ArticleNucleic acids research2012
Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
31 citing papers in PubMed, 45 citations in OpenAlex.
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- RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding.Chemical reviews · 2024Review
- The Genetic Code Assembles via Division and Fusion, Basic Cellular Events.Life (Basel, Switzerland) · 2023Article
- Screening for Primordial RNA-Peptide Interactions Using High-Density Peptide Arrays.Life (Basel, Switzerland) · 2023Article
- Widespread autogenous mRNA-protein interactions detected by CLIP-seq.Nucleic acids research · 2022Article
- Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses.Nucleic acids research · 2022Article
- Driving forces in the origins of life.Open biology · 2021Article
- RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcriptionTranscription · 2020Article
- Frameshifting preserves key physicochemical properties of proteins.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences.Nucleic acids research · 2019Article
- RNA-protein interactions in an unstructured context.FEBS letters · 2018Review
- Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states.Biology direct · 2017Article
- Fuento: functional enrichment for bioinformatics.Bioinformatics (Oxford, England) · 2017Article
- mRNA/protein sequence complementarity and its determinants: The impact of affinity scales.PLoS computational biology · 2017Article
- Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence.Biology direct · 2017Review
- Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding.Scientific reports · 2015Article
- Malleable nature of mRNA-protein compositional complementarity and its functional significance.Nucleic acids research · 2015Article
- Revealing the density of encoded functions in a viral RNA.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
A potential connection between physico-chemical properties of mRNAs and cognate proteins, with implications concerning both the origin of the genetic code and mRNA-protein interactions, is unexplored. We compare pyrimidine content of naturally occurring mRNA coding sequences with the propensity of cognate protein sequences to interact with pyrimidines. The latter is captured by polar requirement, a measure of solubility of amino acids in aqueous solutions of pyridines, heterocycles closely related to pyrimidines. We find that the higher the pyrimidine content of an mRNA, the stronger the average propensity of its cognate protein's amino acids to interact with pyridines. Moreover, window-averaged pyrimidine profiles of individual mRNAs strongly mirror polar-requirement profiles of cognate protein sequences. For example, 4953 human proteins exhibit a correlation between the two with |R| > 0.8. In other words, pyrimidine-rich mRNA regions quantitatively correspond to regions in cognate proteins containing residues soluble in pyrimidine mimetics and vice versa. Finally, by studying randomized genetic code variants we show that the universal genetic code is highly optimized to preserve these correlations. Overall, our findings redefine the stereo-chemical hypothesis concerning code's origin and provide evidence of direct complementary interactions between mRNAs and cognate proteins before development of ribosomal decoding, but also presently, especially if both are unstructured.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.