title: Coding theory based models for protein translation initiation in prokaryotic organisms.
abstract: Our research explores the feasibility of using communication theory, error control (EC) coding theory specifically, for quantitatively modeling the protein translation initiation mechanism. The messenger RNA (mRNA) of Escherichia coli K-12 is modeled as a noisy (errored), encoded signal and the ribosome as a minimum Hamming distance decoder, where the 16S ribosomal RNA (rRNA) serves as a template for generating a set of valid codewords (the codebook). We tested the E. coli based coding models on 5' untranslated leader sequences of prokaryotic organisms of varying taxonomical relation to E. coli including: Salmonella typhimurium LT2, Bacillus subtilis, and Staphylococcus aureus Mu50. The model identified regions on the 5' untranslated leader where the minimum Hamming distance values of translated mRNA sub-sequences and non-translated genomic sequences differ the most. These regions correspond to the Shine-Dalgarno domain and the non-random domain. Applying the EC coding-based models to B. subtilis, and S. aureus Mu50 yielded results similar to those for E. coli K-12. Contrary to our expectations, the behavior of S. typhimurium LT2, the more taxonomically related to E. coli, resembled that of the non-translated sequence group.
authors.affiliation: Computational Biology Department, Sandia National Laboratories, Albuquerque, NM 87185, USA. eemay@sandia.vgov
authors.forename: Elebeoba E
authors.initials: EE
authors.lastname: May
authors.forename: Mladen A
authors.initials: MA
authors.lastname: Vouk
authors.forename: Donald L
authors.initials: DL
authors.lastname: Bitzer
authors.forename: David I
authors.initials: DI
authors.lastname: Rosnick
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics*; D005815:Genetic Code / Q000235:genetics*; D016680:Genome, Bacterial; D016247:Information Storage and Retrieval / Q000379:methods*; D007257:Information Theory; D008957:Models, Genetic; D016366:Open Reading Frames / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D001426:Bacterial Proteins