Escherichia coli K-12 substr. MG1655 Enzyme: tRNA (Gm18) 2'-O-methyltransferase

Gene: trmH Accession Numbers: EG10967 (EcoCyc), b3651, ECK3641

Synonyms: spoU

Regulation Summary Diagram: ?

Regulation summary diagram for trmH

TrmH is the methyltransferase responsible for 2'-O-methylation of ribose at position G18 in certain tRNAs [Persson97]. Unlike Type I enzymes (e.g. from Thermus thermophilus) that can modify all tRNA species, the E. coli enzyme is a Type II enzyme that only modifies a subset of tRNAs. The catalytic domain of TrmH is responsible for substrate selectivity [Ochi13].

TrmH belongs to the SPOUT superfamily of methyltransferases [Anantharaman02] and was identified early as a member of a protein family predicted to include rRNA methylases [Koonin93].

[Persson97] reported no growth defect of a trmH in LB or MOPS-glucose medium, while [Urbonavicius02] found a lower growth rate in rich-MOPS medium compared to wild type. The ΔspoU3 insertion-deletion allele of trmH causes phenotypes due to polar effects on recG gene expression [Kalman92]. A trmH trmA truB triple mutant shows a defect in the tRNA modifications Gm18, m5U54, and Ψ55 as well as translation defects, heat sensitivity, and a growth defect [Urbonavicius02].

Interestingly, tRNATyr lacking the Gm18 modification elicits release of interferon-α in human peripheral blood, while the modified tRNA does not [Jockel12, Gehrig12].

TrmH: "tRNA methylation" [Persson97]

Review: [El12]

Citations: [Kinghorn02, Gustafsson96]

Locations: cytosol

Map Position: [3,822,538 -> 3,823,227] (82.39 centisomes, 297°)
Length: 690 bp / 229 aa

Molecular Weight of Polypeptide: 25.343 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011937 , CGSC:33877 , DIP:DIP-35977N , EchoBASE:EB0960 , EcoGene:EG10967 , EcoliWiki:b3651 , ModBase:P0AGJ2 , OU-Microarray:b3651 , PortEco:trmH , PR:PRO_000024115 , Pride:P0AGJ2 , Protein Model Portal:P0AGJ2 , RefSeq:NP_418108 , RegulonDB:EG10967 , SMR:P0AGJ2 , String:511145.b3651 , Swiss-Model:P0AGJ2 , UniProt:P0AGJ2

Relationship Links: InterPro:IN-FAMILY:IPR001537 , InterPro:IN-FAMILY:IPR022724 , InterPro:IN-FAMILY:IPR029026 , InterPro:IN-FAMILY:IPR029028 , Pfam:IN-FAMILY:PF00588 , Pfam:IN-FAMILY:PF12105

In Paralogous Gene Group: 435 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for trmH

GO Terms:

Biological Process: GO:0002938 - tRNA guanine ribose methylation Inferred from experiment [Persson97]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11]
GO:0030488 - tRNA methylation Author statement [Persson97]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0009020 - tRNA (guanosine-2'-O-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Ochi13, Persson97]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11]
GO:0008173 - RNA methyltransferase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for trmH 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]

Last-Curated ? 31-Jul-2013 by Keseler I , SRI International

Enzymatic reaction of: tRNA (Gm18) 2'-O-methyltransferase

Synonyms: tRNA guanosine 2'-methyltransferase

EC Number:

a guanosine18 in tRNA + S-adenosyl-L-methionine <=> a 2'-O-methylguanosine18 in tRNA + S-adenosyl-L-homocysteine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of tRNA (Gm18) 2'-O-methyltransferase with features indicated

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 119
UniProt: S-adenosyl-L-methionine; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 139
UniProt: S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 148
UniProt: S-adenosyl-L-methionine; via amide nitrogen; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3651 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10967; confirmed by SwissProt match.


Anantharaman02: Anantharaman V, Koonin EV, Aravind L (2002). "SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases." J Mol Microbiol Biotechnol 4(1);71-5. PMID: 11763972

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

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

El12: El Yacoubi B, Bailly M, de Crecy-Lagard V (2012). "Biosynthesis and function of posttranscriptional modifications of transfer RNAs." Annu Rev Genet 46;69-95. PMID: 22905870

Gehrig12: Gehrig S, Eberle ME, Botschen F, Rimbach K, Eberle F, Eigenbrod T, Kaiser S, Holmes WM, Erdmann VA, Sprinzl M, Bec G, Keith G, Dalpke AH, Helm M (2012). "Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity." J Exp Med 209(2);225-33. PMID: 22312113

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

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.

Gustafsson96: Gustafsson C, Reid R, Greene PJ, Santi DV (1996). "Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes." Nucleic Acids Res 24(19);3756-62. PMID: 8871555

Jockel12: Jockel S, Nees G, Sommer R, Zhao Y, Cherkasov D, Hori H, Ehm G, Schnare M, Nain M, Kaufmann A, Bauer S (2012). "The 2'-O-methylation status of a single guanosine controls transfer RNA-mediated Toll-like receptor 7 activation or inhibition." J Exp Med 209(2);235-41. PMID: 22312111

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

Kalman92: Kalman M, Murphy H, Cashel M (1992). "The nucleotide sequence of recG, the distal spo operon gene in Escherichia coli K-12." Gene 110(1);95-9. PMID: 1544582

Kinghorn02: Kinghorn SM, O'Byrne CP, Booth IR, Stansfield I (2002). "Physiological analysis of the role of truB in Escherichia coli: a role for tRNA modification in extreme temperature resistance." Microbiology 148(Pt 11);3511-20. PMID: 12427942

Koonin93: Koonin EV, Rudd KE (1993). "SpoU protein of Escherichia coli belongs to a new family of putative rRNA methylases." Nucleic Acids Res 21(23);5519. PMID: 8265370

Ochi13: Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H (2013). "The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and non-substrate tRNA via an induced-fit process." J Biol Chem. PMID: 23867454

Persson97: Persson BC, Jager G, Gustafsson C (1997). "The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activity." Nucleic Acids Res 25(20);4093-7. PMID: 9321663

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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."

Urbonavicius02: Urbonavicius J, Durand JM, Bjork GR (2002). "Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri." J Bacteriol 184(19);5348-57. PMID: 12218021

Other References Related to Gene Regulation

Gentry93: Gentry D, Bengra C, Ikehara K, Cashel M (1993). "Guanylate kinase of Escherichia coli K-12." J Biol Chem 1993;268(19);14316-21. PMID: 8390989

Lemke11: Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL (2011). "Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA." Proc Natl Acad Sci U S A 108(14);5712-7. PMID: 21402902

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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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