Kimura S, Suzuki T. 2010. Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res. 2010 Mar;38(4):1341-52.
Abstract
In bacterial 16S rRNAs, methylated nucleosides are clustered within the decoding center, and these nucleoside modifications are thought to modulate translational fidelity. The N(4), 2(prime)-O-dimethylcytidine (m(4)Cm) at position 1402 of the Escherichia coli 16S rRNA directly interacts with the P-site codon of the mRNA. The biogenesis and function of this modification remain unclear. We have identified two previously uncharacterized genes in E. coli that are required for m(4)Cm formation. mraW (renamed rsmH) and yraL (renamed rsmI) encode methyltransferases responsible for the N(4) and 2'-O-methylations of C1402, respectively. Recombinant RsmH and RsmI proteins employed the 30S subunit (not the 16S rRNA) as a substrate to reconstitute m(4)Cm1402 in the presence of S-adenosylmethionine (Ado-Met) as the methyl donor, suggesting that m(4)Cm1402 is formed at a late step during 30S assembly in the cell. A luciferase reporter assay indicated that the lack of N(4) methylation of C1402 increased the efficiency of non-AUG initiation and decreased the rate of UGA read-through. These results suggest that m(4)Cm1402 plays a role in fine-tuning the shape and function of the P-site, thus increasing decoding fidelity. PMID: 19965768

References

Carrión M, Gómez MJ, Merchante-Schubert R, Dongarrá S, Ayala JA. 1999. mraW, an essential gene at the dcw cluster of Escherichia coli codes for a cytoplasmic protein with methyltransferase activity. Biochimie, 81(8-9):879-88. PMID: 10572301

Pucci MJ, Thanassi JA, Discotto LF, Kessler RE, Dougherty TJ. 1997. Identification and characterization of cell wall-cell division gene clusters in pathogenic gram-positive cocci. J Bacteriol, 179(17):5632-5. PMID: 9287029

Organization and transcription of the division cell wall (dcw) cluster in Neisseria gonorrhoeae.
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The division and cell wall gene cluster of Enterococcus hirae S185.
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Notes for the Plant-Prokaryote project research project:

At5g10910 is a S-adenosyl-L-methionine-dependent methyltransferase, highly homologous to ubiquitous bacterial methyltransferase MraW. Only recently (March 2010) the function for this highly conserved bacterial family was determined: Mraw (now renamed to RsmH) was shown to methylate 16S rRNA at the N4 position of C1402 nucleotide within the P site of the ribosome (Kimura et al., 2010).

In the same study At1g45110, the member of another conserved protein family shared between bacteria and plants (formerly annotated in SEED as "Tetrapyrrole (Corrin-Porphyrin) methylase family protein UPF0011") was shown to methylate 2(prime)-O-ribose at the same position C1402 of 16S rRNA (Kimura et al., 2010). These two families nearly always co-occur.

Observations for At5g10910:

1.At5g10910 is highly homologous to ubiquitous bacterial methyltransferase MraW (e-58, but shares only modest similarity with eukaryotic counterparts (e-16). It's best prokaryotic homologs occur in Actinobacteria (class), Firmicutes, Chlamydiae/Verrucomicrobia group, etc. Methyltransferase MraW is present (in a single copy) in the vast majority of bacterial genomes sequenced today (in 640 out of 725 analyzed), not present in Archaea

2. The MraW gene family is involved in highly conserved clustering with cell division and cell wall biosynthesis genes. This has been noted over a several years ago in SEED and also independently by several groups in different bacterial taxa: in Firmicutes (Pucci et al., 1997; Duez et al., 1998), Enterobacteriaceae (Carrión et al., 1999), Neisseriaceae (Francis et al., 2000), but no specific function has been determined at the time

3. MraW Methyltransferase was determined to be essential (under conditions tested) in Mycobacterium tuberculosis and Mycoplasma genitalium, but non-essential in E. coli, B. subtilis and P. aeruginosa

4. In Arabidopsis At5g10910 is targeted to chloroplast and is co-expressed with other chloroplast-targeted proteins: plastid transcriptionally active PTAC12 (At2g34640) and Embryo defective 2083, an ATP-dependent peptidase, which has significant similarity with bacterial cell division protein FtsH. This functional association parallels what is implicated by gene clustering in bacteria

Hypothesis: At5g10910 is a SAM-dependent methyltransferase, involved in a highly conserved cellular process, common to eubacteria and chloroplast, such cellular (plastid) division or transcription
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Observations for At1g45110:

1.At1g45110 is highly homologous (e-70) to ubiquitous hypothetical bacterial methyltransferase (formerly annotated in SEED as "Tetrapyrrole methylase family protein UPF0011"), but does not appear to have clear homologs in any eukaryotes other than plants. It's best prokaryotic homologs occur in cyanobacteria, Deltaproteobacteria, Bacteroidetes, etc. This methyltransferase is present (in a single copy) in the vast majority of bacterial genomes sequenced today (in ~600 out of 725 analyzed), not present in Archaea

2. This family is involved in highly conserved clustering in bacterial genomes with several genes controlling RNA modification and transcription (see SS:"Heat shock dnaK gene cluster" for details):
DNA replication intiation control protein YabA,
DNA polymerase III delta prime subunit,
COG4123: Predicted O-methyltransferase,
Ribosomal RNA small subunit methyltransferase E,
Ribonuclease PH
Chaperone proteins DnaJ and DnaK
Heat shock protein GrpE

3. In Arabidopsis At1g45110 is predicted to be targeted to chloroplast and/or mitochondria. It's co-expression pattern parallels functional association implicated by gene clustering in bacteria; as well as co-expression pattern of At5g10910 (see above):
- with plastid transcriptionally active PTAC11 (At2g02740, WRIRLY3)
- with DNAJ heat shock family protein (At3g17830)
- with RNA methyltransferase family protein (At3g21300)

Hypothesis: At1g45110 is a tetrapyrrole family methyltransferase, involved in a highly conserved cellular process, common to eubacteria and chloroplast (and mitochondria?), such as RNA modification (or transcription?)