Escherichia coli K-12 substr. MG1655 Protein: protein involved in threonylcarbamoyladenosine biosynthesis

Gene: tsaE Accession Numbers: EG11757 (EcoCyc), b4168, ECK4164

Synonyms: yjeE

Regulation Summary Diagram: ?

Regulation summary diagram for tsaE

Subunit composition of protein involved in threonylcarbamoyladenosine biosynthesis = [TsaE]2
         protein involved in threonylcarbamoyladenosine biosynthesis = TsaE

TsaE is involved in the biosynthesis of the threonylcarbamoyladenosine (t6A) residue at position 37 of ANN-decoding tRNAs. A mixture of purified TsaD, TsaB, TsaC, and TsaE proteins catalyzes formation of t6A in the presence of a tRNA substrate, ATP, threonine and bicarbonate in vitro [Deutsch12].

The three essential proteins TsaE, TsaB and TsaD form an interaction network. TsaB can interact with both TsaE and TsaD directly, and the interactions appear to be mutually exclusive [Handford09].

TsaE is essential for growth in complex media under aerobic conditions [Freiberg01, AllaliHassani04, Baba06, Handford09], but not under anaerobic conditions [Mangat08]. The protein is broadly conserved in bacteria and contains motifs characteristic of P-loop ATPases. TsaE possesses extremely low ATPase activity (kcat = 12 h-1) and binds ADP with a Kd of 32 mM [AllaliHassani04]. Weak ATPase activity with a Km of 169 µM and a Kcat of 0.0026 s-1 was also measured by [Handford09]. Depletion of the protein results in the formation of enlarged, elongated cells with an unusual distribution of DNA [Handford09].

Purified TsaE forms a heterogeneous mixture of oligomers in vitro and likely in vivo as well [Karst09, Handford09]. In a bacterial two-hybrid system, TsaE interacts with TsaB and itself [Handford09]. A crystal structure of Haemophilus influenzae TsaE shows a nucleotide binding fold, and the protein was shown to exhibit very slow ATPase activity [Teplyakov02, AllaliHassani04].

rstA was identified as a multicopy suppressor of the lethal phenotype of a strain with a conditional tsaE deletion [Campbell07]. Other multicopy suppressors indicate a link between purine biosynthesis and TsaE function [Handford09]. Other genetic interactions were found [Hashimoto11]. Expression of tsaE is induced by norfloxacin and other fluoroquinolone antibiotics [Mangat08].

TsaE: "threonylcarbamoyl-6(six)-adenosine" [Deutsch12]

Reviews: [Brown05, Msadek09]

Citations: [Rajagopala10, Meng12]

Gene Citations: [Kitagawa96, Tsui94, Tsui94a, Tsui96]

Locations: cytosol

Map Position: [4,393,608 -> 4,394,069] (94.7 centisomes, 341°)
Length: 462 bp / 153 aa

Molecular Weight of Polypeptide: 16.853 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013649 , EchoBASE:EB1707 , EcoGene:EG11757 , EcoliWiki:b4168 , ModBase:P0AF67 , OU-Microarray:b4168 , PortEco:yjeE , RefSeq:NP_418589 , RegulonDB:EG11757 , Swiss-Model:P0AF67

Relationship Links: Pfam:IN-FAMILY:PF02367

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for tsaE

GO Terms:

Biological Process: GO:0070526 - threonylcarbamoyladenosine biosynthetic process Inferred from experiment Inferred by computational analysis [GOA01a, Deutsch12]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Handford09]
GO:0042802 - identical protein binding Inferred from experiment [Karst09]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

Gene Class: ORFs Conserved-ORFs

Essentiality data for tsaE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Created 07-May-2009 by Keseler I , SRI International
Last-Curated ? 22-Aug-2012 by Keseler I , SRI International

Sequence Features

Protein sequence of protein involved in threonylcarbamoyladenosine biosynthesis with features indicated

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 35 -> 42
UniProt: ATP; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b4168 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11757; confirmed by SwissProt match.


AllaliHassani04: Allali-Hassani A, Campbell TL, Ho A, Schertzer JW, Brown ED (2004). "Probing the active site of YjeE: a vital Escherichia coli protein of unknown function." Biochem J 384(Pt 3);577-84. PMID: 15324301

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

Brown05: Brown ED (2005). "Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology." Biochem Cell Biol 83(6);738-46. PMID: 16333325

Campbell07: Campbell TL, Ederer C, Allali-Hassani A, Brown ED (2007). "Isolation of the rstA gene as a multicopy suppressor of YjeE, an essential ATPase of unknown function in Escherichia coli." J Bacteriol 189(8):3318-21. PMID: 17293428

Deutsch12: Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D (2012). "Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside." J Biol Chem 287(17);13666-73. PMID: 22378793

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

Freiberg01: Freiberg C, Wieland B, Spaltmann F, Ehlert K, Brotz H, Labischinski H (2001). "Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria." J Mol Microbiol Biotechnol 3(3);483-9. PMID: 11361082

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

Handford09: Handford JI, Ize B, Buchanan G, Butland GP, Greenblatt J, Emili A, Palmer T (2009). "Conserved network of proteins essential for bacterial viability." J Bacteriol 191(15):4732-49. PMID: 19376873

Hashimoto11: Hashimoto C, Sakaguchi K, Taniguchi Y, Honda H, Oshima T, Ogasawara N, Kato J (2011). "Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, which are involved in a universal tRNA modification in Escherichia coli." J Bacteriol 193(21);6075-9. PMID: 21873492

Karst09: Karst JC, Foucher AE, Campbell TL, Di Guilmi AM, Stroebel D, Mangat CS, Brown ED, Jault JM (2009). "The ATPase activity of an 'essential' Bacillus subtilis enzyme, YdiB, is required for its cellular function and is modulated by oligomerization." Microbiology 155(Pt 3);944-56. PMID: 19246765

Kitagawa96: Kitagawa R, Mitsuki H, Okazaki T, Ogawa T (1996). "A novel DnaA protein-binding site at 94.7 min on the Escherichia coli chromosome." Mol Microbiol 1996;19(5);1137-47. PMID: 8830270

Mangat08: Mangat CS, Brown ED (2008). "Known bioactive small molecules probe the function of a widely conserved but enigmatic bacterial ATPase, YjeE." Chem Biol 15(12);1287-95. PMID: 19101473

Meng12: Meng J, Kanzaki G, Meas D, Lam CK, Crummer H, Tain J, Xu HH (2012). "A genome-wide inducible phenotypic screen identifies antisense RNA constructs silencing Escherichia coli essential genes." FEMS Microbiol Lett 329(1);45-53. PMID: 22268863

Msadek09: Msadek T (2009). "Grasping at shadows: revealing the elusive nature of essential genes." J Bacteriol 191(15);4701-4. PMID: 19465656

Rajagopala10: Rajagopala SV, Yamamoto N, Zweifel AE, Nakamichi T, Huang HK, Mendez-Rios JD, Franca-Koh J, Boorgula MP, Fujita K, Suzuki K, Hu JC, Wanner BL, Mori H, Uetz P (2010). "The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology." BMC Genomics 11;470. PMID: 20701780

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Teplyakov02: Teplyakov A, Obmolova G, Tordova M, Thanki N, Bonander N, Eisenstein E, Howard AJ, Gilliland GL (2002). "Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis." Proteins 48(2);220-6. PMID: 12112691

Tsui94: Tsui HC, Leung HC, Winkler ME (1994). "Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12." Mol Microbiol 13(1);35-49. PMID: 7984093

Tsui94a: Tsui HC, Winkler ME (1994). "Transcriptional patterns of the mutL-miaA superoperon of Escherichia coli K-12 suggest a model for posttranscriptional regulation." Biochimie 76(12);1168-77. PMID: 7748952

Tsui96: Tsui HC, Feng G, Winkler ME (1996). "Transcription of the mutL repair, miaA tRNA modification, hfq pleiotropic regulator, and hflA region protease genes of Escherichia coli K-12 from clustered Esigma32-specific promoters during heat shock." J Bacteriol 178(19);5719-31. PMID: 8824618

UniProt08: UniProt Consortium (2008). "UniProt version 14.6 released on 2008-12-16." Database.

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

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

Other References Related to Gene Regulation

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

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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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