title: Differentiation of single-cell organisms according to elongation stages crucial for gene expression efficacy.
abstract: We analyzed the interrelation between the efficiency of a gene expression and the nucleotide composition of all protein-coding sequences in 38 unicellular organisms whose complete genomic sequences are known. These organisms comprise 37 prokaryotic (29 eubacteria and eight archaebacteria) and one eukaryotic (yeast) species. We demonstrated that frequency analysis of gene codon composition fails to reflect adequately the gene expression efficiency of all these organisms. We constructed a measure, the elongation efficiency index, that considers simultaneously the information on codon frequencies and the degree of mRNA local self-complementarity. This measure recognizes the ribosome-coding genes as highly expressed in all the unicellular organisms studied. According to our analysis, these species fall into five groups differentiated by the process that makes the key contribution to the elongation rate.
authors.affiliation: Laboratory of Molecular Evolution, Institute of Cytology and Genetics, Prospekt Lavrentieva 10, 630090, Novosibirsk, Russia. likho@bionet.nsc.ru
authors.forename: Vitali A
authors.initials: VA
authors.lastname: Likhoshvai
authors.forename: Yuri G
authors.initials: YG
authors.lastname: Matushkin
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D019843:Archaeal Proteins / Q000096:biosynthesis / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D001482:Base Composition; D003062:Codon / Q000235:genetics; D005656:Fungal Proteins / Q000096:biosynthesis / Q000235:genetics; D015870:Gene Expression; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D008957:Models, Genetic; D010441:Peptide Chain Elongation, Translational / Q000235:genetics*; D019642:RNA, Archaeal / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012269:Ribosomal Proteins / Q000096:biosynthesis / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D003062:Codon; D005656:Fungal Proteins; D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012331:RNA, Fungal; D012333:RNA, Messenger; D012269:Ribosomal Proteins