Finding Missing tRNA Modification Genes: A Comparative Genomics Goldmine

Crécy‐Lagard, Valérie de

doi:10.1007/978-3-540-74268-5_8

Cited by 6 publications

(5 citation statements)

References 99 publications

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“…In our hands, YibK and LasT have no activity on the position 34 in tRNA Leu5 [30], which further narrows down the prediction of this activity for YgdE or YfiF. Interestingly, the yfiF gene has been independently analyzed by de Crecy-Lagard and predicted to encode a tRNA:m 2 A37 MTase (TrmG) [44] based on the similarity of its genomic location (58 min of the E. coli chromosome) with the location experimentally determined for the trmG gene (56–61 min) [45]. While we cannot exclude the possibility that YfiF is involved in m 2 A methylation, we would like to note that methylation of an endocyclic carbon atom (C2 in m 2 A) is chemically more difficult than methylation of ribose or of an exocyclic amino group, and may require a different mechanism, such as formation of a covalent protein-nucleic acid intermediate that has been observed in m 5 U or m 5 C MTases acting on RNA or DNA [46].…”

Section: Resultsmentioning

confidence: 84%

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

et al. 2007

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Background: SPOUT methyltransferases (MTases) are a large class of S-adenosyl-L-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. In 2001, when no crystal structures were available for any of these proteins, Anantharaman, Koonin, and Aravind identified homology between SpoU and TrmD MTases and defined the SPOUT superfamily. Since then, multiple crystal structures of knotted MTases have been solved and numerous new homologous sequences appeared in the databases. However, no comprehensive comparative analysis of these proteins has been carried out to classify them based on structural and evolutionary criteria and to guide functional predictions.

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Section: Resultsmentioning

confidence: 84%

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

et al. 2007

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“…As a part of a large-scale project aiming at identification of new RNA MTases ( 33 ) we searched for families from the RFM superfamily ( 34 ), whose pattern of phylogenetic occurrence, as indicated in the COG database ( 35 ), exhibited similarity to patterns of occurrence of known RNA methylations without known enzymes ( 1 , 36 ). In the course of this analysis, we identified the COG2384 family as potential candidates for the so far uncharacterized enzymes responsible for the biosynthesis of m 1 A modification present at the position 22 of tRNA Ser and tRNA Tyr in B. subtilis and M. capricolum , but not present in E. coli , Mycobacteria and Archaea [among organisms, for which tRNA sequences are available ( 3 )].…”

Section: Resultsmentioning

confidence: 99%

The YqfN protein of Bacillus subtilis is the tRNA: m 1 A22 methyltransferase (TrmK)

Roovers

Kamińska

Tkaczuk

et al. 2008

Nucleic Acids Research

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N1-methylation of adenosine to m1A occurs in several different positions in tRNAs from various organisms. A methyl group at position N1 prevents Watson–Crick-type base pairing by adenosine and is therefore important for regulation of structure and stability of tRNA molecules. Thus far, only one family of genes encoding enzymes responsible for m1A methylation at position 58 has been identified, while other m1A methyltransferases (MTases) remain elusive. Here, we show that Bacillus subtilis open reading frame yqfN is necessary and sufficient for N1-adenosine methylation at position 22 of bacterial tRNA. Thus, we propose to rename YqfN as TrmK, according to the traditional nomenclature for bacterial tRNA MTases, or TrMet(m1A22) according to the nomenclature from the MODOMICS database of RNA modification enzymes. tRNAs purified from a ΔtrmK strain are a good substrate in vitro for the recombinant TrmK protein, which is sufficient for m1A methylation at position 22 as are tRNAs from Escherichia coli, which natively lacks m1A22. TrmK is conserved in Gram-positive bacteria and present in some Gram-negative bacteria, but its orthologs are apparently absent from archaea and eukaryota. Protein structure prediction indicates that the active site of TrmK does not resemble the active site of the m1A58 MTase TrmI, suggesting that these two enzymatic activities evolved independently.

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“…It is suggested that YfiF may be a methyltransferase [2] and a member of the SPOUT family, having the activity of methyltransferase [3]. TrmL is a methyltransferase that catalyzes 2ʹ‐O methylation at the nucleotide 34 in tRNA Leu CmAA and tRNA Leu cmnm5UmAA [59].…”

Section: Discussionmentioning

confidence: 99%

“…The Escherichia coli genome contains 4499 genes totally, but the function of approximately 240 genes including yfiF are unknown [1]. YfiF is predicted as a methyltransferase of tRNA m 2 A37, termed TrmG [2], a member of the SPOUT family and has the activity of methyltransferase using bioinformatics analysis [3]. Further, YfiF belongs to proteins associated with ribosomes by isotope labeling method and immunoblotting [4].…”

Section: Introductionmentioning

confidence: 99%

YfiF, an unknown protein, affects initiation timing of chromosome replication in Escherichia coli

Gezi

et al. 2021

J Basic Microbiol

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The Escherichia coli YfiF protein is functionally unknown, being predicted as a transfer RNA/ribosomal RNA (tRNA/rRNA) methyltransferase. We find that absence of the yfiF gene delays initiation of chromosome replication and the delay is reversed by ectopic expression of YfiF, whereas excess YfiF causes an early initiation. A slight decrease in both cell size and number of origin per mass is observed in ΔyfiF cells. YfiF does not genetically interact with replication proteins such as DnaA, DnaB, and DnaC. Interestingly, YfiF is associated with ribosome modulation factor (RMF), hibernation promotion factor (HPF), and the tRNA methyltransferase TrmL. Defects in replication initiation of Δrmf, Δhpf, and ΔtrmL can be rescued by overexpression of YfiF, indicating that YfiF is functionally identical to RMF, HPF, and TrmL in terms of replication initiation. Also, YfiF interacts with the rRNA methyltransferase RsmC. Moreover, the total amount of proteins and DnaA content per cell decreases or increases in the absence of YfiF or the presence of excess YfiF. These facts suggest that YfiF is a ribosomal dormancy‐like factor, affecting ribosome function. Thus, we propose that YfiF is involved in the correct timing of chromosome replication by changing the DnaA content per cell as a result of affecting ribosome function.

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Finding Missing tRNA Modification Genes: A Comparative Genomics Goldmine

Cited by 6 publications

References 99 publications

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

The YqfN protein of Bacillus subtilis is the tRNA: m 1 A22 methyltransferase (TrmK)

YfiF, an unknown protein, affects initiation timing of chromosome replication in Escherichia coli

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