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Sosorev AY, Parashchuk OD, Chicherin IV, Trubitsyn AA, Trukhanov VA, Baleva MV, Piunova UE, Kharlanov OG, Kamenski P, Paraschuk DY. Probing of nucleic acid compaction using low-frequency Raman spectroscopy. Phys Chem Chem Phys 2024; 26:17467-17475. [PMID: 38864440 DOI: 10.1039/d3cp05857c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Compaction of nucleic acids, namely DNA and RNA, determines their functions and involvement in vital cell processes including transcription, replication, DNA repair and translation. However, experimental probing of the compaction of nucleic acids is not straightforward. In this study, we suggest an approach for this probing using low-frequency Raman spectroscopy. Specifically, we show theoretically, computationally and experimentally the quantifiable correlation between the low-frequency Raman intensity from nucleic acids, magnitude of thermal fluctuations of atomic positions, and the compaction state of biomolecules. Noteworthily, we highlight that the LF Raman intensity differs by an order of magnitude for different samples of DNA, and even for the same sample in the course of long-term storage. The feasibility of the approach is further shown by assessment of the DNA compaction in the nuclei of plant cells. We anticipate that the suggested approach will enlighten compaction of nucleic acids and their dynamics during the key processes of the cell life cycle and under various factors, facilitating advancement of molecular biology and medicine.
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Affiliation(s)
- Andrey Yu Sosorev
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
- Enikolopov Institute of Synthetic Polymeric Materials, Russian Academy of Sciences, Profsoyuznaya 70, Moscow 117393, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, Moscow 117997, Russia
| | - Olga D Parashchuk
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
| | - Ivan V Chicherin
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia
| | - Artem A Trubitsyn
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
| | - Vasiliy A Trukhanov
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
| | - Maria V Baleva
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia
| | - Ulyana E Piunova
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia
| | - Oleg G Kharlanov
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia
| | - Dmitry Yu Paraschuk
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
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Levitskii SA, Baleva MV, Chicherin IV, Krasheninnikov IA, Kamenski PA. Protein Biosynthesis in Mitochondria: Past Simple, Present Perfect, Future Indefinite. BIOCHEMISTRY (MOSCOW) 2021; 85:257-263. [PMID: 32564730 DOI: 10.1134/s0006297920030013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mitochondria are obligate organelles of most eukaryotic cells that perform many different functions important for cellular homeostasis. The main role of mitochondria is supplying cells with energy in a form of ATP, which is synthesized in a chain of oxidative phosphorylation reactions on the organelle inner membrane. It is commonly believed now that mitochondria have the endosymbiotic origin. In the course of evolution, they have lost most of their genetic material as a result of genome reduction and gene transfer to the nucleus. The majority of mitochondrial proteins are synthesized in the cytosol and then imported to the mitochondria. However, almost all known mitochondria still contain genomes that are maintained and expressed. The processes of protein biosynthesis in the mitochondria - mitochondrial translation - substantially differs from the analogous processes in bacteria and the cytosol of eukaryotic cells. Mitochondrial translation is characterized by a high degree of specialization and specific regulatory mechanisms. In this review, we analyze available information on the common principles of mitochondrial translation with emphasis on the molecular mechanisms of translation initiation in the mitochondria of yeast and mammalian cells.
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Affiliation(s)
- S A Levitskii
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M V Baleva
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I V Chicherin
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I A Krasheninnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - P A Kamenski
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia.
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Yeast Mitochondrial Translation Initiation Factor 3 Interacts with Pet111p to Promote COX2 mRNA Translation. Int J Mol Sci 2020; 21:ijms21103414. [PMID: 32408541 PMCID: PMC7279496 DOI: 10.3390/ijms21103414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes code for several core components of respiratory chain complexes. Thus, mitochondrial translation is of great importance for the organelle as well as for the whole cell. In yeast, mitochondrial translation initiation factor 3, Aim23p, is not essential for the organellar protein synthesis; however, its absence leads to a significant quantitative imbalance of the mitochondrial translation products. This fact points to a possible specific action of Aim23p on the biosynthesis of some mitochondrial protein species. In this work, we examined such peculiar effects of Aim23p in relation to yeast mitochondrial COX2 mRNA translation. We show that Aim23p is indispensable to this process. According to our data, this is mediated by Aimp23p interaction with the known specific factor of the COX2 mRNA translation, Pet111p. If there is no Aim23p in the yeast cells, an increased amount of Pet111p ensures proper COX2 mRNA translation. Our results demonstrate the additional non-canonical function of initiation factor 3 in yeast mitochondrial translation.
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Derbikova K, Kuzmenko A, Levitskii S, Klimontova M, Chicherin I, Baleva MV, Krasheninnikov IA, Kamenski P. Biological and Evolutionary Significance of Terminal Extensions of Mitochondrial Translation Initiation Factor 3. Int J Mol Sci 2018; 19:ijms19123861. [PMID: 30518034 PMCID: PMC6321546 DOI: 10.3390/ijms19123861] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 01/14/2023] Open
Abstract
Protein biosynthesis in mitochondria is organized in a bacterial manner. However, during evolution, mitochondrial translation mechanisms underwent many organelle-specific changes. In particular, almost all mitochondrial translation factors, being orthologous to bacterial proteins, are characterized by some unique elements of primary or secondary structure. In the case of the organellar initiation factor 3 (IF3), these elements are several dozen amino acids long N- and C-terminal extensions. This study focused on the terminal extensions of baker's yeast mitochondrial IF3, Aim23p. By in vivo deletion and complementation analysis, we show that at least one extension is necessary for Aim23p function. At the same time, human mitochondrial IF3 is fully functional in yeast mitochondria even without both terminal extensions. While Escherichia coli IF3 itself is poorly active in yeast mitochondria, adding Aim23p terminal extensions makes the resulting chimeric protein as functional as the cognate factor. Our results show that the terminal extensions of IF3 have evolved as the "adaptors" that accommodate the translation factor of bacterial origin to the evolutionary changed protein biosynthesis system in mitochondria.
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Affiliation(s)
- Ksenia Derbikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Anton Kuzmenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
- Institute of Molecular Genetics, Russian Academy of Science, 119991 Moskva, Russia.
| | - Sergey Levitskii
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Maria Klimontova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
- Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany.
| | - Ivan Chicherin
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Maria V Baleva
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | | | - Piotr Kamenski
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
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