A central fragment of ribosomal protein S26 containing the eukaryote-specific motif YxxPKxYxK is a key component of the ribosomal binding site of mRNA region 5' of the E site codon

Sharifulin, Dmitri E.; Khairulina, Yulia S.; Иванов, А. В.; Meschaninova, Mariya I.; Ven’yaminova, A. G.; Graifer, D. M.; Карпова, Г. Г.

doi:10.1093/nar/gkr1212

Cited by 21 publications

(29 citation statements)

References 37 publications

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“…Rps26 is positioned on the solvent side of the 40S platform and is a crucial component of the 40S ribosome-binding site for mRNA (Ben-Shem et al 2011;Sharifulin et al 2012). Available structural data show that the binding site of eIF3 on the 40S subunit overlaps with Rps26 as well as the other Upf1-interacting ribosomal proteins (Fig.…”

Section: Discussionmentioning

confidence: 99%

Yeast Upf1 CH domain interacts with Rps26 of the 40S ribosomal subunit

Min

Roy

Amrani

et al. 2013

RNA

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The central nonsense-mediated mRNA decay (NMD) regulator, Upf1, selectively targets nonsense-containing mRNAs for rapid degradation. In yeast, Upf1 preferentially associates with mRNAs that are NMD substrates, but the mechanism of its selective retention on these mRNAs has yet to be elucidated. Previously, we demonstrated that Upf1 associates with 40S ribosomal subunits. Here, we define more precisely the nature of this association using conventional and affinity-based purification of ribosomal subunits, and a two-hybrid screen to identify Upf1-interacting ribosomal proteins. Upf1 coimmunoprecipitates specifically with epitope-tagged 40S ribosomal subunits, and Upf1 association with high-salt washed or puromycin-released 40S subunits was found to occur without simultaneous eRF1, eRF3, Upf2, or Upf3 association. Two-hybrid analyses and in vitro binding assays identified a specific interaction between Upf1 and Rps26. Using mutations in domains of UPF1 known to be crucial for its function, we found that Upf1:40S association is modulated by ATP, and Upf1:Rps26 interaction is dependent on the N-terminal Upf1 CH domain. The specific association of Upf1 with the 40S subunit is consistent with the notion that this RNA helicase not only triggers rapid decay of nonsense-containing mRNAs, but may also have an important role in dissociation of the premature termination complex.

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Section: Discussionmentioning

confidence: 99%

Yeast Upf1 CH domain interacts with Rps26 of the 40S ribosomal subunit

Min

Roy

Amrani

et al. 2013

RNA

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“…[79][80][81] The ribosomal protein S26 lacking a eubacterial counterpart, Residue -base contacts (< 5Å distance) observed between 40s ribosomal proteins and the hcV IRes RNa, are listed is a key component of the ribosomal binding site of the mRNA region 5′ of the codon positioned at the exit site. 82 Cross-linking, gel digestion and mass spectroscopy experiments also suggest that IRES interacts with the 40S ribosomal proteins S3, S10, S14, S16, S18 and p40. [29][30][31][32]83 Most of these proteins are found in the vicinity of the IRES RNA (Fig.…”

Section: Discussionmentioning

confidence: 99%

Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA

2014

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In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.

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“…Rp uS3 is known as one of the main components of the mRNA entry site of the ribosome, therefore it has been suggested that cross-linking of mRNA analogs to this protein in the binary complexes takes place at the entry site [25,41]. However, in the ribosomal complexes containing P site bound tRNA cross-linking of the mRNA analogs to rp uS3 might happen in the very mRNA binding site.…”

Section: Peptides Of Rp Us3 Cross-linked To Mrna Analogsmentioning

confidence: 99%