RPG: the Ribosomal Protein Gene database

Nakao, Akihiro; Yoshihama, Maki; Kenmochi, Naoya

doi:10.1093/nar/gkh004

Cited by 177 publications

(170 citation statements)

References 9 publications

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“…A valuable compilation of data on the ribosomal proteins and their genes in many organisms is available at http ://ribosome.med.miyazaki-u.ac.jp (Nakao et al 2004).…”

Section: Genes Encoding Ribosomal Proteins and Their Derivativesmentioning

confidence: 99%

Ribosome-omics of the human ribosome

Gupta

Warner

2014

RNA

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The torrent of RNA-seq data becoming available not only furnishes an overview of the entire transcriptome but also provides tools to focus on specific areas of interest. Our focus on the synthesis of ribosomes asked whether the abundance of mRNAs encoding ribosomal proteins (RPs) matched the equimolar need for the RPs in the assembly of ribosomes. We were at first surprised to find, in the mapping data of ENCODE and other sources, that there were nearly 100-fold differences in the level of the mRNAs encoding the different RPs. However, after correcting for the mapping ambiguities introduced by the presence of more than 2000 pseudogenes derived from RP mRNAs, we show that for 80%-90% of the RP genes, the molar ratio of mRNAs varies less than threefold, with little tissue specificity. Nevertheless, since the RPs are needed in equimolar amounts, there must be sluggish or regulated translation of the more abundant RP mRNAs and/or substantial turnover of unused RPs. In addition, seven of the RPs have subsidiary genes, three of which are pseudogenes that have been "rescued" by the introduction of promoters and/or upstream introns. Several of these are transcribed in a tissue-specific manner, e.g., RPL10L in testis and RPL3L in muscle, leading to potential variation in ribosome structure from one tissue to another. Of the 376 introns in the RP genes, a single one is alternatively spliced in a tissue-specific manner.

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“…A valuable compilation of data on the ribosomal proteins and their genes in many organisms is available at http ://ribosome.med.miyazaki-u.ac.jp (Nakao et al 2004).…”

Section: Genes Encoding Ribosomal Proteins and Their Derivativesmentioning

confidence: 99%

Ribosome-omics of the human ribosome

Gupta

Warner

2014

RNA

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“…Protein sequences of human RPL27, RPL37a and RPL41 were retrieved from Ribosomal Protein Gene (RPG) database [12]. The protein identifiers used are: NP_000979 for RPL27, NP_000989 for RPL37a and NP_001030344.1; NP_0667927.1 for RPL41.…”

Section: A Multiple Sequence Alignmentmentioning

confidence: 99%

Bioinformatics Analysis of the Ribosomal Proteins,RPL27, RPL37a and RPL41: 3-D Protein Modeling and Protein-protein Interaction Prediction

Chan¹,

Sim²

2013

IJBBB

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Abstract-Ribosomal proteins (RPs) are constituents of ribosome important for protein biosynthesis but likely to have extraribosomal functions. Many RPs are associated with various diseases and cancers. A previous study reported RPL27, RPL37a and RPL41 gene to be downregulated in nasopharyngeal carcinoma (NPC) derived cell lines compared to their normal counterpart. However, their actual physiological roles in organogenesis or tumorigenesis have not been properly defined. In this paper, we report on the findings of structural prediction of these three genes and infer their interactions with other proteins using structural neighbor prediction and molecular docking strategies. Our results revealed that RPL27 interact with SYNJ2 and UBC9. RPL27 is predicted to mediate RNA binding protein and deregulate sumolyation. RPL37a is suggested to interact with CTNNB1, SCMH1 and ATBF1. It is predicted to deregulate Wnt degradation pathway, inhibit β-catenin migration and regulate homeotic transcription. Our studies on RPL41 did not allow logical inference on possible interacting factors. Nevertheless, results on RPL27 and RPL37a provide rational data for the elucidation of their molecular activities.Index Terms-Protein modeling, extraribosomal functions, protein-protein interaction prediction, ribosomal protein.

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“…In 2004 seventy-nine distinct mammalian CRPs were identified. Their amino acid sequences and biochemical properties have been described (Nakao et al, 2004). At present, many CRPs and MRPs from different species have been identified (http://ribosome.miyazaki-med.ac.jp/).…”

Section: Introductionmentioning

confidence: 99%

Systematic identification of seven ribosomal protein genes in bighead carp and their expression in response to microcystin-LR

et al. 2016

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-Microcystin-LR (MCLR) is one of the most toxic cyanotoxins produced in algal blooms. The toxic effects of MCLR on the expression of some organelles genes (mitochondrion, endoplasmic reticulum, and cytoskeleton etc) have been widely investigated, but little is known how it impacts on the expression of ribosomal genes. In this study we identified seven ribosomal protein genes RPS6, RPS12, RPS24, RPS27a, RPL12, RPL27 and RPL29 in bighead carp (Aristichthys nobilis), whose expression was regulated by MCLR. The amino acid sequences of those 7 genes shared more than 90% identity with corresponding sequences from zebrafish, and were well conserved throughout evolution. The 3D structure prediction showed that the structures of these ribosomal proteins were conserved, but had species specificity. Q-PCR analysis revealed that expression of seven genes changed dramatically at 3 hr, then went back to a moderate change-level at 24 hr in almost all tested tissues (liver, kidney, intestine, heart, spleen and gill) post MCLR injection, but in brain expression of the seven genes stayed same as the normal level. This study will help us to know not only about the evolution and functions of ribosomal proteins in anti-MCLR response in bighead carp, but also about the MCLR toxicity and its impact on aquaculture and human health.

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RPG: the Ribosomal Protein Gene database

Cited by 177 publications

References 9 publications

Ribosome-omics of the human ribosome

Ribosome-omics of the human ribosome

Bioinformatics Analysis of the Ribosomal Proteins,RPL27, RPL37a and RPL41: 3-D Protein Modeling and Protein-protein Interaction Prediction

Systematic identification of seven ribosomal protein genes in bighead carp and their expression in response to microcystin-LR

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