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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References
Ancel LW, Fontana W (2000) Plasticity, evolvability, and modularity in RNA. J Exp Zool (Mol Dev Evol) 288:242-283
Babajilde A, Farber R, Hofacker IL, Inman J, Lapedes AS, Stadler PF (2001) Exploring protein sequence space using knowledge based potentials. J Theor Biol 212:35-46
Bajaj M, Blundell T (1984) Evolution and the tertiary structure of proteins. Annu Rev Biophys Bioeng 13:453-492
Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nature Rev 5:101-113
Bartel DP (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297
Baulcombe D (2004) RNA silencing in plants. Nature 431:356-363
Bhan A, Galas DJ, Dewey TG (2002) A duplication growth model of gene expression networks. Bioinformatics 18:1486-1493
Billoud B, Guerrucci MA, Masselot M, Deutsch JS (2000) Cirripede phylogeny using a novel approach: molecular morphometrics. Mol Biol Evol 17:1435-1445
Caetano-Anollés G (2001) Novel strategies to study the role of mutation and nucleic acid structure in evolution. Plant Cell Tissue Org Culture 67:115-132
Caetano-Anollés G (2002a) Evolved RNA secondary structure and the rooting of the universal tree of life. J Mol Evol 54:333-345
Caetano-Anollés G (2002b) Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res 30:2527-2587
Caetano-Anollés G (2005) Grass evolution inferred from chromosomal rearrangements and geo-metrical and statistical features in RNA structure. J Mol Evol 60:635-652
Caetano-Anollés G, Caetano-Anollés D (2003) An evolutionarily structured universe of protein architecture. Genome Res 13:1563-1571
Caetano-Anollés G, Caetano-Anollés D (2005) Universal sharing patterns in proteomes and evolu-tion of protein fold architecture and life. J Mol Evol 60:484-498
Caetano-Anollés G, Kim H-S, Mittenthal JE (2007) The origins of modern metabolism inferred from phylogenomic analysis of protein architecture. Proc Natl Acad Sci USA 104:9358-9363
Chandonia J-M, Kim S-H (2006) Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. BMC Struct Biol 6:7
Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, DeJong P, Wilson RK, Paabo S, Rocchi M, Eichler EE (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437:88-93
Chothia C, Gough J, Vogel C, Teichmann SA (2003) Evolution of the protein repertoire. Science 300:1701-1703
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Towards automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287
Collins LJ, Moulton V, Penny D (2000) Use of RNA secondary structure for studying the evolu-tion of RNase P and RNase MRP. J Mol Evol 51:194-204
Delsuc F. Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nature Rev Genet 6:361-375
Doolittle RF (2005) Evolutionary aspects of whole-genome biology. Curr Opin Struct Biol 15:248-253
Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2:919-929
Efimov AV (1997) Structural trees for protein superfamilies. Proteins 28:241-260
Eliceiri GL (1999) Small nucleolar RNAs. Cell Mol Life Sci 56:22-31
Fontana W (2002) Modelling ‘evo-devo’ with RNA. BioEssays 24:1164-1177
Fontana W, Konings DA, Stadler PF, Schuster P (1993) Statistics of RNA secondary structures. Biopolymers 33:1389-1404
Frank DN, Pace NR (1998) Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem 67:153-180
Gerstein M (1998) Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins Struct Funct Genet 33:518-534
Gerstein M, Hegyi H (1998) Comparing genomes in terms of protein structure: Surveys of a finite parts list. FEMS Microbiol Rev 22:277-304
Gilbert W (1986) The RNA world. Nature 319:618
Gladyshev GP, Ershov YA (1982) Principles of the thermodynamics of biological systems. J Theor Biol 94:301-343
Grant A, Lee D, Orengo C (2004) Progress towards mapping the universe of protein folds. Genome Biol 5:107
Grishin NV (2001) Fold change in evolution of protein structures. J Struct Biol 134:167-185
Gultyaev PA, van Batenburg FHD, Pleij CWA (2002) Selective pressures on RNA hairpins in vivo and in vitro. J Mol Evol 54:1-8
Gutteridge A, Thornton JM (2005) Understanding nature’s catalytic toolkit. Trends Biochem Sci 30:622-629
Harrison A, Pearl F, Mott R, Thornton J, Orengo C (2002) Quantifying the similarities within fold space. J Mol Biol 323:909-926
Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 401:C47-C52
Hermann T, Patel DJ (1999) Stitching together RNA tertiary architectures. J Mol Biol 294:829-849
Higgs PG (1993) RNA secondary structure: a comparison of real and random sequences. J Phys I France 3:43-59
Higgs PG (1995) Thermodynamic properties of transfer RNA: a computational study. J Chem Soc Faraday Trans 91:2531-2540
Higgs PG (2000) RNA secondary structure: physical and computational aspects. Q Rev Biophys 33:199-253
Hou J, Sims GE, Zhang C, Kim S-H (2003) A global representation of the protein fold space. Proc Natl Acad Sci USA 100:2386-2390
House CH, Fitz-Gibbon ST (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54:539-547
Hutvágner G, Zamore PD (2002) RNAi: nature abhors a double-strand. Curr Opin Genet Develop 12:225-232
Kacser H, Beeby R (1984) On the origin of enzyme species by means of natural selection. J Mol Evol 20:38-51
Keefe AD, Szostak JW (2001) Functional proteins from a random-sequence library. Nature 410:715-718
Keenan RJ, Freymann DM, Stroud RM, Walter P (2001) The signal recognition particle. Annu Rev Biochem 70:755-775
Kim H-S, Mittenthal J, Caetano-Anollés G (2006) MANET: tracing evolution of protein architec-ture in metabolic networks. BMC Bioinformatics 7:351
Kitano H (2002) Computational systems biology. Nature 420:206-210
Koonin EV, Aravind L, Kondrashov AS (2000) The impact of comparative genomics on our understanding of evolution. Cell 101:573-576
Kunin V, Cases I, Enright AJ, de Lorenzo V, Ouzounis CA (2003) Myriads of protein families, and still counting. Genome Biol 4:401
Kurland CG, Collins LJ, Penny D (2006) Genomics and the irreducible nature of eukaryote cells. Science 312:1011-1014
Kyrpides N (1999) Genomes Online Database (GOLD): a monitor of complete and ongoing genome projects worldwide. Bioinformatics 15:773-774
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843-854
Lin J, Gerstein M (2000). Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 10:808-818
Maizels N, Weiner AM (1994) Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci 91:6729-6734
Mossell E (2003) On the impossibility of reconstructing ancestral data and phylogenies. J Comp Biol 10:669-678
Murzin A (1998) How far divergent evolution goes in proteins. Curr Op Struct Biol 8:380-387
Murzin A, Brenner SE, Hubbard T, Clothia C (1995) SCOP: a structural classification of proteins for the investigation of sequences and structures. J Mol Biol 247:536-540
O’Malley MA, Dupré J (2005) Fundamental issues in systems biology. BioEssays 27:1270-1276
Ochman H, Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096-1098
Orengo CA, Michie AD, Jones S, Jones DJ, Swindells MB, Thornton JM (1997) CATH: a hierar-chic classification of protein domain structures. Structure 5:1093-1108
Page RDM, Holmes EC (1998) Molecular evolution: a phylogenetic approach. Blackwell Science, Oxford
Pastor-Satorras R, Smith E, Sole R (2003) Evolving protein interaction networks through gene duplication. J Theor Biol 222:199-210
Penny D, Hendy MD, Poole AM (2003) Testing fundamental evolutionary hypotheses. J Theor Biol 223:377-385
Philippe H, Laurent J (1998) How good are deep phylogenetic trees? Curr Opin Genet Dev 8:616-623
Ponting CP, Russell RR (2002) The natural history of protein domains. Annu Rev Biophys Biomol Struct 31:45-71
Poole A, Jeffares DC, Penny D (1998) The path from the RNA world. J Mol Evol 46:1-17
Przytycka T, Aurora R, Rose GD (1999) A protein taxonomy based on secondary structure. Nat Struct Biol 6:672-682
Qian J, Luscombe NM, Gerstein M (2001) Protein family and fold occurrence in genomes: power-law behavior and evolutionary model. J Mol Biol 313:673-681
Riley M, Labedan B (1997) Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. J Mol Biol 268:857-868
Rokas A, Holland PWK (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15:454-459
Rzetsky A, Gomez SM (2001) Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics 17:988-996
Schmidt S, Sunyaev S, Bork P, Dandekar T (2003) Metabolites: a helping hand for pathway evolu-tion? Trends Biochem Sci 28:336-341
Schultes EA, Bartel DP (2000) One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289:448-452
Schultes EA, Hraber PT, LaBean TH (1999) Estimating the contributions of selection and self-organization in RNA secondary structure. J Mol Evol 49:76-83
Schumann GL, D’Arcy CJ (2006) Essential plant pathology. APS Press, St Paul, Minnesota
Schuster P, Stadler PF (2003) Networks in molecular evolution. Complexity 8:34-42
Seffens W, Digby D (1999) mRNA have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 27:1578-1584
Sober E, Steel M (2002) Testing the hypothesis of common ancestry. J Theor Biol 218:395-408
Söding J, Lupas AN (2003) More than the sum of their parts: on the evolution of proteins from peptides. BioEssays 25:837-846
Stegger G, Hofman H, Fortsch J, Gross HJ, Randles JW, Sanger HL, Riesner D (1984) Conformational transitions in viroids and virusoids: comparison of results from energy mini-mization algorithm and from experimental data. J Biomol Struct Dynam 2:543-571
Storz G (2002) An expanding universe of noncoding RNAs. Science 296:1260-1263
Sun F-J, Caetano-Anollés G (2008) The origin and evolution of tRNA inferred from phylogenetic analysis of structure. J Mol Evol 66:21-35
Sun F-J, Fleudépine S, Bousquet-Antonelli C, Caetano-Anollés G, Deragon J-M (2007) Common evolutionary trends for tRNA-derived SINE RNA structures. Trends Genet 23:26-33
Swain TD, Taylor DJ (2003) Structural rRNA characters support monophyly of raptorial limbs and paraphyly of limb specialization in water fleas. Proc R Soc London B 270:887-896
Taylor WR (2002) A ‘periodic table’ for protein structures. Nature 416:657-660
Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA (2004) Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol 14:208-216
Vukmirovic OG, Tilghman SM (2000) Exploring genome space. Nature 405:820-822
Wagner A (2003) How the global structure of protein interaction networks evolves. Proc R Soc Lond B 270:457-466
Wang M, Caetano-Anollés G (2006) Evolution inferred from domain combination in proteins. Mol Biol Evol 23:2444-2454
Wang M, Boca SM, Kalelkar R, Mittenthal JE, Caetano-Anollés G (2006) A phylogenomic recon-struction of the protein world based on a genomic census of protein fold architecture. Complexity 12:27-40
Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G (2007) Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res 17:1572-1585
Washietl S, Hofacker IL, Lukasser M, Hüttenhofer A, Stadler PF (2005) Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol 23:1383-1389
White SH (1994) Global statistics of protein sequences: implications for the origin, evolution, and prediction of structure. Annu Rev Biophys Biomol Struct 23:407-439
Woese CR (2000) The universal ancestor. Proc Natl Acad Sci USA 95:6854-6859
Wolf YI, Brenner SE, Bash PA, Koonin EV (1999) Distribution of protein folds in the three superkingdoms of life. Genome Res 9:17-26
Wolf YI, Rogozin IB, Grishin NV, Koonin EV (2002) Genome trees and the tree of life. Trends Genet 18:472-479
Yang S, Doolittle RF, Bourne PE (2005) Phylogeny determined by protein domain content. Proc Natl Acad Sci USA 102:373-378
Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JHD, Noller HF (2001) Crystal structure of the ribosome at 5.5 Å resolution. Science 292:883-896
Zhang C, Kim SH (2000) A comprehensive analysis of the Greek key motifs in protein β-barrels and β-sandwiches. Proteins 40:409-419
Zhang C, Kim SH (2003) Overview of structural genomics: from structure to function. Curr Op Chem Biol 7:28-32
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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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