title: A systems approach to model natural variation in reactive properties of bacterial ribosomes.
abstract: BACKGROUND
  Natural variation in protein output from translation in bacteria and archaea may be an organism-specific property of the ribosome. This paper adopts a systems approach to model the protein output as a measure of specific ribosome reactive properties in a ribosome-mediated translation apparatus. We use the steady-state assumption to define a transition state complex for the ribosome, coupled with mRNA, tRNA, amino acids and reaction factors, as a subsystem that allows a focus on the completed translational output as a measure of specific properties of the ribosome.
  
  
  RESULTS
  In analogy to the steady-state reaction of an enzyme complex, we propose a steady-state translation complex for mRNA from any gene, and derive a maximum specific translation activity, Ta(max), as a property of the ribosomal reaction complex. Ta(max) has units of a-protein output per time per a-specific mRNA. A related property of the ribosome, T a(max), has units of a-protein per time per total RNA with the relationshipT a(max) = rho(a)Ta(max), where rho(a) represents the fraction of total RNA committed to translation outpout of P(a) from gene a message. Ta(max) as a ribosome property is analogous to k(cat) for a purified enzyme, and Ta(max) is analogous to enzyme specific activity in a crude extract.
  
  
  CONCLUSIONS
  Analogy to an enzyme reaction complex led us to a ribosome reaction model for measuring specific translation activity of a bacterial ribosome. We propose to use this model to design experimental tests of our hypothesis that specific translation activity is a ribosomal property that is subject to natural variation and natural selection much like Vmax and Km for any specific enzyme.
authors.affiliation: Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA. jhjacksn@msu.edu
authors.forename: Julius H
authors.initials: JH
authors.lastname: Jackson
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Schmidt
authors.forename: Patricia A
authors.initials: PA
authors.lastname: Herring
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D002384:Catalysis; D007700:Kinetics; D008957:Models, Genetic; D014176:Protein Biosynthesis / Q000235:genetics; D012329:RNA, Bacterial / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D012345:RNA, Transfer, Amino Acid-Specific / Q000378:metabolism; D012269:Ribosomal Proteins / Q000096:biosynthesis; D012270:Ribosomes / Q000378:metabolism*; D013045:Species Specificity; D049490:Systems Biology / Q000379:methods*
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger; D012345:RNA, Transfer, Amino Acid-Specific; D012269:Ribosomal Proteins