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

Nucleic Acids Research
Mario Hlevnjak, Bojan Zagrovic


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


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

❮ Previous
Next ❯


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

❮ Previous
Next ❯

Software Mentioned


Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.