Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis.
Codon bias is related to metabolic functions in translationally biased organisms, and two facts are argued about. First, genes with high codon bias describe in meaningful ways the metabolic characteristics of the organism; important metabolic pathways corresponding to crucial characteristics of the lifestyle of an organism, such as photosynthesis, nitrification, anaerobic versus aerobic respiration, sulfate reduction, methanogenesis, and others, happen to involve especially biased genes. Second, gene transcriptional levels of sets of experiments representing a significant variation of biological conditions strikingly confirm, in the case of Saccharomyces cerevisiae, that metabolic preferences are detectable by purely statistical analysis: the high metabolic activity of yeast during fermentation is encoded in the high bias of enzymes involved in the associated pathways, suggesting that this genome was affected by a strong evolutionary pressure that favored a predominantly fermentative metabolism of yeast in the wild. The ensemble of metabolic pathways involving enzymes with high codon bias is rather well defined and remains consistent across many species, even those that have not been considered as translationally biased, such as Helicobacter pylori, for instance, reveal some weak form of translational bias for this genome. We provide numerical evidence, supported by experimental data, of these facts and conclude that the metabolic networks of translationally biased genomes, observable today as projections of eons of evolutionary pressure, can be analyzed numerically and predictions of the role of specific pathways during evolution can be derived. The new concepts of Comparative Pathway Index, used to compare organisms with respect to their metabolic networks, and Evolutionary Pathway Index, used to detect evolutionarily meaningful bias in the genetic code from transcriptional data, are introduced.
Carbone
Alessandra
A
Génomique Analytique, Université Pierre et Marie Curie, INSERM U511, 91 Bd de l'Hôpital, 75013 Paris, France. carbone@ihes.fr
Madden
Richard
R
D000641:Ammonia / Q000378:metabolism; D001420:Bacteria, Aerobic / Q000378:metabolism; D019143:Evolution, Molecular; D005288:Ferredoxins / Q000378:metabolism; D016680:Genome, Bacterial; D016681:Genome, Fungal; D023281:Genomics; D018698:Glutamic Acid / Q000096:biosynthesis; D006019:Glycolysis; D008660:Metabolism / Q000235:genetics*; D008697:Methane / Q000378:metabolism; D010788:Photosynthesis; D014176:Protein Biosynthesis / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012694:Serine / Q000378:metabolism; D013045:Species Specificity; D014158:Transcription, Genetic / Q000235:genetics*
D005288:Ferredoxins; D018698:Glutamic Acid; D012694:Serine; D000641:Ammonia; D008697:Methane