Coding theory based models for protein translation initiation in prokaryotic organisms.

Conference · Sat Mar 01 04:00:00 EST 2003

OSTI ID:917456

May, Elebeoba Eni; Bitzer, Donald L ^[1]; Rosnick, David I ^[2]; Vouk, Mladen A ^[3]

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1. North Carolina State University, Raleigh, NC
2. North Carolina State University, Raleigh, NC
3. North Carolina State University, Raleigh, NC

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.

• Research Organization: Sandia National Laboratories
• Sponsoring Organization: USDOE
• DOE Contract Number: AC04-94AL85000
• OSTI ID: 917456
• Report Number(s): SAND2003-0942C
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
BACILLUS SUBTILIS
COMMUNICATIONS
ESCHERICHIA COLI
MESSENGER-RNA
PROCESSING
PROTEINS
RIBOSOMAL RNA
RIBOSOMES
SALMONELLA TYPHIMURIUM
SIMULATION
STAPHYLOCOCCUS