Phylogenomic analysis of 16S rRNA:(guanine‐N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino‐methyltransferases

Bujnicki, Janusz M.

doi:10.1096/fj.00-0076com

Cited by 41 publications

(33 citation statements)

References 26 publications

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“…Members of the Trm11p family exhibited the DPPY tetrapeptide in motif IV (Fig. 7), a variant of a [D-N-S]-P-P-[Y-F-W-H] motif found in the majority of MTases that modify exocyclic amino groups of bases in DNA and RNA, including rRNA:m 2 G MTases: RsmC/RsmD specific for bacterial 16S rRNA (12) and Tgs1p specific for eukaryotic mRNA:cap-m 7 G (45).…”

Section: Results Mmentioning

confidence: 99%

Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA

Purushothaman

Bujnicki

Grosjean

et al. 2005

Molecular and Cellular Biology

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107

157

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tRNAs are transcribed as precursor molecules by RNA polymerase III, then the primary transcripts undergo posttranscriptional maturation before becoming functional. tRNA maturation includes the removal of leader and trailer sequences, the addition of a CCA at the 3Ј end, sometimes the splicing of an intron, and the modification of numerous nucleotides (34,42,57). In yeast tRNA, modified nucleotides are detected at 35 different positions out of 76. They are formed posttranscriptionally and require various types of enzymatic activities such as 2Ј-O-ribose methyltransferases (MTases), base MTases, pseudouridylases, deaminases, thiolases, reductases, and oxidases. Base and ribose methylations are by far the most frequent modifications in tRNA (26,57). In yeast, cytoplasmic tRNAs sequenced so far contain 15 methylated bases and five 2Ј-O-methylriboses, while mitochondrially encoded tRNA possess only 4 methylated bases, none of which are unique to mitochondria (57). It is likely that the formation of all these methylated nucleotides is catalyzed by unisite-or multisitespecific MTases. The first identified yeast tRNA MTase (Trm) Trm1p, is required for the formation of N 2 ,N 2 -dimethylguanosine at position 26 (m 2 2 G26) in cytoplasmic and mitochondrial tRNA (19). Later, several tRNA MTases were identified, by either genetic screening, bioinformatic analysis, or biochemical genomics (34). Out of the 10 tRNA MTases that have been characterized to date in yeast, only Trm6p and Trm61p, which form a heterodimer required for the formation of m 1 A58, are essential for cell growth (2). Deletion of either TRM5 or TRM7 leads to a severe growth defect (8, 51), while the genes encoding other Trm proteins can be deleted without apparent cell growth defects under laboratory conditions.With the exception of only one tetrahydrofolate-dependent enzyme (17), all known MTases acting on nucleic acids use S-adenosyl-L-methionine (AdoMet) as a cofactor (10,14). Although AdoMet-dependent MTases can be classified into at least six unrelated superfamilies based on structural and evolutionary considerations (54), all DNA MTases and most RNA MTases belong to the largest class I of Rossmann fold-like MTases (RFMs) (11). A characteristic feature of these enzymes is the presence of nine common motifs that map onto the catalytic face of the common fold, with motifs I to III involved in AdoMet binding, and motif IV and often motifs VI, VIII, and X involved in binding to the target nucleotide and in methyl transfer reactions (20).Using a combination of protein fold recognition and modeling-based identification of potential catalytic and RNA-binding residues, we previously identified 20 putative RNA MTases (termed MTase candidates or Mtcs) (14) and then tested their involvement in tRNA methylation. Here, we report the characterization of the activity responsible for the formation of m 2 G10 in yeast tRNA. The enzyme is composed of at least two subunits: Trm11p is the catalytic subunit that contains the RFM domain, and Trm112p shows similarity to an u...

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Section: Results Mmentioning

confidence: 99%

Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA

Purushothaman

Bujnicki

Grosjean

et al. 2005

Molecular and Cellular Biology

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107

157

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“…In order to identify the gene responsible for methylation of U1498 in the small ribosomal subunit of E. coli, we selected for analysis several genes predicted to encode RNA MTases whose function have not been determined. These include yjhP (Katz et al 2003), yfiC (Katz et al 2003), ybiN (Bujnicki 2000;Bujnicki and Rychlewski 2002;Katz et al 2003), yebU (Reid et al 1999;Katz et al 2003), ygjO (Bujnicki 2000;Bujnicki and Rychlewski 2002), yfiF (Koonin and Rudd 1993) and yggJ (Forouhar et al 2003). Each of the genes was replaced with a kanamycin resistance cassette using the method of Datsenko and Wanner (2000).…”

Section: Resultsmentioning

confidence: 99%

Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family

Basturea¹,

Rudd²,

Deutscher³

2006

RNA

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A variety of RNA methyltransferases act during ribosomal RNA maturation to modify nucleotides in a site-specific manner. However, of the 10 base-methylated nucleotides present in the small ribosomal subunit of Escherichia coli, only three enzymes responsible for modification of four bases are known. Here, we show that the protein encoded by yggJ, a member of the uncharacterized DUF558 protein family of predicted alpha/beta (trefoil) knot methyltransferases is responsible for methylation at U1498 in 16S rRNA. The gene is well-conserved across bacteria and plants, and likely performs the same function in other organisms. A yggJ deletion strain lacks the methyl group at U1498 as well as the specific methyltransferase activity. Moreover, purified recombinant YggJ specifically methylates m 3 U1498 in vitro. The deletion strain was unaffected in exponential growth in rich or minimal media at multiple temperatures, but it was defective when grown in competition with isogenic wild-type cells. Based on these data, we conclude that yggJ is the founding member of a family of RNA base methyltransferases, and propose that it be renamed rsmE.

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“…Therefore, our finding that HemK, which shows high similarity to the ␥ subclass of DNA-(adenine-N6) MTases throughout the primary sequence of the catalytic domain (6), exhibits protein MTase activity was surprising. The group of DNA-(adenine-N6) MTase is a fairly large family and includes a few DNA-(cytosine-N4) and RNA-(guanine-N2) MTases (32,33), but no member of the family has been reported to methylate proteins. Considering the structural characteristics of the class 1 RFs, i.e., molecular mimicry of tRNA (34), the substrate recognition and catalytic mechanism of the HemK are very interesting from a molecular evolutionary standpoint.…”

Section: Discussionmentioning

confidence: 99%

HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination

Nakahigashi

Kubo

Narita

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

115

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HemK, a universally conserved protein of unknown function, has high amino acid similarity with DNA-(adenine-N6) methyl transferases (MTases). A certain mutation in hemK gene rescues the photosensitive phenotype of a ferrochelatase-deficient (hemH) mutant in Escherichia coli. A hemK knockout strain of E. coli not only suffered severe growth defects, but also showed a global shift in gene expression to anaerobic respiration, as determined by microarray analysis, and this shift may lead to the abrogation of photosensitivity by reducing the oxidative stress. Suppressor mutations that abrogated the growth defects of the hemK knockout strain were isolated and shown to be caused by a threonine to alanine change at codon 246 of polypeptide chain release factor (RF) 2, indicating that hemK plays a role in translational termination. Consistent with such a role, the hemK knockout strain showed an enhanced rate of read-through of nonsense codons and induction of transfer-mRNA-mediated tagging of proteins within the cell. By analysis of the methylation of RF1 and RF2 in vivo and in vitro, we showed that HemK methylates RF1 and RF2 in vitro within the tryptic fragment containing the conserved GGQ motif, and that hemK is required for the methylation within the same fragment of, at least, RF1 in vivo. This is an example of a protein MTase containing the DNA MTase motif and also a protein-(glutamine-N5) MTase.

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Phylogenomic analysis of 16S rRNA:(guanine‐N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino‐methyltransferases

Cited by 41 publications

References 26 publications

Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA

Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA

Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family

HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination

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