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Pletnev P, Guseva E, Zanina A, Evfratov S, Dzama M, Treshin V, Pogorel'skaya A, Osterman I, Golovina A, Rubtsova M, Serebryakova M, Pobeguts OV, Govorun VM, Bogdanov AA, Dontsova OA, Sergiev PV. Comprehensive Functional Analysis of Escherichia coli Ribosomal RNA Methyltransferases. Front Genet 2020; 11:97. [PMID: 32174967 PMCID: PMC7056703 DOI: 10.3389/fgene.2020.00097] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 01/29/2020] [Indexed: 11/13/2022] Open
Abstract
Ribosomal RNAs in all organisms are methylated. The functional role of the majority of modified nucleotides is unknown. We systematically questioned the influence of rRNA methylation in Escherichia coli on a number of characteristics of bacterial cells with the help of a set of rRNA methyltransferase (MT) gene knockout strains from the Keio collection. Analysis of ribosomal subunits sedimentation profiles of the knockout strains revealed a surprisingly small number of rRNA MT that significantly affected ribosome assembly. Accumulation of the assembly intermediates was observed only for the rlmE knockout strain whose growth was retarded most significantly among other rRNA MT knockout strains. Accumulation of the 17S rRNA precursor was observed for rsmA(ksgA) knockout cells as well as for cells devoid of functional rsmB and rlmC genes. Significant differences were found among the WT and the majority of rRNA MT knockout strains in their ability to sustain exogenous protein overexpression. While the majority of the rRNA MT knockout strains supported suboptimal reporter gene expression, the strain devoid of the rsmF gene demonstrated a moderate increase in the yield of ectopic gene expression. Comparative 2D protein gel analysis of rRNA MT knockout strains revealed only minor perturbations of the proteome.
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Affiliation(s)
- Philipp Pletnev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ekaterina Guseva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Zanina
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey Evfratov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Margarita Dzama
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Vsevolod Treshin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra Pogorel'skaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ilya Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna Golovina
- Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Marina Serebryakova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V Pobeguts
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Alexey A Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia
| | - Olga A Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
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