Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases

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Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases is …
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scholarly articleQ13442814

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P6179Dimensions Publication ID1019541723
P356DOI10.1186/1756-0500-7-440
P932PMC publication ID4119055
P698PubMed publication ID25012753
P5875ResearchGate publication ID263862528

P50authorAlfonso Benitez-paezQ42790463
P2093author name stringMauricio Corredor
Sonia Cárdenas-Brito
Jeanneth Mosquera-Rendón
Juan D Pineda
P2860cites workPurification and characterization of transfer RNA (guanine-1)methyltransferase from Escherichia coliQ70238866
Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P siteQ71666175
Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilisQ72991207
Translational defects of Escherichia coli mutants deficient in the Um(2552) 23S ribosomal RNA methyltransferase RrmJ/FTSJQ73800291
A conserved rRNA methyltransferase regulates ribosome biogenesisQ81026237
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferaseQ21263012
MUSCLE: a multiple sequence alignment method with reduced time and space complexityQ21284290
Comparative genomics and evolution of proteins involved in RNA metabolismQ24515041
Improvement of reading frame maintenance is a common function for several tRNA modificationsQ24535753
Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase familyQ24541405
Gapped BLAST and PSI-BLAST: a new generation of protein database search programsQ24545170
ProbCons: Probabilistic consistency-based multiple sequence alignmentQ24557418
Identification of a plasmid-borne chloramphenicol-florfenicol resistance gene in Staphylococcus sciuriQ39475015
Emergence of tetracycline resistance in Helicobacter pylori: multiple mutational changes in 16S ribosomal DNA and other genetic lociQ39671183
The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activityQ39721356
Erythromycin resistance by ribosome modificationQ39779280
1-Methylguanosine deficiency of tRNA influences cognate codon interaction and metabolism in Salmonella typhimuriumQ39839155
Cloning and restriction mapping of the trmA gene coding for transfer ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-12Q40334658
Role of helix 44 of 16S rRNA in the fidelity of translation initiation.Q41510482
The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA.Q41768024
Distinction between the Cfr methyltransferase conferring antibiotic resistance and the housekeeping RlmN methyltransferase.Q41774206
The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivoQ41991276
armA and aminoglycoside resistance in Escherichia coliQ42184041
Genetic mapping and cloning of the gene (trmC) responsible for the synthesis of tRNA (mnm5s2U)methyltransferase in Escherichia coli K12.Q42248131
RNA-methyltransferase TrmA is a dual-specific enzyme responsible for C5-methylation of uridine in both tmRNA and tRNA.Q42824088
Impairing methylations at ribosome RNA, a point mutation-dependent strategy for aminoglycoside resistance: the rsmG caseQ46468772
A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: methylation of 23S ribosomal RNA at A2503.Q46642614
Genetic basis for dissemination of armA.Q48129108
Deficiency of 1-methylguanosine in tRNA from Salmonella typhimurium induces frameshifting by quadruplet translocationQ50159368
Mutational analysis of two highly conserved UGG sequences of 23 S rRNA from Escherichia coli.Q54575118
PAL: an object-oriented programming library for molecular evolution and phylogenetics.Q55034934
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extensionQ24603117
MUSCLE: multiple sequence alignment with high accuracy and high throughputQ24613456
SMART 7: recent updates to the protein domain annotation resourceQ24622634
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNAQ24634123
The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNAQ24685082
Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria--evolutionary implicationsQ24813844
Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesisQ24815421
Post-transcriptional nucleotide modification and alternative folding of RNAQ25255871
Recognition of cognate transfer RNA by the 30S ribosomal subunitQ27631606
Methyltransferase That Modifies Guanine 966 of the 16 S rRNA: FUNCTIONAL IDENTIFICATION AND TERTIARY STRUCTUREQ27640940
Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymesQ27652124
Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmGQ27656590
Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilusQ27662428
Structural Basis for Methyl Transfer by a Radical SAM EnzymeQ27667611
Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNAQ27677448
Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m³U1498) from crystal and solution structuresQ27682056
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutionsQ27860462
Profile hidden Markov modelsQ27860536
ProtTest: selection of best-fit models of protein evolutionQ27860845
T-Coffee: A novel method for fast and accurate multiple sequence alignmentQ27860999
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum LikelihoodQ27861000
A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNAQ28488970
rRNA modifications and ribosome functionQ28610126
An improved general amino acid replacement matrixQ29547248
Many paths to methyltransfer: a chronicle of convergenceQ29616667
Update on activities at the Universal Protein Resource (UniProt) in 2013Q29617361
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policyQ29617901
SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase foldQ29618153
SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.Q30787418
The tylosin resistance gene tlrB of Streptomyces fradiae encodes a methyltransferase that targets G748 in 23S rRNA.Q30917937
Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometryQ33188085
BioLayout(Java): versatile network visualisation of structural and functional relationshipsQ33218316
YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407.Q33242538
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferasesQ33276931
Sequence and structural evolution of the KsgA/Dim1 methyltransferase familyQ33380449
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.Q33435992
Two novel point mutations in clinical Staphylococcus aureus reduce linezolid susceptibility and switch on the stringent response to promote persistent infectionQ33604815
Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutantQ33722967
Two Genetic Loci for Resistance to Kasugamycin in Escherichia coliQ33782124
Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coliQ33852617
Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coliQ33857959
Characterization of Streptococcus pneumoniae TrmD, a tRNA methyltransferase essential for growthQ33999417
The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coliQ34100768
Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coliQ34108217
YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptorsQ34139029
Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA.Q34194595
Mechanism of kasugamycin resistance in Escherichia coliQ34207042
YhiQ is RsmJ, the methyltransferase responsible for methylation of G1516 in 16S rRNA of E. coliQ34232122
Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activityQ34243886
Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNAQ34365923
Purification, cloning, and characterization of the 16 S RNA m2G1207 methyltransferase from Escherichia coliQ34485696
Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA.Q34570067
Identification of Escherichia coli m2G methyltransferases: II. The ygjO gene encodes a methyltransferase specific for G1835 of the 23 S rRNA.Q34570072
Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteriaQ34604506
The Cfr rRNA methyltransferase confers resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibioticsQ34721545
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.Q34816382
YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962.Q34825806
The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC)Q34977098
The yggH Gene of Escherichia coli Encodes a tRNA (m 7 G46) MethyltransferaseQ34977384
Inactivation of the indigenous methyltransferase RlmN in Staphylococcus aureus increases linezolid resistanceQ35005203
Alteration of Ribosomal Protein S4 by Mutation Linked to Kasugamycin-Resistance in Escherichia coliQ35093348
Plasmid-mediated high-level resistance to aminoglycosides in Enterobacteriaceae due to 16S rRNA methylationQ35165835
Regulation of expression and catalytic activity of Escherichia coli RsmG methyltransferaseQ35853461
Mutations in rsmG, encoding a 16S rRNA methyltransferase, result in low-level streptomycin resistance and antibiotic overproduction in Streptomyces coelicolor A3(2)Q35879223
Identification of the RsmG methyltransferase target as 16S rRNA nucleotide G527 and characterization of Bacillus subtilis rsmG mutantsQ35949990
The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy.Q36246613
Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-L-methionine methyl synthase RlmN trapped by mutagenesisQ36402114
Bringing order to translation: the contributions of transfer RNA anticodon-domain modificationsQ36776984
Inactivation of KsgA, a 16S rRNA methyltransferase, causes vigorous emergence of mutants with high-level kasugamycin resistanceQ37032849
P4510describes a project that usesggplot2Q326489
P921main subjectnon-coding RNAQ427087
P304page(s)440
P577publication date2014-07-10
P1433published inBMC Research NotesQ15762797
P1476titleEvolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases
P478volume7

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cites work (P2860)
Q64882262Bacillus subtilis exhibits MnmC-like tRNA modification activities.
Q92753112Genome-Wide Identification and Transcriptional Expression of the METTL21C Gene Family in Chicken
Q35891241Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species.
Q89870676The critical function of the plastid rRNA methyltransferase, CMAL, in ribosome biogenesis and plant development

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