ArticleProceedings of the National Academy of Sciences of the United States of America2009
Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 92 citations in OpenAlex.
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- Highly Multiplexed Spatial Transcriptomics in Bacteria.bioRxiv : the preprint server for biology · 2024Article
- The high-density lipoprotein binding protein HDLBP is an unusual RNA-binding protein with multiple roles in cancer and disease.RNA biology · 2024Review
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- mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria.Cell reports · 2023Article
- Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains.Molecular biology and evolution · 2023Article
- A survey of lineage-specific genes inPlant direct · 2023Article
- HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins.Nature communications · 2022Article
- Dynamics of Bacterial Signal Recognition Particle at a Single Molecule Level.Frontiers in microbiology · 2021Article
- Records of RNA locations in living yeast revealed through covalent marks.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Posttranslational insertion of small membrane proteins by the bacterial signal recognition particle.PLoS biology · 2020Article
- Mechanisms and consequences of subcellular RNA localization across diverse cell types.Traffic (Copenhagen, Denmark) · 2020Review
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises.Frontiers in microbiology · 2020Review
- VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences.Nucleic acids research · 2019Article
- A secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis.PLoS genetics · 2019Article
- Interplay between coding and exonic splicing regulatory sequences.Genome research · 2019Article
- Vesicles FromFrontiers in microbiology · 2019Article
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Posttranscriptional processes often involve specific signals in mRNAs. Because mRNAs of integral membrane proteins across evolution are usually translated at distinct locations, we searched for universally conserved specific features in this group of mRNAs. Our analysis revealed that codons of very hydrophobic amino acids, highly represented in integral membrane proteins, are composed of 50% uracils (U). As expected from such a strong U bias, the calculated U profiles of mRNAs closely resemble the hydrophobicity profiles of their encoded proteins and may designate genes encoding integral membrane proteins, even in the absence of information on ORFs. We also show that, unexpectedly, the U-richness phenomenon is not merely a consequence of the codon composition of very hydrophobic amino acids, because counterintuitively, the relatively hydrophilic serine and tyrosine, also encoded by U-rich codons, are overrepresented in integral membrane proteins. Interestingly, although the U-richness phenomenon is conserved, there is an evolutionary trend that minimizes usage of U-rich codons. Taken together, the results suggest that U-richness is an evolutionarily ancient feature of mRNAs encoding integral membrane proteins, which might serve as a physiologically relevant distinctive signature to this group of mRNAs.
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