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Abstract
The olfactory sense plays a key role in animals'life time. The main gene related with olfaction was olfactory receptor (OR) gene. This review introduced the structure, expression regulation, distribution, molecular evolution and polymorphism of OR gene. The relationship between OR gene and olfactory function and olfactory deficits was also discussed.
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102
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Chen M, Peng Z, He S. Olfactory receptor gene family evolution in stickleback and medaka fishes. SCIENCE CHINA-LIFE SCIENCES 2010; 53:257-66. [PMID: 20596836 DOI: 10.1007/s11427-010-0025-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 08/20/2009] [Indexed: 11/27/2022]
Abstract
Interaction of olfactory receptor (OR) genes with environmental odors is regarded as the first step of olfaction. In this study, OR genes of two fish, medaka (Oryzias latipes) and stickleback (Gasterosteus aculeatus), were identified and an evolutional analysis was conducted. The selection pressure of different TM regions and complete coding region were compared. Three TM regions (TM4, TM5 and TM6) were found to have higher average Ka/Ks values, which might be partly caused by positive selection as suggested by subsequent positive selection analysis. Further analysis showed that many PTSs overlap, or are adjacent to previously deduced binding sites in mammals. These results support the hypothesis that binding sites of fish OR genes may evolved under positive selection.
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Affiliation(s)
- Ming Chen
- Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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103
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Abstract
The olfactory properties of 6 amino acids were assessed in 20 human subjects using psychophysical tests of detectability, discriminability, and chemesthesis. Mean olfactory detection thresholds were found to be 10 microM for D-methionine, 80 microM for L-methionine, 200 microM for L-cysteine, 220 microM for D-cysteine, 75 mM for D-proline, and 100 mM for L-proline. When presented at clearly detectable and intensity-matched concentrations, the subjects readily discriminated between the odors of the L-forms of cysteine, methionine, and proline, whereas they failed to distinguish between the L- and D-forms of a given amino acid. The subjects also failed in localizing the side of monorhinal stimulation with all 6 amino acids when presented at the same concentrations as in the discrimination tasks. These results suggest that amino acids may contribute to the flavor of food not only as taste stimuli but also as olfactory stimuli perceived via ortho- or retronasal smelling. In contrast, it is unlikely that amino acids contribute to flavor perception via chemesthesis. Given that the odors of 4 of the 6 amino acids tested here were detected at concentrations lower than their corresponding taste detection thresholds, this may have important implications for the widespread use of amino acids as food additives as well as for the evaluation of off-flavors caused by amino acids.
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Affiliation(s)
- Matthias Laska
- IFM Biology, Linköping University, SE-581 83 Linköping, Sweden.
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104
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Niimura Y. Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents. Hum Genomics 2010; 4:107-18. [PMID: 20038498 PMCID: PMC3525206 DOI: 10.1186/1479-7364-4-2-107] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs), which form the largest multigene family in vertebrates. Identification of the entire repertories of OR genes using bioinformatics methods from the whole-genome sequences of diverse organisms revealed that the numbers of OR genes vary enormously, ranging from ~1,200 in rats and ~400 in humans to ~150 in zebrafish and ~15 in pufferfish. Most species have a considerable fraction of pseudogenes. Extensive phylogenetic analyses have suggested that the numbers of gene gains and losses are extremely large in the OR gene family, which is a striking example of the birth-and-death evolution. It appears that OR gene repertoires change dynamically, depending on each organism's living environment. For example, higher primates equipped with a well-developed vision system have lost a large number of OR genes. Moreover, two groups of OR genes for detecting airborne odorants greatly expanded after the time of terrestrial adaption in the tetrapod lineage, whereas fishes retain diverse repertoires of genes that were present in aquatic ancestral species. The origin of vertebrate OR genes can be traced back to the common ancestor of all chordate species, but insects, nematodes and echinoderms utilise distinctive families of chemoreceptors, suggesting that chemoreceptor genes have evolved many times independently in animal evolution.
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Affiliation(s)
- Yoshihito Niimura
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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105
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Bushley KE, Turgeon BG. Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships. BMC Evol Biol 2010; 10:26. [PMID: 20100353 PMCID: PMC2823734 DOI: 10.1186/1471-2148-10-26] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 01/26/2010] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes, found in fungi and bacteria, which biosynthesize peptides without the aid of ribosomes. Although their metabolite products have been the subject of intense investigation due to their life-saving roles as medicinals and injurious roles as mycotoxins and virulence factors, little is known of the phylogenetic relationships of the corresponding NRPSs or whether they can be ranked into subgroups of common function. We identified genes (NPS) encoding NRPS and NRPS-like proteins in 38 fungal genomes and undertook phylogenomic analyses in order to identify fungal NRPS subfamilies, assess taxonomic distribution, evaluate levels of conservation across subfamilies, and address mechanisms of evolution of multimodular NRPSs. We also characterized relationships of fungal NRPSs, a representative sampling of bacterial NRPSs, and related adenylating enzymes, including alpha-aminoadipate reductases (AARs) involved in lysine biosynthesis in fungi. RESULTS Phylogenomic analysis identified nine major subfamilies of fungal NRPSs which fell into two main groups: one corresponds to NPS genes encoding primarily mono/bi-modular enzymes which grouped with bacterial NRPSs and the other includes genes encoding primarily multimodular and exclusively fungal NRPSs. AARs shared a closer phylogenetic relationship to NRPSs than to other acyl-adenylating enzymes. Phylogenetic analyses and taxonomic distribution suggest that several mono/bi-modular subfamilies arose either prior to, or early in, the evolution of fungi, while two multimodular groups appear restricted to and expanded in fungi. The older mono/bi-modular subfamilies show conserved domain architectures suggestive of functional conservation, while multimodular NRPSs, particularly those unique to euascomycetes, show a diversity of architectures and of genetic mechanisms generating this diversity. CONCLUSIONS This work is the first to characterize subfamilies of fungal NRPSs. Our analyses suggest that mono/bi-modular NRPSs have more ancient origins and more conserved domain architectures than most multimodular NRPSs. It also demonstrates that the alpha-aminoadipate reductases involved in lysine biosynthesis in fungi are closely related to mono/bi-modular NRPSs. Several groups of mono/bi-modular NRPS metabolites are predicted to play more pivotal roles in cellular metabolism than products of multimodular NRPSs. In contrast, multimodular subfamilies of NRPSs are of more recent origin, are restricted to fungi, show less stable domain architectures, and biosynthesize metabolites which perform more niche-specific functions than mono/bi-modular NRPS products. The euascomycete-only NRPS subfamily, in particular, shows evidence for extensive gain and loss of domains suggestive of the contribution of domain duplication and loss in responding to niche-specific pressures.
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Affiliation(s)
- Kathryn E Bushley
- Department of Plant Pathology & Plant-Microbe Biology, 334 Plant Science Bldg. Cornell University, Ithaca, NY, 14853, USA
| | - B Gillian Turgeon
- Department of Plant Pathology & Plant-Microbe Biology, 334 Plant Science Bldg. Cornell University, Ithaca, NY, 14853, USA
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106
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Matsui A, Go Y, Niimura Y. Degeneration of olfactory receptor gene repertories in primates: no direct link to full trichromatic vision. Mol Biol Evol 2010; 27:1192-200. [PMID: 20061342 DOI: 10.1093/molbev/msq003] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Odor molecules in the environment are detected by olfactory receptors (ORs), being encoded by a large multigene family in mammalian genomes. It is generally thought that primates are vision oriented and dependent weakly on olfaction. Previous studies suggested that Old World monkeys (OWMs) and hominoids lost many functional OR genes after the divergence from New World monkeys (NWMs) due to the acquisition of well-developed trichromatic vision. To examine this hypothesis, here we analyzed OR gene repertoires of five primate species including NWMs, OWMs, and hominoids for which high-coverage genome sequences are available, together with two prosimians and tree shrews with low-coverage genomes. The results showed no significant differences in the number of functional OR genes between NWMs (marmosets) and OWMs/hominoids. Two independent analyses, identification of orthologous genes among the five primates and estimation of the numbers of ancestral genes by the reconciled tree method, did not support a sudden loss of OR genes at the branch of the OWMs/hominoids ancestor but suggested a gradual loss in every lineage. Moreover, we found that humans retain larger numbers of ancestral OR genes that were in the common ancestor of NWMs/OWMs/hominoids than orangutans and macaques and that the OR gene repertoire in humans is more similar to that of marmosets than those of orangutans and macaques. These results suggest that the degeneration of OR genes in primates cannot simply be explained by the acquisition of trichromatic vision, and our sense of smell may not be inferior to other primate species.
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Affiliation(s)
- Atsushi Matsui
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
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107
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108
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Steiger SS, Fidler AE, Mueller JC, Kempenaers B. Evidence for adaptive evolution of olfactory receptor genes in 9 bird species. ACTA ACUST UNITED AC 2009; 101:325-33. [PMID: 19965911 DOI: 10.1093/jhered/esp105] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
It has been suggested that positive selection, in particular selection favoring a change in the protein sequence, plays a role in the evolution of olfactory receptor (OR) gene repertoires in fish and mammals. ORs are 7-transmembrane domain (TM) proteins, members of the G-protein-coupled receptor superfamily in vertebrate genomes, and responsible for odorant binding and discrimination. OR gene repertoires in birds are surprisingly large and diverse, suggesting that birds have a keen olfactory sense. The aim of this study is to investigate signatures of positive selection in an expanded OR clade (group-gamma-c) that seems to be a characteristic of avian genomes. Using maximum-likelihood methods that estimate the d(N)/d(S) ratios and account for the effects of recombination, we show here that there is evidence for positive selection in group-gamma-c partial OR coding sequences of 9 bird species that are likely to have different olfactory abilities: the blue tit (Cyanistes caeruleus), the black coucal (Centropus grillii), the brown kiwi (Apteryx australis), the canary (Serinus canaria), the galah (Eolophus roseicapillus), the kakapo (Strigops habroptilus), the mallard (Anas platyrhynchos), the red jungle fowl (Gallus gallus), and the snow petrel (Pagodroma nivea). Positively selected codons were predominantly located in TMs, which in other vertebrates are involved in odorant binding. Our data suggest that 1) at least some avian OR genes have been subjected to adaptive evolution, 2) the extent of such adaptive evolution differs between bird species, and 3) positive selective pressures may have been stronger on the group-gamma-c OR genes of species that have well-developed olfactory abilities.
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Affiliation(s)
- Silke S Steiger
- Department of Behavioral Ecology and Evolutionary Genetics, Max-Planck Institute for Ornithology, PO Box 1564, 82305 Starnberg.
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109
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YY1's DNA-binding motifs in mammalian olfactory receptor genes. BMC Genomics 2009; 10:576. [PMID: 19958529 PMCID: PMC2791781 DOI: 10.1186/1471-2164-10-576] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 12/03/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND YY1 is an epigenetic regulator for a large number of mammalian genes. While performing genome-wide YY1 binding motif searches, we discovered that the olfactory receptor (OLFR) genes have an unusual cluster of YY1 binding sites within their coding regions. The statistical significance of this observation was further analyzed. RESULTS About 45% of the olfactory genes in the mouse have a range of 4-8 YY1 binding sites within their respective 1 kb coding regions. Statistical analyses indicate that this enrichment of YY1 motifs has likely been driven by unknown selection pressures at the DNA level, but not serendipitously by some peptides enriched within the OLFR genes. Similar patterns are also detected in the OLFR genes of all mammals analyzed, but not in the OLFR genes of the fish lineage, suggesting a mammal-specific phenomenon. CONCLUSION YY1, or YY1-related transcription factors, may help regulate olfactory receptor genes. Furthermore, the protein-coding regions of vertebrate genes can contain cis-regulatory elements for transcription factor binding as well as codons.
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110
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Abstract
The sense of smell relies on the diversity of olfactory receptor (OR) repertoires in vertebrates. It has been hypothesized that different types of ORs are required in terrestrial and marine environments. Here we show that viviparous sea snakes, which do not rely on a terrestrial environment, have significantly lost ORs compared with their terrestrial relatives, supporting the hypothesis. On the other hand, oviparous sea snakes, which rely on a terrestrial environment for laying eggs, still maintain their ORs, reflecting the importance of the terrestrial environment for them. Furthermore, we found one Colubroidea snake (including sea snakes and their terrestrial relatives)-specific OR subfamily which had diverged widely during snake evolution after the blind snake-Colubroidea snake split. Interestingly, no pseudogenes are included in this subfamily in sea snakes, and this subfamily seems to have been expanding rapidly even in an underwater environment. These findings suggest that the Colubroidea-specific ORs detect nonvolatile odorants.
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Affiliation(s)
- T Kishida
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan.
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111
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Lajoie M, Bertrand D, El-Mabrouk N. Inferring the evolutionary history of gene clusters from phylogenetic and gene order data. Mol Biol Evol 2009; 27:761-72. [PMID: 19903657 DOI: 10.1093/molbev/msp271] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Gene duplication is frequent within gene clusters and plays a fundamental role in evolution by providing a source of new genetic material upon which natural selection can act. Although classical phylogenetic inference methods provide some insight into the evolutionary history of a gene cluster, they are not sufficient alone to differentiate single- from multiple gene duplication events and to answer other questions regarding the nature and size of evolutionary events. In this paper, we present an algorithm allowing to infer a set of optimal evolutionary histories for a gene cluster in a single species, according to a general cost model involving variable length duplications (in tandem or inverted), deletions, and inversions. We applied our algorithm to the human olfactory receptor and protocadherin gene clusters, showing that the duplication size distribution differs significantly between the two gene families. The algorithm is available through a web interface at http://www-lbit.iro.umontreal.ca/DILTAG/.
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Affiliation(s)
- Mathieu Lajoie
- Département d'informatique et de recherche opérationnelle Université de Montréal, Montréal, Canada.
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112
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Zhou S, Stone EA, Mackay TFC, Anholt RRH. Plasticity of the chemoreceptor repertoire in Drosophila melanogaster. PLoS Genet 2009; 5:e1000681. [PMID: 19816562 PMCID: PMC2750752 DOI: 10.1371/journal.pgen.1000681] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 09/10/2009] [Indexed: 11/18/2022] Open
Abstract
For most organisms, chemosensation is critical for survival and is mediated by large families of chemoreceptor proteins, whose expression must be tuned appropriately to changes in the chemical environment. We asked whether expression of chemoreceptor genes that are clustered in the genome would be regulated independently; whether expression of certain chemoreceptor genes would be especially sensitive to environmental changes; whether groups of chemoreceptor genes undergo coordinated rexpression; and how plastic the expression of chemoreceptor genes is with regard to sex, development, reproductive state, and social context. To answer these questions we used Drosophila melanogaster, because its chemosensory systems are well characterized and both the genotype and environment can be controlled precisely. Using customized cDNA microarrays, we showed that chemoreceptor genes that are clustered in the genome undergo independent transcriptional regulation at different developmental stages and between sexes. Expression of distinct subgroups of chemoreceptor genes is sensitive to reproductive state and social interactions. Furthermore, exposure of flies only to odor of the opposite sex results in altered transcript abundance of chemoreceptor genes. These genes are distinct from those that show transcriptional plasticity when flies are allowed physical contact with same or opposite sex members. We analyzed covariance in transcript abundance of chemosensory genes across all environmental conditions and found that they segregated into 20 relatively small, biologically relevant modules of highly correlated transcripts. This finely pixilated modular organization of the chemosensory subgenome enables fine tuning of the expression of the chemoreceptor repertoire in response to ecologically relevant environmental and physiological conditions. Rapid adaptation and phenotypic plasticity to the chemical environment are essential prerequisites for survival; and, consequently, large families of genes that mediate the recognition of olfactory and gustatory cues have evolved. We asked how flexible the expression of these genes is in the face of rapidly changing conditions encountered during an individual's lifetime. We used the fruit fly, Drosophila melanogaster, to address this question, since both the genetic composition and environmental rearing conditions can be controlled precisely in this experimentally amenable model organism. By measuring expression levels of all chemosensory genes simultaneously, we identified genes that show altered expression at different developmental stages, during aging, in males and females, following mating, and in different social conditions. We asked whether chemosensory genes are regulated independently or whether their regulation is structured. We found that chemosensory genes that are located in close proximity to one another on the chromosome are often regulated independently. However, statistical analysis showed that groups of chemosensory genes are coordinately expressed in response to a range of environmental conditions, revealing an underlying modular organization of the phenotypic plasticity of the chemosensory receptor repertoire.
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Affiliation(s)
- Shanshan Zhou
- Department of Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Eric A. Stone
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Trudy F. C. Mackay
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert R. H. Anholt
- Department of Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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113
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Katafuchi T, Yasue H, Osaki T, Minamino N. Calcitonin receptor-stimulating peptide: Its evolutionary and functional relationship with calcitonin/calcitonin gene-related peptide based on gene structure. Peptides 2009; 30:1753-62. [PMID: 19540291 DOI: 10.1016/j.peptides.2009.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 06/09/2009] [Accepted: 06/10/2009] [Indexed: 12/21/2022]
Abstract
This review focuses on the evolutionary and functional relationship of calcitonin receptor-stimulating peptide (CRSP) with calcitonin (CT)/calcitonin gene-related peptide (CGRP) in mammals. CRSP shows high sequence identity with CGRP, but distinct biological properties. CRSP genes (CRSPs) have been identified in mammals such as pigs and dogs of the Laurasiatheria, but not in primates and rodents of the Euarchontoglires or in non-placental mammals. CRSPs have genomic organizations highly similar to those of CT/CGRP genes (CT/CGRPs), which are located along with CGRPs in a locus between CYP2R1 and INSC, while the other members of the CGRP superfamily, adrenomedullin and amylin, show genomic organizations and locations distinct from CT, CGRP, and CRSP. Thus, we categorized these three peptides into the CT/CGRP/CRSP family. Non-placental mammals having one and placental mammals having multiple CT/CGRP/CRSP family genes suggests that multiplicity of CT/CGRP started at an early stage of mammalian evolution. In the placental mammals, Laurasiatheria generally possesses multiple CRSPs and only one CT/CGRP, while Euarchontoglires possesses CT/CGRP and CGRPbeta but no CRSP, indicating an increase in the diversity and multiplicity of this family of genes in mammalian evolution. Phylogenetic analysis suggests that some CRSPs have been generated very recently in mammalian evolution. Taken together, the increase in the number and complexity of the CT/CGRP/CRSP family genes may have due to evolutionary pressure to facilitate adaptation during mammalian evolution. In this regard, it is important to elucidate the physiological roles of CT, CGRP and CRSP from the viewpoint of the CT/CGRP/CRSP family even in Euarchontoglires.
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Affiliation(s)
- Takeshi Katafuchi
- Department of Pharmacology, National Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka, Japan
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114
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Libants S, Carr K, Wu H, Teeter JH, Chung-Davidson YW, Zhang Z, Wilkerson C, Li W. The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage. BMC Evol Biol 2009; 9:180. [PMID: 19646260 PMCID: PMC2728731 DOI: 10.1186/1471-2148-9-180] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 07/31/2009] [Indexed: 01/26/2023] Open
Abstract
Background In gnathostomes, chemosensory receptors (CR) expressed in olfactory epithelia are encoded by evolutionarily dynamic gene families encoding odorant receptors (OR), trace amine-associated receptors (TAAR), V1Rs and V2Rs. A limited number of OR-like sequences have been found in invertebrate chordate genomes. Whether these gene families arose in basal or advanced vertebrates has not been resolved because these families have not been examined systematically in agnathan genomes. Results Petromyzon is the only extant jawless vertebrate whose genome has been sequenced. Known to be exquisitely sensitive to several classes of odorants, lampreys detect fewer amino acids and steroids than teleosts. This reduced number of detectable odorants is indicative of reduced numbers of CR gene families or a reduced number of genes within CR families, or both, in the sea lamprey. In the lamprey genome we identified a repertoire of 59 intact single-exon CR genes, including 27 OR, 28 TAAR, and four V1R-like genes. These three CR families were expressed in the olfactory organ of both parasitic and adult life stages. Conclusion An extensive search in the lamprey genome failed to identify potential orthologs or pseudogenes of the multi-exon V2R family that is greatly expanded in teleost genomes, but did find intact calcium-sensing receptors (CASR) and intact metabotropic glutamate receptors (MGR). We conclude that OR and V1R arose in chordates after the cephalochordate-urochordate split, but before the diversification of jawed and jawless vertebrates. The advent and diversification of V2R genes from glutamate receptor-family G protein-coupled receptors, most likely the CASR, occurred after the agnathan-gnathostome divergence.
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Affiliation(s)
- Scot Libants
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA.
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115
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Laska M, Persson O, Hernandez Salazar LT. Olfactory sensitivity for alkylpyrazines-a comparative study in CD-1 mice and spider monkeys. ACTA ACUST UNITED AC 2009; 311:278-88. [PMID: 19204998 DOI: 10.1002/jez.527] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Using a conditioning paradigm, the olfactory sensitivity of four CD-1 mice for six alkylpyrazines was investigated. With all six stimuli, the animals discriminated concentrations <or=0.1 ppm (parts per million) from the odorless solvent, and with three of the six stimuli the animals were even able to detect concentrations <or=0.1 ppb (parts per billion). Four spider monkeys tested in parallel were found to detect five of the same six stimuli at concentrations <1 ppm and with one stimulus they were able to discriminate concentrations <1 ppb from the solvent. The results showed CD-1 mice to be more sensitive than spider monkeys with five of the six alkylpyrazines tested. There was a significant positive correlation between sensitivity and the number of alkyl groups attached to the pyrazine (Pyr) ring in both species. A comparison of the detection thresholds obtained here to those obtained in human subjects suggests that neither the number of functional olfactory receptor genes nor the absolute or the relative size of the olfactory bulbs reliably predict a species' olfactory sensitivity. These threshold data may provide useful information for the choice of adequate stimulus concentrations in electrophysiological or imaging studies of the olfactory system or investigations of the discriminative abilities of mice and spider monkeys.
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116
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Ji Y, Zhang Z, Hu Y. The repertoire of G-protein-coupled receptors in Xenopus tropicalis. BMC Genomics 2009; 10:263. [PMID: 19508718 PMCID: PMC2709155 DOI: 10.1186/1471-2164-10-263] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 06/09/2009] [Indexed: 01/06/2023] Open
Abstract
Background The G-protein-coupled receptor (GPCR) superfamily represents the largest protein family in the human genome. These proteins have a variety of physiological functions that give them well recognized roles in clinical medicine. In Xenopus tropicalis, a widely used animal model for physiology research, the repertoire of GPCRs may help link the GPCR evolutionary history in vertebrates from teleost fish to mammals. Results We have identified 1452 GPCRs in the X. tropicalis genome. Phylogenetic analyses classified these receptors into the following seven families: Glutamate, Rhodopsin, Adhesion, Frizzled, Secretin, Taste 2 and Vomeronasal 1. Nearly 70% of X. tropicalis GPCRs are represented by the following three types of receptors thought to receive chemosensory information from the outside world: olfactory, vomeronasal 1 and vomeronasal 2 receptors. Conclusion X. tropicalis shares a more similar repertoire of GPCRs with mammals than it does with fish. An examination of the three major groups of receptors related to olfactory/pheromone detection shows that in X. tropicalis, these groups have undergone lineage specific expansion. A comparison of GPCRs in X. tropicalis, teleost fish and mammals reveals the GPCR evolutionary history in vertebrates.
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Affiliation(s)
- Yanping Ji
- Shanghai Institute of Brain Functional Genomics, East China Normal University, 3663 Zhongshan Road N,, Shanghai, 200062, PR China.
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117
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Galtier N, Daubin V. Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci 2009; 363:4023-9. [PMID: 18852109 DOI: 10.1098/rstb.2008.0144] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent.We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.
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Affiliation(s)
- Nicolas Galtier
- CNRS UMR 5554, Institut des Sciences de l'Evolution, Université Montpellier 2, CC64, Place E. Bataillon, 34095 Montpellier, France.
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118
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Myers BR, Sigal YM, Julius D. Evolution of thermal response properties in a cold-activated TRP channel. PLoS One 2009; 4:e5741. [PMID: 19492038 PMCID: PMC2683941 DOI: 10.1371/journal.pone.0005741] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 05/02/2009] [Indexed: 11/18/2022] Open
Abstract
Animals sense changes in ambient temperature irrespective of whether core body temperature is internally maintained (homeotherms) or subject to environmental variation (poikilotherms). Here we show that a cold-sensitive ion channel, TRPM8, displays dramatically different thermal activation ranges in frogs versus mammals or birds, consistent with variations in these species' cutaneous and core body temperatures. Thus, somatosensory receptors are not static through evolution, but show functional diversity reflecting the characteristics of an organism's ecological niche.
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Affiliation(s)
- Benjamin R. Myers
- Department of Physiology; University of California San Francisco, San Francisco, California, United States of America
| | - Yaron M. Sigal
- Department of Physiology; University of California San Francisco, San Francisco, California, United States of America
| | - David Julius
- Department of Physiology; University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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119
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Steiger SS, Fidler AE, Kempenaers B. Evidence for increased olfactory receptor gene repertoire size in two nocturnal bird species with well-developed olfactory ability. BMC Evol Biol 2009; 9:117. [PMID: 19467156 PMCID: PMC2701422 DOI: 10.1186/1471-2148-9-117] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 05/25/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In vertebrates, the molecular basis of the sense of smell is encoded by members of a large gene family, namely olfactory receptor (OR) genes. Both the total number of OR genes and the proportion of intact OR genes in a genome may indicate the importance of the sense of smell for an animal. There is behavioral, physiological, and anatomical evidence that some bird species, in particular nocturnal birds, have a well developed sense of smell. Therefore, we hypothesized that nocturnal birds with good olfactory abilities have evolved (i) more OR genes and (ii) more intact OR genes than closely related and presumably less 'olfaction-dependent' day-active avian taxa. RESULTS We used both non-radioactive Southern hybridization and PCR with degenerate primers to investigate whether two nocturnal bird species that are known to rely on olfactory cues, the brown kiwi (Apteryx australis) and the kakapo (Strigops habroptilus), have evolved a larger OR gene repertoire than their day-active, closest living relatives (for kiwi the emu Dromaius novaehollandiae, rhea Rhea americana, and ostrich Struthio camelus and for kakapo the kaka Nestor meridionalis and kea Nestor notabilis). We show that the nocturnal birds did not have a significantly higher proportion of intact OR genes. However, the estimated total number of OR genes was larger in the two nocturnal birds than in their relatives. CONCLUSION Our results suggest that ecological niche adaptations such as daily activity patterns may have shaped avian OR gene repertoires.
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Affiliation(s)
- Silke S Steiger
- Department of Behavioural Ecology and Evolutionary Genetics, Max-Planck Institute for Ornithology, Eberhard-Gwinner Strasse, 82319 Seewiesen, Germany
| | - Andrew E Fidler
- Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson 7042, New Zealand
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max-Planck Institute for Ornithology, Eberhard-Gwinner Strasse, 82319 Seewiesen, Germany
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120
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Niimura Y. On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species. Genome Biol Evol 2009; 1:34-44. [PMID: 20333175 PMCID: PMC2817399 DOI: 10.1093/gbe/evp003] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2009] [Indexed: 12/27/2022] Open
Abstract
Olfaction is a primitive sense in organisms. Both vertebrates and insects have
receptors for detecting odor molecules in the environment, but the evolutionary
origins of these genes are different. Among studied vertebrates, mammals have
∼1,000 olfactory receptor (OR) genes, whereas teleost fishes have much
smaller (∼100) numbers of OR genes. To investigate the origin and
evolution of vertebrate OR genes, I attempted to determine near-complete OR gene
repertoires by searching whole-genome sequences of 14 nonmammalian chordates,
including cephalochordates (amphioxus), urochordates (ascidian and larvacean),
and vertebrates (sea lamprey, elephant shark, five teleost fishes, frog, lizard,
and chicken), followed by a large-scale phylogenetic analysis in conjunction
with mammalian OR genes identified from nine species. This analysis showed that
the amphioxus has >30 vertebrate-type OR genes though it lacks
distinctive olfactory organs, whereas all OR genes appear to have been lost in
the urochordate lineage. Some groups of genes (θ, κ, and
λ) that are phylogenetically nested within vertebrate OR genes showed
few gene gains and losses, which is in sharp contrast to the evolutionary
pattern of OR genes, suggesting that they are actually non-OR genes. Moreover,
the analysis demonstrated a great difference in OR gene repertoires between
aquatic and terrestrial vertebrates, reflecting the necessity for the detection
of water-soluble and airborne odorants, respectively. However, a minor group
(β) of genes that are atypically present in both aquatic and
terrestrial vertebrates was also found. These findings should provide a critical
foundation for further physiological, behavioral, and evolutionary studies of
olfaction in various organisms.
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Affiliation(s)
- Yoshihito Niimura
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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121
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Sato Y, Hashiguchi Y, Nishida M. Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. BMC SYSTEMS BIOLOGY 2009; 3:23. [PMID: 19232106 PMCID: PMC2653465 DOI: 10.1186/1752-0509-3-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 02/20/2009] [Indexed: 11/10/2022]
Abstract
Background Duplicate genes are considered to have evolved through the partitioning of ancestral functions among duplicates (subfunctionalization) and/or the acquisition of novel functions from a beneficial mutation (neofunctionalization). Additionally, an increase in gene dosage resulting from duplication may also confer an advantageous effect, as has been suggested for histone, tRNA, and rRNA genes. Currently, there is little understanding of the effect of increased gene dosage on subcellular networks like signal transduction pathways. Addressing this issue may provide further insights into the evolution by gene duplication. Results We analyzed the evolution of multiple stickleback phosphodiesterase (PDE, EC: 3.1.4.17) 1C genes involved in the cyclic nucleotide signaling pathway. Stickleback has 8–9 copies of this gene, whereas only one or two loci exist in other model vertebrates. Our phylogenetic and synteny analyses suggested that the multiple PDE1C genes in stickleback were generated by repeated duplications of >100-kbp chromosome segments. Sequence evolution analysis did not provide strong evidence for neofunctionalization in the coding sequences of stickleback PDE1C isoforms. On the other hand, gene expression analysis suggested that the derived isoforms acquired expression in new organs, implying their neofunctionalization in terms of expression patterns. In addition, at least seven isoforms of the stickleback PDE1C were co-expressed with olfactory-type G-proteins in the nose, suggesting that PDE1C dosage is increased in the stickleback olfactory transduction (OT) pathway. In silico simulations of OT implied that the increased PDE1C dosage extends the longevity of the depolarization signals of the olfactory receptor neuron. Conclusion The predicted effect of the increase in PDE1C products on the OT pathway may play an important role in stickleback behavior and ecology. However, this possibility should be empirically examined. Our analyses imply that an increase in gene product sometimes has a significant, yet unexpected, effect on the functions of subcellular networks.
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Affiliation(s)
- Yukuto Sato
- Division of Molecular Marine Biology, Ocean Research Institute, The University of Tokyo, Tokyo, Japan.
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122
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Koonin EV. Evolution of genome architecture. Int J Biochem Cell Biol 2009; 41:298-306. [PMID: 18929678 PMCID: PMC3272702 DOI: 10.1016/j.biocel.2008.09.015] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 09/16/2008] [Accepted: 09/16/2008] [Indexed: 11/26/2022]
Abstract
Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin's conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the "Origin", we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome architectures are, mostly, products of neutral processes or epiphenomena of more general selective processes, such as selection for genome streamlining in successful lineages with large populations. Selection for specific gene arrangements (elements of genome architecture) seems only to modulate the results of these processes.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
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123
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Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. Proc Natl Acad Sci U S A 2009; 106:835-40. [PMID: 19126682 DOI: 10.1073/pnas.0812043106] [Citation(s) in RCA: 202] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. In plants, F-box genes form one of the largest multigene superfamilies and control many important biological functions. However, it is unclear how and why plants have acquired a large number of F-box genes. Here we identified 692, 337, and 779 F-box genes in Arabidopsis, poplar and rice, respectively, and studied their phylogenetic relationships and evolutionary patterns. We found that the plant F-box superfamily can be divided into 42 families, each of which has a distinct domain organization. We also estimated the number of ancestral genes for each family and identified highly conservative versus divergent families. In conservative families, there has been little or no change in the number of genes since the divergence between eudicots and monocots approximately 145 million years ago. In divergent families, however, the numbers have increased dramatically during the same period. In two cases, the numbers of genes in extant species are >100 times greater than that in the most recent common ancestor (MRCA) of the three species. Proteins encoded by highly conservative genes always have the same domain organization, suggesting that they interact with the same or similar substrates. In contrast, proteins of rapidly duplicating genes sometimes have quite different domain structures, mainly caused by unusually frequent shifts of exon-intron boundaries and/or frameshift mutations. Our results indicate that different F-box families, or different clusters of the same family, have experienced dramatically different modes of sequence divergence, apparently having resulted in adaptive changes in function.
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124
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Shi P, Zhang J. Extraordinary diversity of chemosensory receptor gene repertoires among vertebrates. Results Probl Cell Differ 2009; 47:1-23. [PMID: 19145414 DOI: 10.1007/400_2008_4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemosensation (smell and taste) is important to the survival and reproduction of vertebrates and is mediated by specific bindings of odorants, pheromones, and tastants by chemoreceptors that are encoded by several large gene families. This review summarizes recent comparative genomic and evolutionary studies of vertebrate chemoreceptor genes. It focuses on the remarkable diversity of chemoreceptor gene repertoires in terms of gene number and gene sequence across vertebrates and the evolutionary mechanisms that are responsible for generating this diversity. We argue that the great among-species variation of chemoreceptor gene repertoires is a result of adaptations of individual species to their environments and diets.
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Affiliation(s)
- P Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Arthur-Scheunert-Allee 114-116, 650223, Kunming, China.
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125
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Steiger SS, Fidler AE, Valcu M, Kempenaers B. Avian olfactory receptor gene repertoires: evidence for a well-developed sense of smell in birds? Proc Biol Sci 2008; 275:2309-17. [PMID: 18628122 PMCID: PMC2495045 DOI: 10.1098/rspb.2008.0607] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 06/20/2008] [Accepted: 06/20/2008] [Indexed: 11/20/2022] Open
Abstract
Among vertebrates, the sense of smell is mediated by olfactory receptors (ORs) expressed in sensory neurons within the olfactory epithelium. Comparative genomic studies suggest that the olfactory acuity of mammalian species correlates positively with both the total number and the proportion of functional OR genes encoded in their genomes. In contrast to mammals, avian olfaction is poorly understood, with birds widely regarded as relying primarily on visual and auditory inputs. Here, we show that in nine bird species from seven orders (blue tit, Cyanistes caeruleus; black coucal, Centropus grillii; brown kiwi, Apteryx australis; canary, Serinus canaria; galah, Eolophus roseicapillus; red jungle fowl, Gallus gallus; kakapo, Strigops habroptilus; mallard, Anas platyrhynchos; snow petrel, Pagodroma nivea), the majority of amplified OR sequences are predicted to be from potentially functional genes. This finding is somewhat surprising as one previous report suggested that the majority of OR genes in an avian (red jungle fowl) genomic sequence are non-functional pseudogenes. We also show that it is not the estimated proportion of potentially functional OR genes, but rather the estimated total number of OR genes that correlates positively with relative olfactory bulb size, an anatomical correlate of olfactory capability. We further demonstrate that all the nine bird genomes examined encode OR genes belonging to a large gene clade, termed gamma-c, the expansion of which appears to be a shared characteristic of class Aves. In summary, our findings suggest that olfaction in birds may be a more important sense than generally believed.
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Affiliation(s)
- Silke S Steiger
- Department of Behavioural Ecology and Evolutionary Genetics, Max-Planck Institute for Ornithology, PO Box 1564, 82319 Starnberg, Germany.
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126
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Cometto-Muñiz JE, Cain WS, Abraham MH, Gil-Lostes J. Concentration-detection functions for the odor of homologous n-acetate esters. Physiol Behav 2008; 95:658-67. [PMID: 18950650 DOI: 10.1016/j.physbeh.2008.09.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 09/17/2008] [Accepted: 09/19/2008] [Indexed: 10/21/2022]
Abstract
Using air-dilution olfactometry, we measured concentration-response functions for the odor detection of the homologous esters ethyl, butyl, hexyl, and octyl acetate. Stimuli were delivered by means of an 8-station vapor delivery device (VDD-8) specifically designed to capture odor detection performance by humans under environmentally realistic conditions. Groups of 16-17 (half female) normosmic (i.e., having a normal olfaction) non-smokers (ages 18-38) were tested intensively. The method involved a three-alternative forced-choice procedure against carbon-filtered air, with an ascending concentration approach. Delivered concentrations were confirmed by gas chromatography before and during actual testing. A sigmoid (logistic) model provided an excellent fit to the odor detection functions both at the group and individual levels. Odor detection thresholds (ODTs) (defined as the half-way point between chance and perfect detection) decreased from ethyl (245 ppb by volume), to butyl (4.3 ppb), to hexyl acetate (2.9 ppb), and increased for octyl acetate (20 ppb). Interindividual threshold variability was near one and always below two orders of magnitude. The steepness of the functions increased slightly but significantly with carbon chain length. The outcome showed that the present thresholds lie at the very low end of those previously reported, but share with them a similar relative trend across n-acetates. On this basis, we suggest that a recent quantitative structure-activity relationship (QSAR) for ODTs can be applied to these and additional optimized data, and used to describe and predict not just ODTs but the complete underlying psychometric odor functions.
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Affiliation(s)
- J Enrique Cometto-Muñiz
- Chemosensory Perception Laboratory, Department of Surgery (Otolaryngology), University of California, San Diego, La Jolla, CA 92093-0957, USA.
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127
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Thomas JH, Robertson HM. The Caenorhabditis chemoreceptor gene families. BMC Biol 2008; 6:42. [PMID: 18837995 PMCID: PMC2576165 DOI: 10.1186/1741-7007-6-42] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Accepted: 10/06/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. RESULTS Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. CONCLUSION Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.
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Affiliation(s)
- James H Thomas
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois, Urbana-Champaign, IL, USA
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128
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Olfactory discrimination of aliphatic odorants at 1 ppm: too easy for CD-1 mice to show odor structure-activity relationships? J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2008; 194:971-80. [PMID: 18810459 DOI: 10.1007/s00359-008-0370-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 08/25/2008] [Accepted: 09/05/2008] [Indexed: 02/02/2023]
Abstract
Using an operant conditioning paradigm we tested the ability of CD-1 mice to discriminate between 25 odorants comprising members of five homologous series of aliphatic odorants (C4-C8) presented at a gas phase concentration of 1 ppm. We found (a) that all mice significantly discriminated between all 50 stimulus pairs that involved odorants sharing the same functional group, but differing in carbon chain length, as well as between all 50 stimulus pairs that involved odorants sharing the same carbon chain length but differing in functional group, (b) a significant negative correlation between discrimination performance and structural similarity of odorants in terms of differences in carbon chain length with the acetic esters and the 2-ketones, but not with the 1-alcohols, n-aldehydes, and n-carboxylic acids tested, and (c) that odorant pairs differing in functional group were significantly better discriminated than odorant pairs differing in carbon chain length. These findings demonstrate that CD-1 mice have excellent discrimination ability for structurally related aliphatic odorants, that correlations between discrimination performance and structural similarity of odorants are odorant class-specific rather than a general phenomenon, and that both carbon chain length and type of functional group play an important role for odor quality coding in mice.
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129
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Differential loss of embryonic globin genes during the radiation of placental mammals. Proc Natl Acad Sci U S A 2008; 105:12950-5. [PMID: 18755893 DOI: 10.1073/pnas.0804392105] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The differential gain and loss of genes from homologous gene families represents an important source of functional variation among the genomes of different species. Differences in gene content between species are primarily attributable to lineage-specific gene gains via duplication and lineage-specific losses via deletion or inactivation. Here, we use a comparative genomic approach to investigate this process of gene turnover in the beta-globin gene family of placental mammals. By analyzing genomic sequence data from representatives of each of the main superordinal clades of placental mammals, we were able to reconstruct pathways of gene family evolution during the basal radiation of this physiologically and morphologically diverse vertebrate group. Our analysis revealed that an initial expansion of the nonadult portion of the beta-globin gene cluster in the ancestor of placental mammals was followed by the differential loss and retention of ancestral gene lineages, thereby generating variation in the complement of embryonic globin genes among contemporary species. The sorting of epsilon-, gamma-, and eta-globin gene lineages among the basal clades of placental mammals has produced species differences in the functional types of hemoglobin isoforms that can be synthesized during the course of embryonic development.
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130
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Wu DD, Irwin DM, Zhang YP. Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair. BMC Evol Biol 2008; 8:241. [PMID: 18721477 PMCID: PMC2528016 DOI: 10.1186/1471-2148-8-241] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 08/23/2008] [Indexed: 01/14/2023] Open
Abstract
Background Hair is unique to mammals. Keratin associated proteins (KRTAPs), which contain two major groups: high/ultrahigh cysteine and high glycine-tyrosine, are one of the major components of hair and play essential roles in the formation of rigid and resistant hair shafts. Results The KRTAP family was identified as being unique to mammals, and near-complete KRTAP gene repertoires for eight mammalian genomes were characterized in this study. An expanded KRTAP gene repertoire was found in rodents. Surprisingly, humans have a similar number of genes as other primates despite the relative hairlessness of humans. We identified several new subfamilies not previously reported in the high/ultrahigh cysteine KRTAP genes. Genes in many subfamilies of the high/ultrahigh cysteine KRTAP genes have evolved by concerted evolution with frequent gene conversion events, yielding a higher GC base content for these gene sequences. In contrast, the high glycine-tyrosine KRTAP genes have evolved more dynamically, with fewer gene conversion events and thus have a lower GC base content, possibly due to positive selection. Conclusion Most of the subfamilies emerged early in the evolution of mammals, thus we propose that the mammalian ancestor should have a diverse KRTAP gene repertoire. We propose that hair content characteristics have evolved and diverged rapidly among mammals because of rapid divergent evolution of KRTAPs between species. In contrast, subfamilies of KRTAP genes have been homogenized within each species due to concerted evolution.
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Affiliation(s)
- Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China.
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131
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Vieira FG, Sánchez-Gracia A, Rozas J. Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biol 2008; 8:R235. [PMID: 18039354 PMCID: PMC2258175 DOI: 10.1186/gb-2007-8-11-r235] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 06/08/2007] [Accepted: 11/08/2007] [Indexed: 01/18/2023] Open
Abstract
The comparative analysis of the odorant binding protein family in 12 Drosophila genomes allowed the identification of 595 putative family member genes and revealed insights into the evolution of this family in these species. Background Chemoreception is a widespread mechanism that is involved in critical biologic processes, including individual and social behavior. The insect peripheral olfactory system comprises three major multigene families: the olfactory receptor (Or), the gustatory receptor (Gr), and the odorant-binding protein (OBP) families. Members of the latter family establish the first contact with the odorants, and thus constitute the first step in the chemosensory transduction pathway. Results Comparative analysis of the OBP family in 12 Drosophila genomes allowed the identification of 595 genes that encode putative functional and nonfunctional members in extant species, with 43 gene gains and 28 gene losses (15 deletions and 13 pseudogenization events). The evolution of this family shows tandem gene duplication events, progressive divergence in DNA and amino acid sequence, and prevalence of pseudogenization events in external branches of the phylogenetic tree. We observed that the OBP arrangement in clusters is maintained across the Drosophila species and that purifying selection governs the evolution of the family; nevertheless, OBP genes differ in their functional constraints levels. Finally, we detect that the OBP repertoire evolves more rapidly in the specialist lineages of the Drosophila melanogaster group (D. sechellia and D. erecta) than in their closest generalists. Conclusion Overall, the evolution of the OBP multigene family is consistent with the birth-and-death model. We also found that members of this family exhibit different functional constraints, which is indicative of some functional divergence, and that they might be involved in some of the specialization processes that occurred through the diversification of the Drosophila genus.
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Affiliation(s)
- Filipe G Vieira
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av, Diagonal 645, Barcelona 08028, Spain.
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132
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Hiroi M, Tanimura T, Marion-Poll F. Hedonic taste in Drosophila revealed by olfactory receptors expressed in taste neurons. PLoS One 2008; 3:e2610. [PMID: 18612414 PMCID: PMC2440521 DOI: 10.1371/journal.pone.0002610] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Accepted: 06/04/2008] [Indexed: 01/01/2023] Open
Abstract
Taste and olfaction are each tuned to a unique set of chemicals in the outside world, and their corresponding sensory spaces are mapped in different areas in the brain. This dichotomy matches categories of receptors detecting molecules either in the gaseous or in the liquid phase in terrestrial animals. However, in Drosophila olfactory and gustatory neurons express receptors which belong to the same family of 7-transmembrane domain proteins. Striking overlaps exist in their sequence structure and in their expression pattern, suggesting that there might be some functional commonalities between them. In this work, we tested the assumption that Drosophila olfactory receptor proteins are compatible with taste neurons by ectopically expressing an olfactory receptor (OR22a and OR83b) for which ligands are known. Using electrophysiological recordings, we show that the transformed taste neurons are excited by odor ligands as by their cognate tastants. The wiring of these neurons to the brain seems unchanged and no additional connections to the antennal lobe were detected. The odor ligands detected by the olfactory receptor acquire a new hedonic value, inducing appetitive or aversive behaviors depending on the categories of taste neurons in which they are expressed i.e. sugar- or bitter-sensing cells expressing either Gr5a or Gr66a receptors. Taste neurons expressing ectopic olfactory receptors can sense odors at close range either in the aerial phase or by contact, in a lipophilic phase. The responses of the transformed taste neurons to the odorant are similar to those obtained with tastants. The hedonic value attributed to tastants is directly linked to the taste neurons in which their receptors are expressed.
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Affiliation(s)
- Makoto Hiroi
- UMR n°1272, Physiologie de l'Insecte: Signalisation and Communication, INRA / UPMC / AgroParisTech, Route de Saint Cyr, Versailles, France
- Department of Biology, Graduate School of Sciences, Kyushu University, Ropponmatsu, Fukuoka, Japan
| | - Teiichi Tanimura
- Department of Biology, Graduate School of Sciences, Kyushu University, Ropponmatsu, Fukuoka, Japan
| | - Frédéric Marion-Poll
- UMR n°1272, Physiologie de l'Insecte: Signalisation and Communication, INRA / UPMC / AgroParisTech, Route de Saint Cyr, Versailles, France
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133
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Go Y, Niimura Y. Similar Numbers but Different Repertoires of Olfactory Receptor Genes in Humans and Chimpanzees. Mol Biol Evol 2008; 25:1897-907. [DOI: 10.1093/molbev/msn135] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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134
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Steiger SS, Fidler AE, Kempenaers B. Detection of olfactory receptor transcripts in bird testes. ACTA ACUST UNITED AC 2008; 99:624-8. [PMID: 18567612 DOI: 10.1093/jhered/esn051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The sense of smell is mediated through olfactory receptors (ORs) expressed in olfactory sensory neurons of the olfactory epithelium. Interestingly, some OR genes also function in another context: they are expressed in nonolfactory testicular tissue and in sperm of mammals and fish where they mediate sperm flagellar motility. The presence of OR transcripts in testicular tissue of both mammals and fish suggests that this is a conserved trait among vertebrates. In birds, sperm competition is widespread and its outcome depends, in part, on sperm motility. Thus, avian testicular OR gene expression might be particularly interesting to study, especially in the context of current ideas on postcopulatory sexual selection. Using reverse transcription-polymerase chain reaction with degenerate primers specific for OR genes and subsequent cloning, we here demonstrate that multiple OR gene transcripts are present in chicken (Gallus gallus domesticus) testes. Moreover, we show that they belong to the class-gamma OR gene clade. We discuss the potential significance and evolutionary implications of avian testicular OR gene expression.
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Affiliation(s)
- Silke S Steiger
- Max-Planck Institute for Ornithology, Department of Behavioural Ecology & Evolutionary Genetics, PO Box 1564, 82319 Starnberg, Germany.
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135
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Kishida T. Pattern of the divergence of olfactory receptor genes during tetrapod evolution. PLoS One 2008; 3:e2385. [PMID: 18568087 PMCID: PMC2435047 DOI: 10.1371/journal.pone.0002385] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Accepted: 04/22/2008] [Indexed: 11/19/2022] Open
Abstract
The olfactory receptor (OR) multigene family is responsible for the sense of smell in vertebrate species. OR genes are scattered widely in our chromosomes and constitute one of the largest gene families in eutherian genomes. Some previous studies revealed that eutherian OR genes diverged mainly during early mammalian evolution. However, the exact period when, and the ecological reason why eutherian ORs strongly diverged has remained unclear. In this study, I performed a strict data mining effort for marsupial opossum OR sequences and bootstrap analyses to estimate the periods of chromosomal migrations and gene duplications of OR genes during tetrapod evolution. The results indicate that chromosomal migrations occurred mainly during early vertebrate evolution before the monotreme-placental split, and that gene duplications occurred mainly during early mammalian evolution between the bird-mammal split and marsupial-placental split, coinciding with the reduction of opsin genes in primitive mammals. It could be thought that the previous chromosomal dispersal allowed the OR genes to subsequently expand easily, and the nocturnal adaptation of early mammals might have triggered the OR gene expansion.
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136
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GARDINER ANASTASIA, BARKER DANIEL, BUTLIN ROGERK, JORDAN WILLIAMC, RITCHIE MICHAELG. Drosophilachemoreceptor gene evolution: selection, specialization and genome size. Mol Ecol 2008; 17:1648-57. [DOI: 10.1111/j.1365-294x.2008.03713.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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137
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Conceição IC, Aguadé M. High incidence of interchromosomal transpositions in the evolutionary history of a subset of or genes in Drosophila. J Mol Evol 2008; 66:325-32. [PMID: 18330486 DOI: 10.1007/s00239-008-9071-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 12/17/2007] [Accepted: 01/25/2008] [Indexed: 01/17/2023]
Abstract
In insects, the odorant receptor (Or) multigene family is an intermediate-sized family with genes present in all chromosomes, indicating that duplication followed by interchromosomal transposition played an important role in the early stages of the family evolution. Here, we have explored the occurrence of interchromosomal transpositions in more recent stages through the comparative analysis of a subset of Or genes in Drosophila, where the gene content of chromosomal arms is highly conserved. The studied subset consisted of 11 Or genes located on the left arm of chromosome 3 (Muller's D element) in D. melanogaster. Our study focused on the number and chromosomal arm location of these members of the family across the 12 Drosophila species with complete genome sequences. In contrast to previous results from in situ hybridization comparative mapping that were mainly based on single-copy genes, our study, based on members of a multigene family of moderate size, revealed repeated interchromosomal transposition events and a complex history of some of the studied genes.
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Affiliation(s)
- Inês C Conceição
- Departament de Genètica, Universitat de Barcelona, Av. Diagonal, 645, Barcelona 08028, Spain
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138
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139
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Glöckner G, Golderer G, Werner-Felmayer G, Meyer S, Marwan W. A first glimpse at the transcriptome of Physarum polycephalum. BMC Genomics 2008; 9:6. [PMID: 18179708 PMCID: PMC2258281 DOI: 10.1186/1471-2164-9-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 01/07/2008] [Indexed: 01/03/2023] Open
Abstract
Background Physarum polycephalum, an acellular plasmodial species belongs to the amoebozoa, a major branch in eukaryote evolution. Its complex life cycle and rich cell biology is reflected in more than 2500 publications on various aspects of its biochemistry, developmental biology, cytoskeleton, and cell motility. It now can be genetically manipulated, opening up the possibility of targeted functional analysis in this organism. Methods Here we describe a large fraction of the transcribed genes by sequencing a cDNA library from the plasmodial stage of the developmental cycle. Results In addition to the genes for the basic metabolism we found an unexpected large number of genes involved in sophisticated signaling networks and identified potential receptors for environmental signals such as light. In accordance with the various developmental options of the plasmodial cell we found that many P. polycephalum genes are alternatively spliced. Using 30 donor and 30 acceptor sites we determined the splicing signatures of this species. Comparisons to various other organisms including Dictyostelium, the closest relative, revealed that roughly half of the transcribed genes have no detectable counterpart, thus potentially defining species specific adaptations. On the other hand, we found highly conserved proteins, which are maintained in the metazoan lineage, but absent in D. discoideum or plants. These genes arose possibly in the last common ancestor of Amoebozoa and Metazoa but were lost in D. discoideum. Conclusion This work provides an analysis of up to half of the protein coding genes of Physarum polycephalum. The definition of splice motifs together with the description of alternatively spliced genes will provide a valuable resource for the ongoing genome project.
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Affiliation(s)
- Gernot Glöckner
- Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstr, 11, D-07745 Jena, Germany.
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140
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141
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Genomic drift and copy number variation of sensory receptor genes in humans. Proc Natl Acad Sci U S A 2007; 104:20421-6. [PMID: 18077390 DOI: 10.1073/pnas.0709956104] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The number of sensory receptor genes varies extensively among different mammalian species. This variation is believed to be caused partly by physiological requirements of animals and partly by genomic drift due to random duplication and deletion of genes. If the contribution of genomic drift is substantial, each species should contain a significant amount of copy number variation (CNV). We therefore investigated CNVs in sensory receptor genes among 270 healthy humans by using published CNV data. The results indicated that olfactory receptor (OR), taste receptor type 2, and vomeronasal receptor type 1 genes show a high level of intraspecific CNVs. In particular, >30% of the approximately 800 OR gene loci in humans were polymorphic with respect to copy number, and two randomly chosen individuals showed a copy number difference of approximately 11 in functional OR genes on average. There was no significant difference in the amount of CNVs between functional and nonfunctional OR genes. Because pseudogenes are expected to evolve in a neutral fashion, this observation suggests that functional OR genes also have evolved in a similar manner with respect to copy number change. In addition, we found that the evolutionary change of copy number of OR genes approximately follows the Gaussian process in probability theory, and the copy number divergence between populations has increased with evolutionary time. We therefore conclude that genomic drift plays an important role for generating intra- and interspecific CNVs of sensory receptor genes. Similar results were obtained when all annotated genes were analyzed.
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142
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Young JM, Waters H, Dong C, Fülle HJ, Liman ER. Degeneration of the olfactory guanylyl cyclase D gene during primate evolution. PLoS One 2007; 2:e884. [PMID: 17849013 PMCID: PMC1964805 DOI: 10.1371/journal.pone.0000884] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 08/20/2007] [Indexed: 02/04/2023] Open
Abstract
Background The mammalian olfactory system consists of several subsystems that detect specific sets of chemical cues and underlie a variety of behavioral responses. Within the main olfactory epithelium at least three distinct types of chemosensory neurons can be defined by their expression of unique sets of signal transduction components. In rodents, one set of neurons expresses the olfactory-specific guanylyl cyclase (GC)-D gene (Gucy2d, guanylyl cyclase 2d) and other cell-type specific molecules. GC-D-positive neurons project their axons to a small group of atypical “necklace” glomeruli in the olfactory bulb, some of which are activated in response to suckling in neonatal rodents and to atmospheric CO2 in adult mice. Because GC-D is a pseudogene in humans, signaling through this system appears to have been lost at some point in primate evolution. Principal Findings Here we used a combination of bioinformatic analysis of trace-archive and genome-assembly data and sequencing of PCR-amplified genomic DNA to determine when during primate evolution the functional gene was lost. Our analysis reveals that GC-D is a pseudogene in a large number of primate species, including apes, Old World and New World monkeys and tarsier. In contrast, the gene appears intact and has evolved under purifying selection in mouse, rat, dog, lemur and bushbaby. Conclusions These data suggest that signaling through GC-D-expressing cells was probably compromised more than 40 million years ago, prior to the divergence of New World monkeys from Old World monkeys and apes, and thus cannot be involved in chemosensation in most primates.
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Affiliation(s)
- Janet M. Young
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail: (EL), (JY)
| | - Hang Waters
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Cora Dong
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Hans-Jürgen Fülle
- Departments of Cell and Neurobiology and Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Emily R. Liman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- Program in Neuroscience, University of Southern California, Los Angeles, California, United States of America
- * To whom correspondence should be addressed. E-mail: (EL), (JY)
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143
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Niimura Y, Nei M. Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2007; 2:e708. [PMID: 17684554 PMCID: PMC1933591 DOI: 10.1371/journal.pone.0000708] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/04/2007] [Indexed: 11/25/2022] Open
Abstract
Odor perception in mammals is mediated by a large multigene family of olfactory receptor (OR) genes. The number of OR genes varies extensively among different species of mammals, and most species have a substantial number of pseudogenes. To gain some insight into the evolutionary dynamics of mammalian OR genes, we identified the entire set of OR genes in platypuses, opossums, cows, dogs, rats, and macaques and studied the evolutionary change of the genes together with those of humans and mice. We found that platypuses and primates have <400 functional OR genes while the other species have 800–1,200 functional OR genes. We then estimated the numbers of gains and losses of OR genes for each branch of the phylogenetic tree of mammals. This analysis showed that (i) gene expansion occurred in the placental lineage each time after it diverged from monotremes and from marsupials and (ii) hundreds of gains and losses of OR genes have occurred in an order-specific manner, making the gene repertoires highly variable among different orders. It appears that the number of OR genes is determined primarily by the functional requirement for each species, but once the number reaches the required level, it fluctuates by random duplication and deletion of genes. This fluctuation seems to have been aided by the stochastic nature of OR gene expression.
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Affiliation(s)
- Yoshihito Niimura
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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144
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Abstract
Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.
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Affiliation(s)
- Masatoshi Nei
- Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA.
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145
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Nozawa M, Nei M. Evolutionary dynamics of olfactory receptor genes in Drosophila species. Proc Natl Acad Sci U S A 2007; 104:7122-7. [PMID: 17438280 PMCID: PMC1855360 DOI: 10.1073/pnas.0702133104] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Olfactory receptor (OR) genes are of vital importance for animals to find food, identify mates, and avoid dangers. In mammals, the number of OR genes is large and varies extensively among different orders, whereas, in insects, the extent of interspecific variation appears to be small, although only a few species have been studied. To understand the evolutionary changes of OR genes, we identified all OR genes from 12 Drosophila species, of which the evolutionary time is roughly equivalent to that of eutherian mammals. The results showed that all species examined have similar numbers ( approximately 60) of functional OR genes. Phylogenetic analysis indicated that the ancestral species also had similar numbers of genes, but there were frequent gains and losses of genes that occurred in each evolutionary lineage. It appears that tandem duplication and random inactivation of duplicate genes are the major factors of gene number change. However, chromosomal rearrangements have contributed to the establishment of genome-wide distribution of OR genes. These results suggest that the repertoire of OR genes in Drosophila has been quite stable compared with the mammalian genes. The difference in evolutionary pattern between Drosophila and mammals can be explained partly by the differences of gene expression mechanisms and partly by the environmental and behavioral differences.
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Affiliation(s)
- Masafumi Nozawa
- Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802
- *To whom correspondence may be addressed. E-mail: or
| | - Masatoshi Nei
- Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802
- *To whom correspondence may be addressed. E-mail: or
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146
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Cutoff in detection of eye irritation from vapors of homologous carboxylic acids and aliphatic aldehydes. Neuroscience 2007; 145:1130-7. [PMID: 17270354 DOI: 10.1016/j.neuroscience.2006.12.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/13/2006] [Accepted: 12/14/2006] [Indexed: 01/26/2023]
Abstract
Using neat vapors of selected homologous aldehydes (decanal, undecanal, dodecanal) and carboxylic acids (pentanoic, hexanoic, heptanoic, octanoic, nonanoic), we explored the point where a certain homolog (and all larger ones) becomes undetectable by eye irritation (i.e. by ocular chemesthesis). This phenomenon has been observed in other homologous series that also reach a break-point, or cutoff, in chemesthetic detection. Participants (11<or=n<or=32) were tested using a three-alternative, forced-choice procedure. Flow rate to the eye equaled 4 or 8 l/min and time of exposure was 6 s. The outcome showed that dodecanal and heptanoic acid were the shortest undetectable homologs. When the vapor concentration of the stimuli was increased by heating the liquid source to 37 degrees C, homologs located before the cutoff point (e.g. hexanoic acid) became readily detected by all subjects, whereas homologs located at the cutoff remained largely undetected. In addition, a comparison of calculated values of eye irritation thresholds for aldehydes and acids (from a successful model of ocular chemesthetic potency) with values of saturated vapor concentration at 23 and 37 degrees C indicated that the vapor concentration of dodecanal and heptanoic acid should have been enough to produce detection. The outcome suggests that the cutoff observed does not result from a low vapor concentration but from limitations in the structure or dimension(s) of the molecules that render them unsuitable to interact effectively with human chemesthetic receptors.
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147
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Sugino H. Comparative genomic analysis of the mouse and rat amylase multigene family. FEBS Lett 2007; 581:355-60. [PMID: 17223109 DOI: 10.1016/j.febslet.2006.12.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 12/21/2006] [Accepted: 12/22/2006] [Indexed: 11/21/2022]
Abstract
The rat and mouse amylase gene families were characterized using sequence data from the UCSC genome assembly. We found that the rat genome contains one amylase-1 and two amylase-2 genes, lying close to one another on the same chromosome. Detailed analysis revealed at least six additional amylase pseudogenes in the rat genome in the region adjacent to the amylase-2 genes. In contrast, the mouse has one amylase-1 gene and five amylase-2 genes; the latter are tandemly and systematically arranged on the same chromosome and were generated by segmental duplication. Detailed analysis revealed that the mouse has two amylase pseudogenes, located 5' to the five amylase-2 segments. Thus, the amylase genes of mouse and rat tend to be amplified; the sequences of some of them are fixed while others have become pseudogenes during evolution. This is the second report of amylase genomic organization in mammals and the first in the rodents.
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Affiliation(s)
- Hidehiko Sugino
- Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Suita, Osaka 565-0871, Japan.
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148
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Wyder S, Kriventseva EV, Schröder R, Kadowaki T, Zdobnov EM. Quantification of ortholog losses in insects and vertebrates. Genome Biol 2007; 8:R242. [PMID: 18021399 PMCID: PMC2258195 DOI: 10.1186/gb-2007-8-11-r242] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 10/04/2007] [Accepted: 11/16/2007] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The increasing number of sequenced insect and vertebrate genomes of variable divergence enables refined comparative analyses to quantify the major modes of animal genome evolution and allows tracing of gene genealogy (orthology) and pinpointing of gene extinctions (losses), which can reveal lineage-specific traits. RESULTS To consistently quantify losses of orthologous groups of genes, we compared the gene repertoires of five vertebrates and five insects, including honeybee and Tribolium beetle, that represent insect orders outside the previously sequenced Diptera. We found hundreds of lost Urbilateria genes in each of the lineages and assessed their phylogenetic origin. The rate of losses correlates well with the species' rates of molecular evolution and radiation times, without distinction between insects and vertebrates, indicating their stochastic nature. Remarkably, this extends to the universal single-copy orthologs, losses of dozens of which have been tolerated in each species. Nevertheless, the propensity for loss differs substantially among genes, where roughly 20% of the orthologs have an 8-fold higher chance of becoming extinct. Extrapolation of our data also suggests that the Urbilateria genome contained more than 7,000 genes. CONCLUSION Our results indicate that the seemingly higher number of observed gene losses in insects can be explained by their two- to three-fold higher evolutionary rate. Despite the profound effect of many losses on cellular machinery, overall, they seem to be guided by neutral evolution.
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Affiliation(s)
- Stefan Wyder
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, rue Michel-Servet, 1211 Geneva, Switzerland
| | - Evgenia V Kriventseva
- Swiss Institute of Bioinformatics, rue Michel-Servet, 1211 Geneva, Switzerland
- Department of Structural Biology and Bioinformatics, University of Geneva Medical School, rue Michel-Servet, 1211 Geneva, Switzerland
| | - Reinhard Schröder
- Interf. Institut für Zellbiologie, Abt. Genetik der Tiere, Universität Tübingen, 72076 Tübingen, Germany
| | - Tatsuhiko Kadowaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, rue Michel-Servet, 1211 Geneva, Switzerland
- Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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149
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Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch 2006; 453:125-31. [PMID: 16897042 DOI: 10.1007/s00424-006-0120-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 06/14/2006] [Indexed: 10/24/2022]
Abstract
Sensory organs provide key and, in many cases, species-specific information that allows animals to effectively forage, find mates, and avoid hazards. The primary sensors for the vertebrate senses of vision, taste, and smell are G-protein-coupled receptors (GPCRs) expressed by sensory receptor cells that initiate intracellular signal transduction cascades in response to activation by appropriate stimuli. The identification of sensory GPCRs and their related downstream transduction components from a variety of species has provided an essential tool for understanding the molecular evolution of sensory systems. Expansion of the number of genes encoding sensory GPCRs has, in some cases, expanded the repertoire of signals that animals detect, allowing them to occupy new niches, while, in other cases, evolution has favored a reduction in the repertoire of receptors and their cognate signal transduction components when these signals no longer provide a selective advantage. This review will focus on recent studies that have identified molecular changes in vision, smell, taste, and pheromone detection during primate evolution.
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Affiliation(s)
- Emily R Liman
- Neuroscience Program, Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 3641 Watt Way, Los Angeles, CA 90089, USA.
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