Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA m6A2030 methyltransferase

Gene: rlmJ Accession Numbers: EG12234 (EcoCyc), b3499, ECK3484

Synonyms: yhiR

Regulation Summary Diagram: ?

Regulation summary diagram for rlmJ

RlmJ is the methyltransferase responsible for methylation of 23S rRNA at the N6 position of the A2030 nucleotide. In vitro, RlmJ can methylate A2030 most efficiently in free 23S rRNA, but not in assembled 50S ribosomal subunits [Golovina12]. Lack of RlmJ does not affect ribosome assembly. The abundance of only a limited number of proteins is affected by lack of 23S rRNA modification at A2030 [Golovina12].

Crystal structures of the enzyme have been solved, allowing the identification of substrate binding sites. Site-directed mutagenesis of predicted active site residues confirmed their importance [Punekar13].

rlmJ is a homologue of the H. influenzae competence gene comJ. A mutant with a defect in this gene is unable to utilize DNA as a sole carbon or energy source, despite retaining the ability to be artificially induced to competence. This suggests separate mechanisms for DNA uptake depending on whether it will be used for nutrient acquisition or genetic transformation [Finkel01, Palchevskiy06]. rlmJ is not required for spontaneous plasmid transformation on nutrient plates with high agar concentration [Sun09]. rlmJ was recognised in a screen designed to identify genes that are involved in repressing cell-to-cell plasmid transfer in E. coli K-12 [Matsuda12].

While [Palchevskiy06] found that an rlmJ mutant has a growth defect in stationary phase, [Golovina12] found no growth defect under any of the tested conditions, including stationary phase.

RlmJ: "rRNA large subunit methyltransferase J" [Golovina12]

Citations: [Siibak10]

Locations: cytosol

Map Position: [3,643,408 -> 3,644,250] (78.53 centisomes, 283°)
Length: 843 bp / 280 aa

Molecular Weight of Polypeptide: 31.942 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011428 , DIP:DIP-12371N , EchoBASE:EB2146 , EcoGene:EG12234 , EcoliWiki:b3499 , Mint:MINT-1219143 , OU-Microarray:b3499 , PortEco:yhiR , Protein Model Portal:P37634 , RefSeq:NP_417956 , RegulonDB:EG12234 , SMR:P37634 , String:511145.b3499 , UniProt:P37634

Relationship Links: InterPro:IN-FAMILY:IPR002052 , InterPro:IN-FAMILY:IPR007473 , InterPro:IN-FAMILY:IPR029063 , PDB:Structure:4BLU , PDB:Structure:4BLV , PDB:Structure:4BLW , Pfam:IN-FAMILY:PF04378 , Prosite:IN-FAMILY:PS00092

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0015976 - carbon utilization Inferred from experiment [Palchevskiy06]
GO:0070475 - rRNA base methylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Golovina12]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0008988 - rRNA (adenine-N6-)-methyltransferase activity Inferred from experiment [Golovina12]
GO:0036307 - 23S rRNA (adenine(2030)-N(6))-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, Golovina12]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0008649 - rRNA methyltransferase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer RNA related RNA modification
metabolism carbon utilization

Essentiality data for rlmJ 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 ? 20-Aug-2013 by Keseler I , SRI International

Enzymatic reaction of: 23S rRNA m6A2030 methyltransferase

Synonyms: ribosomal RNA large subunit methyltransferase J

EC Number:

adenine2030 in 23S rRNA + S-adenosyl-L-methionine <=> N6-methyladenine2030 in 23S rRNA + 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 23S rRNA m6A2030 methyltransferase with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 4
[Punekar13, UniProt15]
[Punekar13, UniProt15]
Y → F: 40-fold reduction in catalytic activity.
Y → A: Loss of catalytic activity.
Amino-Acid-Site 4
UniProt: Interaction with substrate rRNA; Sequence Annotation Type: site; Non-Experimental Qualifier: probable.
Mutagenesis-Variant 6
[Punekar13, UniProt15]
UniProt: Loss of catalytic activity.
Mutagenesis-Variant 18
[Punekar13, UniProt15]
[Punekar13, UniProt15]
K → R: 10-fold reduction in catalytic activity.
K → A: Loss of catalytic activity.
Amino-Acid-Sites-That-Bind 19
UniProt: S-adenosyl-L-methionine.
Amino-Acid-Sites-That-Bind 42
UniProt: S-adenosyl-L-methionine; via carbonyl oxygen.
Amino-Acid-Sites-That-Bind 100
UniProt: S-adenosyl-L-methionine.
Amino-Acid-Sites-That-Bind 118
UniProt: S-adenosyl-L-methionine.
Protein-Segment 143 -> 144
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 164
[Punekar13, UniProt15]
UniProt: Loss of catalytic activity.
Amino-Acid-Sites-That-Bind 164
UniProt: S-adenosyl-L-methionine.
Active-Site 164
[Punekar13, UniProt15]
UniProt: Proton acceptor.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

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 b3499 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12234; confirmed by SwissProt match.


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

Finkel01: Finkel SE, Kolter R (2001). "DNA as a nutrient: novel role for bacterial competence gene homologs." J Bacteriol 183(21);6288-93. PMID: 11591672

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."

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

Golovina12: Golovina AY, Dzama MM, Osterman IA, Sergiev PV, Serebryakova MV, Bogdanov AA, Dontsova OA (2012). "The last rRNA methyltransferase of E. coli revealed: The yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA." RNA 18(9);1725-34. PMID: 22847818

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Matsuda12: Matsuda A, Kurono N, Kawano C, Shirota K, Hirabayashi A, Horino M, Etchuya R, Sobue R, Sasaki Y, Miyaue S, Sekoguchi A, Sugiura C, Shibata Y, Ito M, Ando T, Maeda S (2012). "Genome-wide screen for Escherichia coli genes involved in repressing cell-to-cell transfer of non-conjugative plasmids." Biochem Biophys Res Commun 428(4);445-50. PMID: 23131563

Palchevskiy06: Palchevskiy V, Finkel SE (2006). "Escherichia coli Competence Gene Homologs Are Essential for Competitive Fitness and the Use of DNA as a Nutrient." J Bacteriol 188(11);3902-10. PMID: 16707682

Punekar13: Punekar AS, Liljeruhm J, Shepherd TR, Forster AC, Selmer M (2013). "Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ." Nucleic Acids Res 41(20);9537-48. PMID: 23945937

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

Siibak10: Siibak T, Remme J (2010). "Subribosomal particle analysis reveals the stages of bacterial ribosome assembly at which rRNA nucleotides are modified." RNA 16(10);2023-32. PMID: 20719918

Sun09: Sun D, Zhang X, Wang L, Prudhomme M, Xie Z, Martin B, Claverys JP (2009). "Transforming DNA uptake gene orthologs do not mediate spontaneous plasmid transformation in Escherichia coli." J Bacteriol 191(3):713-9. PMID: 19011021

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Oct 6, 2015, BIOCYC14A.