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

Nucleic Acids Research
Mario Hlevnjak, Bojan Zagrovic

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 f...Continue Reading

References

Apr 1, 1966·Proceedings of the National Academy of Sciences of the United States of America·C R WoeseS A Dugre
Sep 29, 1995·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·P M SharpJ F Peden
Sep 5, 1997·Science·F R BlattnerY Shao
Oct 2, 2003·Genome Biology·Douglas A HosackRichard A Lempicki
Dec 19, 2003·Nucleic Acids Research·M A HarrisUNKNOWN Gene Ontology Consortium
Dec 19, 2003·Nucleic Acids Research·Evelyn CamonRolf Apweiler
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Swaine L ChenHarley H McAdams
Dec 22, 2006·Bioinformatics·Isabelle RivalsMarie-Claude Potier
Apr 30, 2008·Journal of Molecular Evolution·Damien C Mathew, Zaida Luthey-Schulten
Jan 2, 2009·IUBMB Life·Eugene V Koonin, Artem S Novozhilov
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Apr 11, 2009·Science·Grzegorz KudlaJoshua B Plotkin
Oct 2, 2009·Journal of Molecular Evolution·Michael YarusRob Knight
Sep 3, 2010·Nature·Michael KerteszEran Segal
Oct 26, 2010·Nucleic Acids Research·Rasko LeinonenGuy Cochrane
Nov 26, 2010·Nature Reviews. Genetics·Joshua B Plotkin, Grzegorz Kudla
Nov 22, 2011·Nucleic Acids Research·UNKNOWN UniProt Consortium
Nov 30, 2011·Nucleic Acids Research·Emily C DimmerRolf Apweiler
Dec 12, 2012·Annals of Neurology·Lorraine V KaliaAnthony E Lang
May 8, 2013·Trends in Molecular Medicine·Angélique DeleersnijderVeerle Baekelandt
Jul 23, 2013·Nucleic Acids Research·Anton A Polyansky, Bojan Zagrovic
Dec 18, 2013·Science·Andrew B StergachisJohn A Stamatoyannopoulos
Jun 29, 2014·Biochimica Et Biophysica Acta·Dezerae CoxHeath Ecroyd

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Citations

Nov 28, 2015·Biology Direct·Anatoly D Altstein
Jul 28, 2017·PLoS Computational Biology·Lukas Bartonek, Bojan Zagrovic
Jun 1, 2018·FEBS Letters·Bojan ZagrovicAnton A Polyansky
Aug 3, 2017·Journal of Chemical Theory and Computation·Anita de RuiterBojan Zagrovic

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