دورية أكاديمية
أعرض في EDS

How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?

التفاصيل البيبلوغرافية
العنوان: How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?
المؤلفون: Sergiev PV; Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia. petya@genebee.msu.su, Golovina AY, Sergeeva OV, Osterman IA, Nesterchuk MV, Bogdanov AA, Dontsova OA
المصدر: Nucleic acids research [Nucleic Acids Res] 2012 Jul; Vol. 40 (12), pp. 5694-705. Date of Electronic Publication: 2012 Mar 12.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
أسماء مطبوعة: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
مواضيع طبية MeSH: Escherichia coli/*genetics , RNA, Bacterial/*metabolism , RNA, Ribosomal/*metabolism, Data Mining ; Enzymes/genetics ; Enzymes/isolation & purification ; Enzymes/metabolism ; Escherichia coli/enzymology ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/isolation & purification ; Escherichia coli Proteins/metabolism ; Gene Expression ; Gene Knockout Techniques ; Genes, Bacterial ; Genome, Bacterial ; Phenotype
مستخلص: 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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المشرفين على المادة: 0 (Enzymes)
0 (Escherichia coli Proteins)
0 (RNA, Bacterial)
0 (RNA, Ribosomal)
تواريخ الأحداث: Date Created: 20120314 Date Completed: 20121001 Latest Revision: 20211021
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC3384335
DOI: 10.1093/nar/gks219
PMID: 22411911
قاعدة البيانات: MEDLINE
الوصف
تدمد:1362-4962
DOI:10.1093/nar/gks219