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Aseev LV, Koledinskaya LS, Boni IV. Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023. Int J Mol Sci 2024; 25:2957. [PMID: 38474204 DOI: 10.3390/ijms25052957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein-protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. The extraribosomal activities of r-proteins have been studied over the decades. In the past decade, our understanding of r-protein functions has advanced significantly due to intensive studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis but also in little-explored bacterial species from various phyla. The aim of this review is to update information on the multiple functions of r-proteins in bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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Zhou YJ, Yang ML, He X, Gu HY, Ren JH, Cheng ST, Fu Z, Zhang ZZ, Chen J. RNA-binding protein RPS7 promotes hepatocellular carcinoma progression via LOXL2-dependent activation of ITGB1/FAK/SRC signaling. J Exp Clin Cancer Res 2024; 43:45. [PMID: 38326908 PMCID: PMC10851485 DOI: 10.1186/s13046-023-02929-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Metastasis is one of the leading cause contributes to treatment failure and poor prognosis of hepatocellular carcinoma (HCC) patients. The underlying mechanism of HCC metastasis remains to be determined. Although several RNA binding proteins (RBPs) have been found to participate in tumorigenesis and progression of liver cancer, the role of RBPs in HCC patients with extrahepatic metastases is poorly understood. METHODS By performing RNA-seq of primary HCC tissues (including HCC with extrahepatic metastasis and those did not develop metastasis), we identified a set of HCC metastasis-associated RBPs candidates. Among which, ribosomal protein S7 (RPS7) was found to be remarkably increased in HCC tissues and be strongly related to HCC poor survival. Overexpression or CRISPR-Cas9-mediated knockout were applied to investigate the role of RPS7 on the metastasis-associated phenotypes of HCC cells. RNA sequencing, RIP, RNA-pull down, dual luciferase reporter assay, nascent RNA capture assay, and RNA decay and so on, were applied to reveal the underlying mechanism of RPS7 induced HCC metastasis. RESULTS Gain- and loss- of function analyses revealed that RPS7 promoted HCC cells adhesion, migration and invasion capabilities, as well as lung metastasis. Mechanistically, we uncovered that lysyl oxidase-like 2 (LOXL2) was a critical downstream target of RPS7. RPS7 could stabilize LOXL2 mRNA by binding to AUUUA motifs in the 3155-3375 region of the 3'UTR of LOXL2 mRNA, thus increased LOXL2 expression via elevating LOXL2 mRNA abundance. Further research revealed that LOXL2 could accelerate focal adhesion formation through maintaining the protein stability of ITGB1 and activating ITGB1-mediated FAK/SRC signaling pathway, and thereby contribute to the pro-metastasis effect of RPS7. CONCLUSIONS Taken together, our data reveal a novel function of RPS7 in HCC metastasis, also reveal the critical roles of the RPS7/LOXL2/ITGB1 axis in HCC metastasis and shed new light on the exploration of molecular drugs against HCC.
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Affiliation(s)
- Yu-Jiao Zhou
- Department of Infectious Disease, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, No.20 Jinyu Road, Yubei District, Chongqing, 401122, China
| | - Min-Li Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xin He
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hui-Ying Gu
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ji-Hua Ren
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Sheng-Tao Cheng
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhou Fu
- Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory of Child Development and Disorders, and the Department of Respiratory Diseases, The Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhen-Zhen Zhang
- Department of Infectious Disease, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, No.20 Jinyu Road, Yubei District, Chongqing, 401122, China.
| | - Juan Chen
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China.
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China.
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Tishchenko SV, Mikhailina AO, Lekontseva NV, Stolboushkina EA, Nikonova EY, Nikonov OS, Nikulin AD. Structural Investigations of RNA–Protein Complexes in Post-Ribosomal Era. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Structural studies of RNA–protein complexes are important for understanding many molecular mechanisms occurring in cells (e.g., regulation of protein synthesis and RNA-chaperone activity of proteins). Various objects investigated at the Institute of Protein Research of the Russian Academy of Sciences are considered. Based on the analysis of the structures of the complexes of the ribosomal protein L1 with specific regions on both mRNA and rRNA, the principles of regulation of the translation of the mRNA of its own operon are presented. The studies of the heterotrimeric translation initiation factor IF2 of archaea and eukaryotes are described, and the data on the interaction of glycyl-tRNA-synthetase with viral IRES are reported. The results of studying the interaction of RNA molecules with one of functionally important sites of the Hfq protein are presented, and the differences in the RNA-binding properties of the Hfq and archaeal Lsm proteins are revealed.
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Nikulin AD. Characteristic Features of Protein Interaction with Single- and Double-Stranded RNA. BIOCHEMISTRY (MOSCOW) 2021; 86:1025-1040. [PMID: 34488578 DOI: 10.1134/s0006297921080125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses differences between the specific protein interactions with single- and double-stranded RNA molecules using the data on the structure of RNA-protein complexes. Proteins interacting with the single-stranded RNAs form contacts with RNA bases, which ensures recognition of specific nucleotide sequences. Formation of such contacts with the double-stranded RNAs is hindered, so that the proteins recognize unique conformations of the RNA spatial structure and interact mainly with the RNA sugar-phosphate backbone.
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Affiliation(s)
- Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Mikhaylina AO, Nikonova EY, Kostareva OS, Piendl W, Erlacher M, Tishchenko SV. Characterization of Regulatory Elements of L11 and L1 Operons in Thermophilic Bacteria and Archaea. BIOCHEMISTRY (MOSCOW) 2021; 86:397-408. [PMID: 33941062 DOI: 10.1134/s0006297921040027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ribosomal protein L1 is a conserved two-domain protein that is involved in formation of the L1 stalk of the large ribosomal subunit. When there are no free binding sites available on the ribosomal 23S RNA, the protein binds to the specific site on the mRNA of its own operon (L11 operon in bacteria and L1 operon in archaea) preventing translation. Here we show that the regulatory properties of the r-protein L1 and its domain I are conserved in the thermophilic bacteria Thermus and Thermotoga and in the halophilic archaeon Haloarcula marismortui. At the same time the revealed features of the operon regulation in thermophilic bacteria suggest presence of two regulatory regions.
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Affiliation(s)
- Alisa O Mikhaylina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Ekaterina Y Nikonova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Olga S Kostareva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Wolfgang Piendl
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, 6020, Austria.
| | - Matthias Erlacher
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck, 6020, Austria.
| | - Svetlana V Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Kostareva OS, Nevskaya NA, Tishchenko SV, Gabdulkhakov AG, Garber MB, Nikonov SV. Influence of Nonconserved Regions of L1 Protuberance of Thermus thermophilus Ribosome on the Affinity of L1 Protein to 23s rRNA. Mol Biol 2018. [DOI: 10.1134/s0026893318010090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mikhaylina AO, Kostareva OS, Nikonova EY, Garber MB, Tishchenko SV. Identification of Ribosomal Protein L1-Binding Sites in Thermus thermophilus and Thermotoga maritima mRNAs. Mol Biol 2018. [DOI: 10.1134/s0026893318010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs. J Theor Biol 2016; 397:115-27. [DOI: 10.1016/j.jtbi.2016.02.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 11/18/2022]
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Ma L, Zhao W, Zheng Q, Chen T, Qi J, Li G, Tong T. Ribosomal L1 domain and lysine-rich region are essential for CSIG/ RSL1D1 to regulate proliferation and senescence. Biochem Biophys Res Commun 2015; 469:593-8. [PMID: 26686419 DOI: 10.1016/j.bbrc.2015.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 12/01/2015] [Indexed: 12/14/2022]
Abstract
The expression change of cellular senescence-associated genes is underlying the genetic foundation of cellular senescence. Using a suppressive subtractive hybridization system, we identified CSIG (cellular senescence-inhibited gene protein; RSL1D1) as a novel senescence-associated gene. CSIG is implicated in various process including cell cycle regulation, apoptosis, and tumor metastasis. We previously showed that CSIG plays an important role in regulating cell proliferation and cellular senescence progression through inhibiting PTEN, however, which domain or region of CSIG contributes to this function? To clarify this question, we investigated the functional importance of ribosomal L1 domain and lysine (Lys) -rich region of CSIG. The data showed that expression of CSIG potently reduced PTEN expression, increased cell proliferation rates, and reduced the senescent phenotype (lower SA-β-gal activity). By contrast, neither the expression of CSIG N- terminal (NT) fragment containing the ribosomal L1 domain nor C-terminal (CT) fragment containing Lys-rich region could significantly altered the levels of PTEN; instead of promoting cell proliferation and delaying cellular senescence, expression of CSIG-NT or CSIG-CT inhibited cell proliferation and accelerated cell senescence (increased SA-β-gal activity) compared to either CSIG over-expressing or control (empty vector transfected) cells. The further immunofluorescence analysis showed that CSIG-CT and CSIG-NT truncated proteins exhibited different subcellular distribution with that of wild-type CSIG. Conclusively, both ribosomal L1 domain and Lys-rich region of CSIG are critical for CSIG to act as a regulator of cell proliferation and cellular senescence.
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Affiliation(s)
- Liwei Ma
- Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing 100191, PR China
| | - Wenting Zhao
- Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing 100191, PR China
| | - Quanhui Zheng
- Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing 100191, PR China
| | - Tianda Chen
- Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing 100191, PR China
| | - Ji Qi
- Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing 100191, PR China
| | - Guodong Li
- Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing 100191, PR China
| | - Tanjun Tong
- Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing 100191, PR China.
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Studying the properties of domain I of the ribosomal protein l1: incorporation into ribosome and regulation of the l1 operon expression. Protein J 2015; 34:103-10. [PMID: 25681234 DOI: 10.1007/s10930-015-9602-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
L1 is a conserved protein of the large ribosomal subunit. This protein binds strongly to the specific region of the high molecular weight rRNA of the large ribosomal subunit, thus forming a conserved flexible structural element--the L1 stalk. L1 protein also regulates translation of the operon that comprises its own gene. Crystallographic data suggest that L1 interacts with RNA mainly by means of its domain I. We show here for the first time that the isolated domain I of the bacterial protein L1 of Thermus thermophilus and Escherichia coli is able to incorporate in vivo into the E. coli ribosome. Furthermore, domain I of T. thermophilus L1 can regulate expression of the L1 gene operon of Archaea in the coupled transcription-translation system in vitro, as well as the intact protein. We have identified the structural elements of domain I of the L1 protein that may be responsible for its regulatory properties.
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11
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Tishchenko S, Kostareva O, Gabdulkhakov A, Mikhaylina A, Nikonova E, Nevskaya N, Sarskikh A, Piendl W, Garber M, Nikonov S. Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions. ACTA ACUST UNITED AC 2015; 71:376-86. [PMID: 25664749 DOI: 10.1107/s1399004714026248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/29/2014] [Indexed: 11/10/2022]
Abstract
Ribosomal protein L1, as part of the L1 stalk of the 50S ribosomal subunit, is implicated in directing tRNA movement through the ribosome during translocation. High-resolution crystal structures of four mutants (T217V, T217A, M218L and G219V) of the ribosomal protein L1 from Thermus thermophilus (TthL1) in complex with a specific 80 nt fragment of 23S rRNA and the structures of two of these mutants (T217V and G219V) in the RNA-unbound form are reported in this work. All mutations are located in the highly conserved triad Thr-Met-Gly, which is responsible for about 17% of all protein-RNA hydrogen bonds and 50% of solvent-inaccessible intermolecular hydrogen bonds. In the mutated proteins without bound RNA the RNA-binding regions show substantial conformational changes. On the other hand, in the complexes with RNA the structures of the RNA-binding surfaces in all studied mutants are very similar to the structure of the wild-type protein in complex with RNA. This shows that formation of the RNA complexes restores the distorted surfaces of the mutant proteins to a conformation characteristic of the wild-type protein complex. Domain I of the mutated TthL1 and helix 77 of 23S rRNA form a rigid body identical to that found in the complex of wild-type TthL1 with RNA, suggesting that the observed relative orientation is conserved and is probably important for ribosome function. Analysis of the complex structures and the kinetic data show that the number of intermolecular contacts and hydrogen bonds in the RNA-protein contact area does not correlate with the affinity of the protein for RNA and cannot be used as a measure of affinity.
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Affiliation(s)
- Svetlana Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Olga Kostareva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Alisa Mikhaylina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Ekaterina Nikonova
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Natalia Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Alena Sarskikh
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Wolfgang Piendl
- Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Stanislav Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
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Kostareva O, Tishchenko S, Nikonova E, Kljashtorny V, Nevskaya N, Nikulin A, Sycheva A, Moshkovskii S, Piendl W, Garber M, Nikonov S. Disruption of shape complementarity in the ribosomal protein L1-RNA contact region does not hinder specific recognition of the RNA target site. J Mol Recognit 2010; 24:524-32. [DOI: 10.1002/jmr.1063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 04/05/2010] [Accepted: 05/22/2010] [Indexed: 11/11/2022]
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13
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Domain II of Thermus thermophilus ribosomal protein L1 hinders recognition of its mRNA. J Mol Biol 2008; 383:301-5. [PMID: 18778715 DOI: 10.1016/j.jmb.2008.08.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 08/19/2008] [Indexed: 10/21/2022]
Abstract
The two-domain ribosomal protein L1 has a dual function as a primary rRNA-binding ribosomal protein and as a translational repressor that binds its own mRNA. Here, we report the crystal structure of a complex between the isolated domain I of L1 from the bacterium Thermus thermophilus and a specific mRNA fragment from Methanoccocus vannielii. In parallel, we report kinetic characteristics measured for complexes formed by intact TthL1 and its domain I with the specific mRNA fragment. Although, there is a close similarity between the RNA-protein contact regions in both complexes, the association rate constant is higher in the case of the complex formed by the isolated domain I. This finding demonstrates that domain II hinders mRNA recognition by the intact TthL1.
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