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Eukaryotic Ribosomal Protein S5 of the 40S Subunit: Structure and Function. Int J Mol Sci 2023; 24:ijms24043386. [PMID: 36834797 PMCID: PMC9958902 DOI: 10.3390/ijms24043386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
The ribosomal protein RPS5 is one of the prime proteins to combine with RNA and belongs to the conserved ribosomal protein family. It plays a substantial role in the process of translation and also has some non-ribosome functions. Despite the enormous studies on the relationship between the structure and function of prokaryotic RPS7, the structure and molecular details of the mechanism of eukaryotic RPS5 remain largely unexplored. This article focuses on the structure of RPS5 and its role in cells and diseases, especially the binding to 18S rRNA. The role of RPS5 in translation initiation and its potential use as targets for liver disease and cancer are discussed.
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Arrangements of nucleotides flanking the start codon in the IRES of the hepatitis C virus in the IRES binary complex with the human 40S ribosomal subunit. Biochimie 2018; 148:72-79. [PMID: 29501734 DOI: 10.1016/j.biochi.2018.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/26/2018] [Indexed: 01/09/2023]
Abstract
Genomic RNA of hepatitis C virus (HCV) has an internal ribosome entry site (IRES), a specific highly structured fragment responsible for its non-canonical translation initiation. The HCV IRES contains a major part of the 5'-untranslated region of the viral RNA and a small portion of the open reading frame (ORF). At the first step of initiation, IRES directly binds to 40S ribosomal subunits so that the AUG start codon appears at the P site region without scanning and without involving initiation factors. However, it is still not entirely clear whether the IRES ORF is correctly loaded into the 40S ribosomal mRNA binding channel in the resulting binary complex. To address this issue, we applied site-directed cross-linking using HCV IRES derivatives bearing a perfluorophenyl azide cross-linker at nucleotides in definite positions relative to the adenine of the AUG start codon. We found that the modifier at the IRES position -3 cross-links to ribosomal proteins uS11 and eS26. These proteins have been identified together with uS7 as those interacting with the mRNA nucleotide in position -3 relative to the first nucleotide of the codon directed to the P site by a cognate tRNA. Thus, our results indicate a certain difference in the locations of the above parts of HCV IRES and canonical mRNAs on 40S subunits. The modifier at the IRES positions +4/5 was attached to uS19, which is specific for ribosomal complexes with the P site tRNA and similar derivatives of model canonical mRNAs when the modifier is in the same positions. However, the cross-linking efficiency of the IRES derivative was drastically lower than that previously observed with derivatives of model mRNAs. This implies that the IRES ORF portion is correctly loaded into the mRNA binding channel only in a tiny fraction of the binary complexes.
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Mailliot J, Martin F. Viral internal ribosomal entry sites: four classes for one goal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9. [PMID: 29193740 DOI: 10.1002/wrna.1458] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/19/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]
Abstract
To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m7 G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. WIREs RNA 2018, 9:e1458. doi: 10.1002/wrna.1458 This article is categorized under: Translation > Ribosome Structure/Function Translation > Translation Mechanisms RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Justine Mailliot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Illkirch-Graffenstaden, France
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN" CNRS UPR9002, Université De Strasbourg, Strasbourg, France
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Xin Z, Jin C, Chao L, Zheng Z, Liehu C, Panpan P, Weizong W, Xiao Z, Qingjie Z, Honggang H, Longjuan Q, Xiao C, Jiacan S. A Matrine Derivative M54 Suppresses Osteoclastogenesis and Prevents Ovariectomy-Induced Bone Loss by Targeting Ribosomal Protein S5. Front Pharmacol 2018; 9:22. [PMID: 29441015 PMCID: PMC5797611 DOI: 10.3389/fphar.2018.00022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/08/2018] [Indexed: 02/02/2023] Open
Abstract
Post-menopausal osteoporosis (PMOP) is a metabolic bone disorder characterized by low bone mass and micro-architectural deterioration of bone tissue. The over-activated osteoclastogenesis, which plays an important role in osteoporosis, has become an important therapeutic target. M54 was a bioactive derivative of the Chinese traditional herb matrine. We found that M54 could suppress RANKL-induced osteoclastogenesis in bone marrow mononuclear cells and RAW264.7 cells through suppressing NF-κB, PI3K/AKT, and MAPKs pathways activity in vitro, and prevent ovariectomy-induced bone loss in vivo. Our previous study has proved that ribosomal protein S5 (RPS5) was a direct target of M19, based on which M54 was synthesized. Thus we deduced that M54 also targeted RPS5. During osteoclastogenesis, the RPS5 level in RAW264.7 cells was significantly down-regulated while M54 could maintain its level. After RPS5 was silenced, the inhibitory effects of M54 on osteoclastogenesis were partially compromised, indicating that M54 took effects through targeting RPS5. In summary, M54 was a potential clinical medicine for post-menopause osteoporosis treatment, and RPS5 is a possible key protein in PMOP.
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Affiliation(s)
- Zhi Xin
- Graduate Management Unit, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Cui Jin
- Graduate Management Unit, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Liu Chao
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Zhang Zheng
- Graduate Management Unit, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Cao Liehu
- Department of Orthopedics, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.,China-South Korea Bioengineering Center, Shanghai, China
| | - Pan Panpan
- Department of Orthopedics, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.,China-South Korea Bioengineering Center, Shanghai, China
| | - Weng Weizong
- Department of Orthopedics, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.,China-South Korea Bioengineering Center, Shanghai, China
| | - Zhai Xiao
- Department of Orthopedics, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhao Qingjie
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Hu Honggang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Qin Longjuan
- Orthopedic Basic and Translational Research Center, Jiangyin, China
| | - Chen Xiao
- Department of Orthopedics, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.,China-South Korea Bioengineering Center, Shanghai, China
| | - Su Jiacan
- Department of Orthopedics, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.,China-South Korea Bioengineering Center, Shanghai, China
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5
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Johnson AG, Grosely R, Petrov AN, Puglisi JD. Dynamics of IRES-mediated translation. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0177. [PMID: 28138065 DOI: 10.1098/rstb.2016.0177] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/19/2022] Open
Abstract
Viral internal ribosome entry sites (IRESs) are unique RNA elements, which use stable and dynamic RNA structures to recruit ribosomes and drive protein synthesis. IRESs overcome the high complexity of the canonical eukaryotic translation initiation pathway, often functioning with a limited set of eukaryotic initiation factors. The simplest types of IRESs are typified by the cricket paralysis virus intergenic region (CrPV IGR) and hepatitis C virus (HCV) IRESs, both of which independently form high-affinity complexes with the small (40S) ribosomal subunit and bypass the molecular processes of cap-binding and scanning. Owing to their simplicity and ribosomal affinity, the CrPV and HCV IRES have been important models for structural and functional studies of the eukaryotic ribosome during initiation, serving as excellent targets for recent technological breakthroughs in cryogenic electron microscopy (cryo-EM) and single-molecule analysis. High-resolution structural models of ribosome : IRES complexes, coupled with dynamics studies, have clarified decades of biochemical research and provided an outline of the conformational and compositional trajectory of the ribosome during initiation. Here we review recent progress in the study of HCV- and CrPV-type IRESs, highlighting important structural and dynamics insights and the synergy between cryo-EM and single-molecule studies.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Alex G Johnson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Alexey N Petrov
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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Chen X, Zhi X, Cao L, Weng W, Pan P, Hu H, Liu C, Zhao Q, Zhou Q, Cui J, Su J. Matrine derivate MASM uncovers a novel function for ribosomal protein S5 in osteoclastogenesis and postmenopausal osteoporosis. Cell Death Dis 2017; 8:e3037. [PMID: 28880271 PMCID: PMC5636967 DOI: 10.1038/cddis.2017.394] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/09/2017] [Accepted: 07/11/2017] [Indexed: 02/08/2023]
Abstract
Postmenopausal osteoporosis (POMP) is a public health problem characterized by decreased bone density and increased fracture risk. Over-activated osteoclastogenesis plays a vital role in POMP. Here we developed a novel bioactive compound MASM (M19) based on sophocarpine. Although it showed no significant effects on osteogenesis and adipogenesis for bone marrow-derived mesenchymal stem cells (BMSCs) in vitro, it could significantly inhibit RANKL/M-CSF induced osteoclastogenesis through suppressing NF-κB, MAPKs and PI3K/Akt pathways in vitro and ameliorate bone loss in ovariectomized mice in vivo. Ribosomal protein s5 (RPS5) has been identified as a target of M19 and regulates PI3K/Akt, NF-κB and MAPKs pathways in osteoclastogenesis. Overexpressions of RPS5 synergistically inhibited osteoclastogenesis with M19 while silencing RPS5 compromised M19 inhibitory effects on osteoclastogenesis in vitro. Among the three pathways, Akt plays a major role in M19 effects. The Akt activator SC79 partially reversed the inhibitory effects on osteoclastogenesis by M19 and RPS5-knocking-down. It indicates that RPS5 serves as a potential candidate target for inhibiting osteoclastogenesis and osteoporosis therapy and M19 is a promising agent for POMP treatment.
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Affiliation(s)
- Xiao Chen
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Second Military Medical University, Yangpu District, Shanghai 200433, China.,China-South Korea Bioengineering Center, Jiading District, Shanghai 201802, China
| | - Xin Zhi
- Graduate Management Unit, Shanghai Changhai Hospital, Second Military Medical University, Yangpu District, Shanghai 200433, China
| | - Liehu Cao
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Second Military Medical University, Yangpu District, Shanghai 200433, China.,China-South Korea Bioengineering Center, Jiading District, Shanghai 201802, China
| | - Weizong Weng
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Second Military Medical University, Yangpu District, Shanghai 200433, China.,China-South Korea Bioengineering Center, Jiading District, Shanghai 201802, China
| | - Panpan Pan
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Second Military Medical University, Yangpu District, Shanghai 200433, China.,China-South Korea Bioengineering Center, Jiading District, Shanghai 201802, China
| | - Honggang Hu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Chao Liu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Qingjie Zhao
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Qirong Zhou
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Second Military Medical University, Yangpu District, Shanghai 200433, China.,China-South Korea Bioengineering Center, Jiading District, Shanghai 201802, China
| | - Jin Cui
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Second Military Medical University, Yangpu District, Shanghai 200433, China.,China-South Korea Bioengineering Center, Jiading District, Shanghai 201802, China
| | - Jiacan Su
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Second Military Medical University, Yangpu District, Shanghai 200433, China.,China-South Korea Bioengineering Center, Jiading District, Shanghai 201802, China
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Kolekar P, Pataskar A, Kulkarni-Kale U, Pal J, Kulkarni A. IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES). Sci Rep 2016; 6:27436. [PMID: 27264539 PMCID: PMC4893748 DOI: 10.1038/srep27436] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 05/17/2016] [Indexed: 02/06/2023] Open
Abstract
Cellular mRNAs are predominantly translated in a cap-dependent manner. However, some viral and a subset of cellular mRNAs initiate their translation in a cap-independent manner. This requires presence of a structured RNA element, known as, Internal Ribosome Entry Site (IRES) in their 5′ untranslated regions (UTRs). Experimental demonstration of IRES in UTR remains a challenging task. Computational prediction of IRES merely based on sequence and structure conservation is also difficult, particularly for cellular IRES. A web server, IRESPred is developed for prediction of both viral and cellular IRES using Support Vector Machine (SVM). The predictive model was built using 35 features that are based on sequence and structural properties of UTRs and the probabilities of interactions between UTR and small subunit ribosomal proteins (SSRPs). The model was found to have 75.51% accuracy, 75.75% sensitivity, 75.25% specificity, 75.75% precision and Matthews Correlation Coefficient (MCC) of 0.51 in blind testing. IRESPred was found to perform better than the only available viral IRES prediction server, VIPS. The IRESPred server is freely available at http://bioinfo.net.in/IRESPred/.
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Affiliation(s)
- Pandurang Kolekar
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, 411 007, India
| | - Abhijeet Pataskar
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, 411 007, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, 411 007, India
| | - Jayanta Pal
- Department of Biotechnology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, 411 007, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, 411 007, India
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8
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Yamamoto H, Collier M, Loerke J, Ismer J, Schmidt A, Hilal T, Sprink T, Yamamoto K, Mielke T, Bürger J, Shaikh TR, Dabrowski M, Hildebrand PW, Scheerer P, Spahn CMT. Molecular architecture of the ribosome-bound Hepatitis C Virus internal ribosomal entry site RNA. EMBO J 2015; 34:3042-58. [PMID: 26604301 DOI: 10.15252/embj.201592469] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/29/2015] [Indexed: 12/12/2022] Open
Abstract
Internal ribosomal entry sites (IRESs) are structured cis-acting RNAs that drive an alternative, cap-independent translation initiation pathway. They are used by many viruses to hijack the translational machinery of the host cell. IRESs facilitate translation initiation by recruiting and actively manipulating the eukaryotic ribosome using only a subset of canonical initiation factor and IRES transacting factors. Here we present cryo-EM reconstructions of the ribosome 80S- and 40S-bound Hepatitis C Virus (HCV) IRES. The presence of four subpopulations for the 80S•HCV IRES complex reveals dynamic conformational modes of the complex. At a global resolution of 3.9 Å for the most stable complex, a derived atomic model reveals a complex fold of the IRES RNA and molecular details of its interaction with the ribosome. The comparison of obtained structures explains how a modular architecture facilitates mRNA loading and tRNA binding to the P-site. This information provides the structural foundation for understanding the mechanism of HCV IRES RNA-driven translation initiation.
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Affiliation(s)
- Hiroshi Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Marianne Collier
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Jochen Ismer
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Andrea Schmidt
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Thiemo Sprink
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Kaori Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tanvir R Shaikh
- Structural Biology Programme, CEITEC, Masaryk University, Brno, Czech Republic
| | - Marylena Dabrowski
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Peter W Hildebrand
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Patrick Scheerer
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
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9
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Mauro VP, Matsuda D. Translation regulation by ribosomes: Increased complexity and expanded scope. RNA Biol 2015; 13:748-55. [PMID: 26513496 DOI: 10.1080/15476286.2015.1107701] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The primary function of ribosomes is to decode mRNAs into polypeptide chains; however, this description is overly simplistic. Accumulating evidence shows that ribosomes themselves can affect the relative efficiency with which various mRNAs are translated and indicates that these effects can be modulated by ribosome heterogeneity. The notion that ribosomes have regulatory capabilities was elaborated more than a decade ago in the ribosome filter hypothesis. Various lines of evidence support this idea and have shown that the translation of some mRNAs is affected by discrete binding interactions with rRNA or ribosomal proteins. Recent work from our laboratory has demonstrated that base-pairing of the Hepatitis C Virus (HCV) internal ribosome entry site (IRES) to 18S rRNA is required for IRES function, but only in the context of more complex ribosomal interactions. The HCV IRES provides an example of the ribosome filter that involves multiple binding interactions between mRNAs and ribosomal subunits.
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Affiliation(s)
- Vincent P Mauro
- a Promosome, LLC , San Diego , CA , USA.,b The Scripps Research Institute , La Jolla , CA , USA
| | - Daiki Matsuda
- b The Scripps Research Institute , La Jolla , CA , USA
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10
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Bhat P, Shwetha S, Sharma DK, Joseph AP, Srinivasan N, Das S. The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function. Nucleic Acids Res 2015; 43:2888-901. [PMID: 25712089 PMCID: PMC4357715 DOI: 10.1093/nar/gkv110] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Translation initiation in Hepatitis C Virus (HCV) is mediated by Internal Ribosome Entry Site (IRES), which is independent of cap-structure and uses a limited number of canonical initiation factors. During translation initiation IRES–40S complex formation depends on high affinity interaction of IRES with ribosomal proteins. Earlier, it has been shown that ribosomal protein S5 (RPS5) interacts with HCV IRES. Here, we have extensively characterized the HCV IRES–RPS5 interaction and demonstrated its role in IRES function. Computational modelling and RNA–protein interaction studies demonstrated that the beta hairpin structure within RPS5 is critically required for the binding with domains II and IV. Mutations disrupting IRES–RPS5 interaction drastically reduced the 80S complex formation and the corresponding IRES activity. Computational analysis and UV cross-linking experiments using various IRES-mutants revealed interplay between domains II and IV mediated by RPS5. In addition, present study demonstrated that RPS5 interaction is unique to HCV IRES and is not involved in 40S–3′ UTR interaction. Further, partial silencing of RPS5 resulted in preferential inhibition of HCV RNA translation. However, global translation was marginally affected by partial silencing of RPS5. Taken together, results provide novel molecular insights into IRES–RPS5 interaction and unravel its functional significance in mediating internal initiation of translation.
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Affiliation(s)
- Prasanna Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Shivaprasad Shwetha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Divya Khandige Sharma
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | | | | | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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11
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Graifer D, Karpova G. Roles of ribosomal proteins in the functioning of translational machinery of eukaryotes. Biochimie 2015; 109:1-17. [DOI: 10.1016/j.biochi.2014.11.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/18/2014] [Indexed: 11/16/2022]
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