ArticleNucleic acids research2012
How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 18 citations in OpenAlex.
- The critical function of the plastid rRNA methyltransferase, CMAL, in ribosome biogenesis and plant development.Nucleic acids research · 2020Article
- Mirror-Image 5S Ribonucleoprotein Complexes.Angewandte Chemie (International ed. in English) · 2020Article
- Comprehensive Functional Analysis ofFrontiers in genetics · 2020Article
- Screening of Potential Genes and Transcription Factors of Postoperative Cognitive Dysfunction via Bioinformatics Methods.Medical science monitor : international medical journal of experimental and clinical research · 2018Article
- E. coli metabolic protein aldehyde-alcohol dehydrogenase-E binds to the ribosome: a unique moonlighting action revealed.Scientific reports · 2016Article
- The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli.Journal of bacteriology · 2014Article
- Modified nucleotides m(2)G966/m(5)C967 of Escherichia coli 16S rRNA are required for attenuation of tryptophan operon.Scientific reports · 2013Article
- Impact of methylations of m2G966/m5C967 in 16S rRNA on bacterial fitness and translation initiation.Nucleic acids research · 2012Article
- 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 (New York, N.Y.) · 2012Article
- Regulation of translation by one-carbon metabolism in bacteria and eukaryotic organelles.The Journal of biological chemistryReview
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Modification of ribosomal RNA is ubiquitous among living organisms. Its functional role is well established for only a limited number of modified nucleotides. There are examples of rRNA modification involvement in the gene expression regulation in the cell. There is a need for large data set analysis in the search for potential functional partners for rRNA modification. In this study, we extracted phylogenetic profile, genome neighbourhood, co-expression and phenotype profile and co-purification data regarding Escherichia coli rRNA modification enzymes from public databases. Results were visualized as graphs using Cytoscape and analysed. Majority linked genes/proteins belong to translation apparatus. Among co-purification partners of rRNA modification enzymes are several candidates for experimental validation. Phylogenetic profiling revealed links of pseudouridine synthetases with RF2, RsmH with translation factors IF2, RF1 and LepA and RlmM with RdgC. Genome neighbourhood connections revealed several putative functionally linked genes, e.g. rlmH with genes coding for cell wall biosynthetic proteins and others. Comparative analysis of expression profiles (Gene Expression Omnibus) revealed two main associations, a group of genes expressed during fast growth and association of rrmJ with heat shock genes. This study might be used as a roadmap for further experimental verification of predicted functional interactions.
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