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      Malleable nature of mRNA-protein compositional complementarity and its functional significance

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      Nucleic Acids Research
      Oxford University Press

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          Abstract

          It has recently been demonstrated that nucleobase-density profiles of typical mRNA coding sequences exhibit a complementary relationship with nucleobase-interaction propensity profiles of their cognate protein sequences. This finding supports the idea that the genetic code developed in response to direct binding interactions between amino acids and appropriate nucleobases, but also suggests that present-day mRNAs and their cognate proteins may be physicochemically complementary to each other and bind. Here, we computationally recode complete Methanocaldococcus jannaschii, Escherichia coli and Homo sapiens mRNA transcriptomes and analyze how much complementary matching of synonymous mRNAs can vary, while keeping protein sequences fixed. We show that for most proteins there exist cognate mRNAs that improve, but also significantly worsen the level of native matching (e.g. by 1.8 viz. 7.6 standard deviations on average for H. sapiens, respectively), with the least malleable proteins in this sense being strongly enriched in nuclear localization and DNA-binding functions. Even so, we show that the majority of recodings for most proteins result in pronounced complementarity. Our results suggest that the genetic code was designed for favorable, yet tunable compositional complementarity between mRNAs and their cognate proteins, supporting the hypothesis that the interactions between the two were an important defining element behind the code's origin.

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          Most cited references21

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Reorganizing the protein space at the Universal Protein Resource (UniProt)

            The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. A key development at UniProt is the provision of complete, reference and representative proteomes. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.
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              Identifying biological themes within lists of genes with EASE.

              EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data. The biological themes returned by EASE recapitulate manually determined themes in previously published gene lists and are robust to varying methods of normalization, intensity calculation and statistical selection of genes. EASE is a powerful tool for rapidly converting the results of functional genomics studies from 'genes' to 'themes'.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                31 March 2015
                08 March 2015
                08 March 2015
                : 43
                : 6
                : 3012-3021
                Affiliations
                Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +43 1 4277 9522; Fax: +43 1 4277 9522; Email: bojan.zagrovic@ 123456univie.ac.at
                Article
                10.1093/nar/gkv166
                4381073
                25753660
                87ca5171-2a37-479c-ab7a-975ee41702e2
                © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 22 February 2015
                : 18 January 2015
                : 03 November 2014
                Page count
                Pages: 10
                Categories
                Computational Biology
                Custom metadata
                31 March 2015

                Genetics
                Genetics

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