key: cord-0005370-7aucxlcy authors: Ogawa, Tomohisa title: Molecular diversity of proteins in biological offense and defense systems date: 2006-11-17 journal: Mol Divers DOI: 10.1007/s11030-006-9048-y sha: 70fd0c98d2eebeab570459cfa8d82ae43367ab14 doc_id: 5370 cord_uid: 7aucxlcy nan The biodiversity of living organisms on Earth is the result of a perpetual evolutional process. One approach to tracing this process is through the application of currently available biomolecular techniques which, in particular, enable gene and protein sequences to be analyzed. The recent advances that have been made in a number of genome projects aimed at determining the genomes of various living species, including the human genome, have enabled scientists to view evolution within the framework of whole genome structures and, subsequently, be able to compare genomes between species. To date, almost every study on molecular evolution has focused on individual genes or proteins. However, in order to be able to understand the evolutionary mechanism of diversified proteins in molecular networks, one must acquire a system-wide perspective, including the us-or-them war of survival. One of the important questions in molecular evolution is: How can new adaptations to proteins recognize the target molecules to be obtained in the complex biological networks? An applicable example of the evolutionary mechanism at work are adaptations in network, biological defense and offense systems. These two systems are essentially equal and identical with the exception of the target protein; i.e. biological defense molecules such as anti-bacterial proteins are produced in humans as offensive molecules against bacteria; conversely, the bacterial toxins are offensive molecules against humans but defensive molecules for the bacterial cell itself. Interactions between species, such as paragenetic and hostile correlations, must affect the evolutional processes of the interacting species. The mechanism by which genes and proteins have evolved in a molecular context is believed to be through the fixation and chance adaptation of errors that occurred in the genome during gene replication and/or repair. Alternative splicing and gene duplication are well-known major mechanisms for generating new functional and evolutionary molecular diversities of proteins [1, 2] . More recently, some hot topics have attracted the attention of many researchers: the role of gene duplication in the emergence of novel functions, adaptive molecular evolution versus neutral drift and the identification of molecular evolutional pathways responsible for various human characteristics pertaining to infection and disease. Rapid adaptive evolution, which is characterized by a higher mutation rate of nonsynonymous nucleotides (causing amino acid change) to synonymous ones (not causing amino acid change) and/ or by the higher mutation rate of coding region/exons compared to those of non-coding/introns, has been identified in several gene families, including that of 'Biological offense & defense systems' and 'Reproduction' (see Table 1 and Ref. [59 -61] ). In this special issue of Molecular Diversity, we focus on the molecular evolution of proteins in biological offense and defense systems: vascular endothelial growth factor (VEGF) family proteins and their receptors, including recently identified snake venom-derived VEGFs (Yasuo Yamazaki and Takashi Morita), snake neurotoxins (Toru Tamiya and Takahiko J. Fujimi) and spider toxins (Pierre Escoubas) in biological offense systems. Furthermore, five unique examples of biological defense systems are described: adaptive rapid evolution of the Siglec family of cell-surface lectins (Takashi Angata), conger eel galectins (Tsuyoshi Shirai et al.), b-defensins (Julia R. Dorin and Colin Semple), RNase A superfamily (Kimberly Dyer and Helene F. Rosenberg) and insects' immunoglobulin superfamily (Shoichiro Kurata). Thus, the readers will be able to get an overall feeling for the field in general as well as acquire some insight into each unique case of proteins in biological offense and defense systems and, consequently into the molecular evolution of proteins. This special issue will no doubt provide interesting reading material. I would like to thank to contributors for their support, and also gratefully acknowledge the help received from the reviewers in evaluating the manuscripts. Many thanks are also extended to professor Dr. Shu-Kun Lin (Editor-in-Chief) for his assistance. [3 -6] Porin protein 1 Bacteria (Neisseria) [7] CSP, TRAP, MSA-2 & PF83 Protozoa [8] Resistance to antibiotics b-lactamase Bacteria (TEM) [9] Toxin Colicin Bacteria [10] Conotoxins GD Mollusc (Conus) [11 -14] Phospholipase A2/Serine protease/Zn protease/3 finger toxins/CTLP GD Reptile (Snake) [15 -20] Spider toxins/Scorpion toxins GD Arthropod [21 -24] Immunity Immunoglobulin VH GD Mammals [25] MHC GD Mammals [26] Enzyme inhibitors a1-Proteinase inhibitor GD Rodents [27] Elafin GD Mammals [28] Polygalacturonase inhibitor Plant (Legume) [29] Type I interferon-omega Mammals [30] Phospholipase A2 inhibitor GD Reptile (Snake) [31] Innate immunity Siglec GD Mammals [32] Class1 chitinase Plant (Arabidopsis) [33] Congerins GD Fish [34, 35] Transferrin Fish [36] Defensin GD Mammals [37, 38] RH, RH50 blood group GD Primates and rodents [39] RNase A GD Mammals [40, 41] Cytidine deaminase Mammals [42] Reproduction Cell recognition 18-kDa fertilization protein/Sperm lysin/TMAP/lysine-R Mollusc (Haliotis) [43 -45] Bindin/suREJ Echinoderm [46, 47] Protamine P1 Primates [48] ZP2/ZP3 Rodents [49] S-Rnase GD Plant [50] Reproduction behavior control Acp26Aa, Acp70A GD Drosophila [51] Androgen-binding protein Rodents [52] Reproductive transcription factor Sry gene Primates [53] Ods homeobox Drosophila [54] Pem homeobox GD Rodents [55] Others Transcription factor Asr2 Plant (Lycopersicon) [56] Fatty acid synthase Human [57] Pten gene Insects [58] Increase of functional diversity by alternative splicing Evolution of alternative splicing after gene duplication Long term trends in the evolution of H(3) HA1 human influenza type A Large-scale search for genes on which positive selection may operate Episodic evolution mediates interspecific transfer of a murine coronavirus Recombination of hepatitis D virus RNA sequences and its implications Sequence evolution of the porBgene of Neisseria gonorrhoeae and Neisseria meningitidis: evidence for positive darwinian selection Natural selection on Plasmodium surface proteins Darwinian evolution can follow only very few mutational paths to fitter proteins Positive selection for colicin diversity in bacteria Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus Evolutionary diversification of multigene families: allelic selection of toxins in predatory cone snails Mechanisms for evolving hypervariability: the case for conopeptides Speciation of cone snails and interspecific hyperdivergence of their venom peptides: potential evolutionary significance of introns Accelerated evolution of Trimeresurus flavoviridis venom gland phospholipase A 2 isozymes Accelerated evolution in the protein-coding regions is universal in crotalinae snake venom gland phospholipase A 2 isozyme genes Accelerated evolution of crotalinae snake venom gland serine proteases Snake venom disintegrins: evolution of structure and function Molecular evolution of snake toxins: is the functional diversity of snake toxins associated with a mechanism of accelerated evolution? Molecular diversity and accelerated evolution of C-type lectin-like proteins from snake venom Dynamic diversification from a putative common ancestor of scorpion toxins affecting sodium, potassium, and chloride channels Adaptive evolution of scorpion sodium channel toxins Adaptive evolution after gene duplication in alpha-KT x 14 subfamily from Buthus martensii Karsch Structure and pharmacology of spider venom neurotoxins Positive darwinian selection observed at the variable-region genes of immunoglobulins Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection Patterns of divergence during evolution of a1-proteinase inhibitors in mammals Accelerated evolution in inhibitor domains of porcine elafin family members Identification of target amino acids that affect interactions of fungal polygalacturonases and their plant inhibitors The evolution of the type I interferon family in mammals Structures of genes encoding phospholipase A2 inhibitors from the serum of Trimeresurus flavoviridis snake Largescale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanisms Rapid evolution in plant chitinases: molecular targets of selection in plantpathogen coevolution Accelerated evolution in the protein-coding region of galectin cDNAs, congerin I and congerin II, from skin mucus of conger eel (Conger myriaster) The speciation of conger eel galectins by rapid adaptive evolution Molecular evolution of transferrin: evidence for positive selection in salmonids Duplication and selection in the evolution of primate beta-defensin genes Evidence of positively selected sites in mammalian alpha-defensins Evolution of Rh blood group genes have experienced gene conversions and positive selection Positive darwinian selection after gene duplication in primate ribonuclease genes Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey Adaptive evolution and antiviral activity of the conserved mammalian cytidine deaminase APOBEC3H Positive darwinian selection on two homologous fertilization proteins: what is the selective pressure driving their divergence? Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein Positive selection in the egg receptor for abalone sperm lysine Adaptive evolution of sperm bindin tracks egg incompatibility in neotropical sea urchins of the genus Echinometra Positive selection in the carbohydrate recognition domains of sea urchin sperm receptor for egg jelly (suREJ) proteins Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive darwinian selection? Adaptive evolution of fertilization proteins within a genus: Variation in ZP2 and ZP3 in Deer Mice (Peromyscus) Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implications for S-allele-specific recognition sites in S-Rnase Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila Reduced nucleotide variability at an androgen-binding protein locus (Abpa) in house mice: evidence for positive natural selection Evolution of Sry genes A rapidly evolving homeobox at the site of a hybrid sterility gene Rapid evolution of a homeodomain: evidence for positive selection Adaptive evolution of the water stress-induced gene Asr2 in Lycopersicon species dwelling in arid habitats Adaptive evolution of the human fatty acid synthase gene: support for the cancer selection and fat utilization hypotheses? Rapid adaptive evolution of the tumor suppressor gene pten in an insect lineage Statistical methods for detecting molecular adaptation Adaptive evolution of genes and gene families The rapid evolution of reproductive proteins