;147(3);787-96. PMID: 6268608

Deeley82: Deeley MC, Yanofsky C (1982). "Transcription initiation at the tryptophanase promoter of Escherichia coli K-12." J Bacteriol 1982;151(2);942-51. PMID: 6284718

Do14: Do QT, Nguyen GT, Celis V, Phillips RS (2014). "Inhibition of Escherichia coli tryptophan indole-lyase by tryptophan homologues." Arch Biochem Biophys 560C;20-26. PMID: 25088962

Dong08: Dong T, Kirchhof MG, Schellhorn HE (2008). "RpoS regulation of gene expression during exponential growth of Escherichia coli K12." Mol Genet Genomics 279(3);267-77. PMID: 18158608

Edwards82: Edwards RM, Yudkin MD (1982). "Location of the gene for the low-affinity tryptophan-specific permease of Escherichia coli." Biochem J 1982;204(2);617-9. PMID: 7052072

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

Field12: Field CM, Summers DK (2012). "Indole inhibition of ColE1 replication contributes to stable plasmid maintenance." Plasmid 67(2);88-94. PMID: 22172706

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

Gaimster14: Gaimster H, Cama J, Hernandez-Ainsa S, Keyser UF, Summers DK (2014). "The indole pulse: a new perspective on indole signalling in Escherichia coli." PLoS One 9(4);e93168. PMID: 24695245

Gartner65: Gartner TK, Riley M (1965). "Genetic analysis of tryptophanase mutants of Escherichia coli." J Bacteriol 89;319-25. PMID: 14255697

Gartner65a: Gartner TK, Riley M (1965). "Isolation of mutants affecting tryptophanase production in Escherichia coli." J Bacteriol 89;313-8. PMID: 14255696

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Gollnick90: Gollnick P, Yanofsky C (1990). "tRNA(Trp) translation of leader peptide codon 12 and other factors that regulate expression of the tryptophanase operon." J Bacteriol 1990;172(6);3100-7. PMID: 2345136

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

Hu14: Hu Y, Kwan BW, Osbourne DO, Benedik MJ, Wood TK (2014). "Toxin YafQ increases persister cell formation by reducing indole signalling." Environ Microbiol. PMID: 25041421

Immken72: Immken L, Apirion D (1972). "Site of action of 3',5'-cyclic adenosine monophosphate in production of tryptophanase in Escherichia coli." Genetics 70(1);175-80. PMID: 4335309

Isaacs94: Isaacs H, Chao D, Yanofsky C, Saier MH (1994). "Mechanism of catabolite repression of tryptophanase synthesis in Escherichia coli." Microbiology 140 ( Pt 8);2125-34. PMID: 7921262

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

Kagamiyama72: Kagamiyama H, Matsubara H, Snell EE (1972). "The chemical structure of tryptophanase from Escherichia coli. 3. Isolation and amino acid sequence of the tryptic peptides." J Biol Chem 247(5);1576-86. PMID: 4551944

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

Ku06: Ku SY, Yip P, Howell PL (2006). "Structure of Escherichia coli tryptophanase." Acta Crystallogr D Biol Crystallogr 62(Pt 7);814-23. PMID: 16790938

KuczynskaWisnik10: 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

KuczynskaWisnik10a: Kuczynska-Wisnik D, Matuszewska E, Laskowska E (2010). "Escherichia coli heat-shock proteins IbpA and IbpB affect biofilm formation by influencing the level of extracellular indole." Microbiology 156(Pt 1);148-57. PMID: 19797360

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

Lelong07: Lelong C, Aguiluz K, Luche S, Kuhn L, Garin J, Rabilloud T, Geiselmann J (2007). "The Crl-RpoS regulon of Escherichia coli." Mol Cell Proteomics 6(4);648-59. PMID: 17224607

Li12c: Li G, Young KD (2012). "Isolation and identification of new inner membrane-associated proteins that localize to cell poles in Escherichia coli." Mol Microbiol 84(2);276-95. PMID: 22380631

Li13c: Li G, Young KD (2013). "Indole production by the tryptophanase TnaA in Escherichia coli is determined by the amount of exogenous tryptophan." Microbiology 159(Pt 2);402-10. PMID: 23397453

Li14a: Li G, Young KD (2014). "A cAMP-independent carbohydrate-driven mechanism inhibits tnaA expression and TnaA enzyme activity in Escherichia coli." Microbiology 160(Pt 9);2079-2088. PMID: 25061041

London72: London J, Goldberg ME (1972). "The tryptophanase from Escherichia coli K-12. I. Purification, physical properties, and quaternary structure." J Biol Chem 247(5);1566-70. PMID: 4551942

London74a: 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

Morino67: Morino Y, Snell EE (1967). "A kinetic study of the reaction mechanism of tryptophanase-catalyzed reactions." J Biol Chem 242(12);2793-9. PMID: 5338506

Ng63: Ng H, Gartner TK (1963). "Selection of mutants of Escherichia coli constitutive for tryptophanase." J Bacteriol 85;245-6. PMID: 13938299

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

Phillips03a: Phillips RS, Demidkina TV, Faleev NG (2003). "Structure and mechanism of tryptophan indole-lyase and tyrosine phenol-lyase." Biochim Biophys Acta 1647(1-2);167-72. PMID: 12686128

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

Phillips89: Phillips RS, Gollnick PD (1989). "Evidence that cysteine 298 is in the active site of tryptophan indole-lyase." J Biol Chem 264(18);10627-32. PMID: 2659590

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

Raibaud73: Raibaud O, Goldberg ME (1973). "The tryptophanase from Escherichia coli K-12. II. Comparison of the thermal stabilities of apo-, holo-, and hybrid enzymes." J Biol Chem 248(10);3451-5. PMID: 4573978

Raibaud76: Raibaud O, Goldberg ME (1976). "Structural and functional interdependence of the protomers of Escherichia coli K 12 tryptophanase during binding of pyridoxal 5'-phosphate." J Biol Chem 251(9);2814-9. PMID: 770472

Raibaud76a: Raibaud O, Goldberg ME (1976). "The dissociated tryptophanase subunit is inactive." J Biol Chem 251(9);2820-4. PMID: 770473

Raibaud77: Raibaud O, Goldberg ME (1977). "The reactivity of one essential cysteine as a conformational probe in Escherichia coli tryptophanase. Application to the study of the structural influence of subunit interactions." Eur J Biochem 73(2);591-9. PMID: 321224

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

Ramirez72: Ramirez JM, Conde F, Del Campo FF (1972). "Transcriptional control of tryptophanase synthesis by cyclic AMP in Escherichia coli." Eur J Biochem 25(3);471-5. PMID: 4339643

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Skrzynia74: Skrzynia C, London J, Goldberg ME (1974). "The tryptophanase from Escherichia coli K12. 3. Further characterization of hybrids between the apo- and holoenzyme." J Biol Chem 249(7);2325-6. PMID: 4594500

Snell75: Snell EE (1975). "Tryptophanase: structure, catalytic activities, and mechanism of action." Adv Enzymol Relat Areas Mol Biol 1975;42;287-333. PMID: 236639

Stancik02: Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN, Slonczewski JL (2002). "pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli." J Bacteriol 184(15);4246-58. PMID: 12107143

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

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

Stewart86a: Stewart V, Yanofsky C (1986). "Role of leader peptide synthesis in tryptophanase operon expression in Escherichia coli K-12." J Bacteriol 167(1);383-6. PMID: 3522554

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

Tokushige89: Tokushige M, Tsujimoto N, Oda T, Honda T, Yumoto N, Ito S, Yamamoto M, Kim EH, Hiragi Y (1989). "Role of cysteine residues in tryptophanase for monovalent cation-induced activation." Biochimie 71(6);711-20. PMID: 2502187

Tsesin07: Tsesin N, Kogan A, Gdalevsky GY, Himanen JP, Cohen-Luria R, Parola AH, Goldgur Y, Almog O (2007). "The structure of apo tryptophanase from Escherichia coli reveals a wide-open conformation." Acta Crystallogr D Biol Crystallogr 63(Pt 9);969-74. PMID: 17704565

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Wang01c: Wang D, Ding X, Rather PN (2001). "Indole can act as an extracellular signal in Escherichia coli." J Bacteriol 183(14);4210-6. PMID: 11418561

Ward76: Ward DF, Yudkin MD (1976). "Mutations in Escherichia coli that relieve catabolite repression of tryptophanase synthesis. Tryptophanase promoter-like mutations." J Gen Microbiol 92(1);133-7. PMID: 1107479

Watanabe72: Watanabe T, Snell EE (1972). "Reversibility of the tryptophanase reaction: synthesis of tryptophan from indole, pyruvate, and ammonia." Proc Natl Acad Sci U S A 69(5);1086-90. PMID: 4556453

Watanabe77: Watanabe T, Snell EE (1977). "The interaction of Escherichia coli tryptophanase with various amino and their analogs. Active site mapping." J Biochem 82(3);733-45. PMID: 334760

Wood47: Wood WA, Gunsalus IC, Umbreit WW (1947). "Function of pyridoxal phosphate: resolution and purification of the tryptophanase enzyme of Escherichia coli." J Biol Chem 170:313-321.

Wood47a: Wood WA, Gunsalus IC, Umbreit WW (1947). "Pyridoxal phosphate as the coenzyme of tryptophanase from Escherichia coli." J Bacteriol 54(1);21. PMID: 20255117

Yanofsky07: Yanofsky C (2007). "RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria." RNA 13(8);1141-54. PMID: 17601995

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Yudkin77: Yudkin MD (1977). "Unstable mutations that relieve catabolite repression of tryptophanase synthesis by Escherichia coli." J Bacteriol 130(1);57-61. PMID: 323244

Zhang09b: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Zheng11: Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE (2011). "Cross-linking measurements of in vivo protein complex topologies." Mol Cell Proteomics 10(10);M110.006841. PMID: 21697552

Other References Related to Gene Regulation

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

Gong03b: Gong F, Yanofsky C (2003). "A transcriptional pause synchronizes translation with transcription in the tryptophanase operon leader region." J Bacteriol 185(21);6472-6. PMID: 14563884

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