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Evolutionary Genomics: Linking Macromolecular Structure, Genomes and Biological Networks

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Book cover Molecular Mechanisms of Plant and Microbe Coexistence

Part of the book series: Soil Biology ((SOILBIOL,volume 15))

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What makes individuals, populations, species and organismal lineages unique? Are genetic complements enough to define phenotypic repertoires? Only 1.5% differences in nucleic acid sequence separate humans from chimpanzee, two species believed to have diverged from each other over six million years ago (Cheng et al. 2005). Yet humans differ notably from chimpanzees and other primates. Are nucleic acid sequence differences at the gene level important? A recent wholegenome analysis of concatenated gene sequences shows that higher organisms have been given more taxonomic resolution than microbes; organisms assigned to separate phyla in Eukarya would clearly belong to a same phylum in the prokaryotic classification (Ciccarelli et al. 2006). Yet they appear to be phenotypically more plastic expressing greater morphological diversity. We may be tempted to state that differences in phenotypes between species are due to limited sets of coding genes that make critical proteins, or to differential regulation of a larger number of protein coding genes. The discovery of a diverse modern RNA world with regulatory function could support the differential regulatory explanation (Bartel 2004). We could also argue that it is not the gene repertoire what counts but the encoded proteins. Protein sequence is extraordinarily diverse and so is the three-dimensional (3D) structure of proteins and their associated functions (Chothia et al. 2003). However, protein sequences encoded in the genomes of the millions of species that currently inhabit earth cover necessarily only a minute fraction (at most one in 10−300) of the enormous permutational space defined by amino acid sequence. Yet the tools of structural genomics and protein structure determination reveal that this limited exploration of sequence space has uncovered considerable diversity in structure and biological function (e.g. enzymatic catalysis; Gutteridge and Thornton 2005). We could also argue that it is the unique modular structure of proteins that makes the difference. A substantial portion of proteins is made of multiple domains, units of compact structure that can combine in different ways to provide structural diversity (Vogel et al. 2004). Are differences at this level crucial?

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Authors and Affiliations

  1. Department of Crop Sciences, University of Illinois at Urbana-Champaign, 332 NSRC, 1101 West Peabody Drive, Urbana, IL, 61801, USA

    Gustavo Caetano-Anollés

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  1. National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India

    Chandra Shekhar Nautiyal

  2. Département de phytologie Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec (Québec), G1V 0A6, Canada

    Patrice Dion

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Caetano-Anollés, G. (2008). Evolutionary Genomics: Linking Macromolecular Structure, Genomes and Biological Networks. In: Nautiyal, C.S., Dion, P. (eds) Molecular Mechanisms of Plant and Microbe Coexistence. Soil Biology, vol 15. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75575-3_6

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