title: Protein functional features are reflected in the patterns of mRNA translation speed.
abstract: BACKGROUND
  The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins.
  
  
  RESULTS
  We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features.
  
  
  CONCLUSIONS
  This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.
authors.affiliation: Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), c/ Darwin, 3, Madrid, 28049, Spain. dlopez@bacmine.com.|Current address: BacMine, S.L. c/ Santiago Grisolía, lab 151, Parque Científico de Madrid, Tres Cantos, Madrid, 28760, Spain. dlopez@bacmine.com.
authors.forename: Daniel
authors.initials: D
authors.lastname: López
authors.affiliation: Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), c/ Darwin, 3, Madrid, 28049, Spain. pazos@cnb.csic.es.
authors.forename: Florencio
authors.initials: F
authors.lastname: Pazos
mesh_terms: D020134:Catalytic Domain; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism*; D016678:Genome; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism; D015003:Yeasts / Q000235:genetics / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D012333:RNA, Messenger; D012343:RNA, Transfer