Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions

One important mechanism for functional innovation during evolution is the duplication of genes and entire genomes. Evidence is accumulating that during the evolution of vertebrates from early deuterostome ancestors entire genomes were duplicated through two rounds of duplications (the 'one-to-two-to-four' rule). The first genome duplication in chordate evolution might predate the Cambrian explosion. The second genome duplication possibly dates back to the early Devonian. Recent data suggest that later in the Devonian, the fish genome was duplicated for a third time to produce up to eight copies of the original deuterostome genome. This last duplication took place after the two major radiations of jawed vertebrate life, the ray-finned fish (Actinopterygia) and the sarcopterygian lineage, diverged. Therefore the sarcopterygian fish, which includes the coelacanth, lungfish and all land vertebrates such as amphibians, reptiles, birds and mammals, tend to have only half the number of genes compared with actinopterygian fish. Although many duplicated genes turned into pseudogenes, or even 'junk' DNA, many others evolved new functions particularly during development. The increased genetic complexity of fish might reflect their evolutionary success and diversity.     

Satellite Ic: a possible link between the satellite DNAs of D. virilis and D. melanogaster.

In this study, we isolated and characterized a previously undetected cryptic satellite DNA comprising 0.1% of the total nuclear genome of D. virilis. This satellite is hidden from detection in neutral CsCl by satellite I and is therefore designated cryptic satellite I or Ic. Sequence analysis reveals that Ic is the repeating heptanucleotide [poly d(AATATAG): d(CTATATT)]. It is more closely related to the three simple sequence satellite DNAs of D. melanogaster, a distantly related species, than it is to any of the major D. virilis satellite DNA sequences. Ic may therefore be a link between the simple sequence satellites of D. virilis and D. melanogaster. As an extension of this theory, we have constructed a "family tree" linking the satellites of D. virilis and D. melanogaster by a series of "simple" operations. Only one intermediate required by this evolutionary scheme has not yet been identified.     

Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis

Pair-rule genes serve two important functions during Drosophila development: they first initiate periodic patterns, and subsequently interact with each other to refine these patterns to the precision required for definition of segmental compartments. Previously, we described a pair-rule input region of the runt gene. Here we further characterize this region through the use of reporter gene constructs and by comparison with corresponding sequences from Drosophila virilis. We find that many but not all regulatory properties of this '7-stripe region' are functionally conserved. Moreover, the similarity between these homologous sequences is surprisingly low. When compared to similar data for gap gene input element, our data suggest that pair-rule target sequences are less constrained during evolution, and that functional elements mediating pair-rule interactions can be dispersed over many kilobases.     

Evolution of CC chemokines in teleost fish: a case study in gene duplication and implications for immune diversity

Chemokines are a superfamily of cytokines responsible for regulating cell migration under both inflammatory and physiological conditions. CC chemokines are the largest subfamily of chemokines, with 28 members in humans. A subject of intense study in mammalian species, the known functional roles of CC chemokines ligands in both developmental and disease conditions continue to expand. They are also an important family for the study of gene copy number variation and tandem duplication in mammalian species. However, little is known regarding the evolutionary origin and status of these ligands in primitive vertebrates such as teleost fish. In this paper, we review the evolution of the teleost fish CC chemokine gene family, noting evidence of widespread tandem gene duplications and examining the implications of this phenomenon on immune diversity. Through extensive phylogenetic analysis of the CC chemokine sets of four teleost species, zebrafish, catfish, rainbow trout, and Atlantic salmon, we identified seven large groups of CC chemokines. It appeared that several major groups of CC chemokines are highly related including the CCL19/21/25 group, the CCL20 group, CCL27/28 group, and the fish-specific group. In the three remaining groups that contained the largest number of members, the CCL17/22 group, the MIP group, and the MCP group, similarities among species members were obscured by rapid, tandem duplications that may contribute to immune diversity.     

Evolution of the bovine lysozyme gene family: Changes in gene expression and reversion of function

Recruitment of lysozyme to a digestive function in ruminant artiodactyls is associated with amplification of the gene. At least four of the approximately ten genes are expressed in the stomach, and several are expressed in nonstomach tissues. Characterization of additional lysozymelike sequences in the bovine genome has identified most, if not all, of the members of this gene family. There are at least six stomachlike lysozyme genes, two of which are pseudogenes. The stomach lysozyme pseudogenes show a pattern of concerted evolution similar to that of the functional stomach genes. At least four nonstomach lysozyme genes exist. The nonstomach lysozyme genes are not monophyletic. A gene encoding a tracheal lysozyme was isolated, and the stomach lysozyme of advanced ruminants was found to be more closely related to the tracheal lysozyme than to the stomach lysozyme of the camel or other nonstomach lysozyme genes of ruminants. The tracheal lysozyme shares with stomach lysozymes of advanced ruminants the deletion of amino acid 103, and several other adaptive sequence characteristics of stomach lysozymes. I suggest here that tracheal lysozyme has reverted from a functional stomach lysozyme. Tracheal lysozyme then represents a second instance of a change in lysozyme gene expression and function within ruminants. Correspondence to: D.M. Irwin     

The genome of the diploid anuran <Emphasis Type="Italic">Xenopus tropicalis</Emphasis> contains a novel array of sarcoplasmic myosin heavy chain genes expressed in larval muscle and larynx

The sarcomeric myosin heavy chain (MyHC) proteins are a family of molecular motors responsible for the transduction of chemical energy into mechanical work in striated muscle. The vertebrate genome contains multiple copies of the MyHC gene, and expression of different isoforms correlates with differences in the physiological properties of muscle fibers. Most MyHC isoforms are found in two arrays, one containing the "fast-twitch" skeletal muscle isoforms and the other the "slow-twitch" or cardiac isoforms. To extend our understanding of MyHC evolution, we have examined the genome of the anuran Xenopus tropicalis. The X. tropicalis genome includes15 full-length MyHC genes organized in seven genomic locations. One unique array of MyHC genes is similar to the mammalian fast-skeletal array, but is not found in amniotes. The isoforms in this array are expressed during larval stages and in muscles of the adult larynx. Duplication of the fast-skeletal MyHC array appears to have led to expression divergence of muscle proteins in the larval and adult stages of the anuran life cycle. A striking similarity of gene order between regions flanking X. tropicalis MyHC arrays and human arrays was evident; genomic organization of MyHC isoforms may thus be highly conserved across tetrapods.     

黑腹果蝇white基因在H2O2影响下卷翅形成中的作用及机理

卷翅是果蝇遗传学上最常用的标记之一,但卷翅形成的具体机制还不清楚.过去的研究发现,理化刺激影响果蝇卷翅的形成.我们最近研究发现,H₂O₂处理不仅会影响果蝇的羽化率,还会使其出现卷翅现象.本研究通过改变H₂O₂浓度、果蝇培养温度和H₂O₂处理时间,探讨影响黑腹果蝇卷翅形成的具体因素,并对其超氧化物歧化酶(SOD)、过氧化氢酶(CAT)和谷胱甘肽过氧化物酶(GSH-PX)活力进行检测,探讨H₂O₂对果蝇抗氧化能力的影响.结果表明: 果蝇的羽化率与H₂O₂浓度成反比.温度、H₂O₂浓度和H₂O₂处理时间的改变均会影响果蝇翅的卷曲程度和卷翅果蝇所占的比例.其中white基因突变果蝇对这3种条件反应最明显,mini-white(white基因回复突变)果蝇却可以拯救该表型,它的反应与野生型OR相似.H₂O₂对含Cy基因的果蝇卷翅的形成也有一定的影响,可以加大果蝇翅的卷曲程度.对SOD、CAT和GSH-PX活力检测发现,H₂O₂处理会使果蝇的抗氧化能力降低.实时荧光定量PCR检测发现,H₂O₂处理会导致果蝇基因表达量发生改变.黑腹果蝇卷翅形成是一个十分复杂的过程,H₂O₂可能作为某种信号分子或是间接影响某种因子参与黑腹果蝇的卷翅形成过程.该卷翅形成过程可能与Cy基因导致的果蝇卷翅过程是同一个信号途径,两者也可能是通过不同的模式进行调控的.     

Association of vitamin D receptor gene polymorphism with the risk of lung cancer: a meta-analysis

Abstract

Relationship between vitamin D receptor (VDR) gene polymorphism and the risk of lung cancer from the published reports are still conflicting. This study was conducted to evaluate the relationship between VDR TaqI (rs731236), BsmI (rs1544410) and ApaI (rs7975232) gene polymorphism and the risk of lung cancer using meta-analysis method. The association studies were identified from PubMed and Cochrane Library on 1 December 2013, and eligible investigations were included and synthesized using meta-analysis method. Six reports were recruited into this meta-analysis for the association of VDR gene polymorphism with lung cancer susceptibility. In the meta-analysis for ApaI gene polymorphism, AA genotype was associated with the risk of lung cancer in Asians. In the meta-analysis for BsmI gene polymorphism, B allele, BB genotype and bb genotype were associated with lung cancer in Asians, and B allele bb genotype were associated with lung cancer risk in overall populations; furthermore, bb genotype was associated with lung cancer risk in Caucasians. In the meta-analysis for TaqI gene polymorphism, t allele and TT genotype were associated with lung cancer in overall populations and in Caucasians. In conclusion, B allele bb genotype t allele and TT genotype were associated with lung cancer risk in overall populations. AA genotype, B allele, BB genotype and bb genotype were associated with the risk of lung cancer in Asians. Furthermore, bb genotype t allele and TT genotype was associated with lung cancer risk in Caucasians. However, more studies should be conducted to confirm it.     

Association of vitamin D receptor gene polymorphism with the risk of renal cell carcinoma: a meta-analysis

Abstract

Relationship between vitamin D receptor (VDR) gene polymorphism and the risk of renal cell carcinoma from the published reports are still conflicting. This study was conducted to evaluate the relationship between VDR ApaI (rs7975232), BsmI (rs1544410), TaqI (rs731236), and Fok1 (rs2228570) gene polymorphism and the risk of renal cell carcinoma using meta-analysis method. The association studies were identified from PubMed, and Cochrane Library on 1 March 2014, and eligible investigations were included and synthesized using meta-analysis method. Five reports were recruited into this meta-analysis for the association of VDR gene polymorphism with renal cell carcinoma susceptibility. In this meta-analysis, the ApaI AA genotype, BsmI BB genotype, Fok1 f allele, and Fok1 FF genotype were associated with the risk of renal cell carcinoma in Asians. However, VDR ApaI, BsmI, TaqI, and Fok1 gene polymorphism were not associated with the risk of renal cell carcinoma in overall populations and in Caucasians. In conclusion, the ApaI AA genotype, BsmI BB genotype, Fok1 f allele, and Fok1 FF genotype were associated with the risk of renal cell carcinoma in Asians. However, more studies should be conducted to confirm it.     

Genome scans of variation and adaptive change: extended analysis of a candidate locus close to the phantom gene region in Drosophila melanogaster

Nucleotide variation in populations originating from the recent range expansion of a species should reflect their adaptation to new habitats as well as their demographic history. A survey of nucleotide variation at 109 noncoding X-chromosome fragments in a European population of Drosophila melanogaster allowed identifying some candidates to have been recently affected by positive selection. Adaptive changes leave a spatial differential footprint that can be used to discriminate among candidates by extending their study to neighboring regions. Here, we surveyed variation at an approximately 190-kb region spanning a locus exhibiting a significantly skewed frequency spectrum. A stretch of approximately 12 kb with reduced variation was detected within a continuously sequenced region that included the focal fragment. Moreover, the regions flanking this stretch exhibited an excess of high-frequency derived variants. Application of maximum likelihood ratio and goodness-of-fit tests suggested that the pattern of variation detected at the studied region (at cytological bands 17C-17D) might have been shaped by a recent selective change, most probably at or around the phantom gene that encodes CYP306A1, a cytochrome P450 enzyme in the ecdysteroidogenic pathway.     

A single amino-acid substitution toggles chloride dependence of the alpha-amylase paralog amyrel in Drosophila melanogaster and Drosophila virilis species

In animals, most α-amylases are chloride-dependent enzymes. A chloride ion is required for allosteric activation and is coordinated by one asparagine and two arginine side chains. Whereas the asparagine and one arginine are strictly conserved, the main chloride binding arginine is replaced by a glutamine in some rare instances, resulting in the loss of chloride binding and activation. Amyrel is a distant paralogue of α-amylase in Diptera, which was not characterized biochemically to date. Amyrel shows both substitutions depending on the species. In Drosophila melanogaster, an arginine is present in the sequence but in Drosophila virilis, a glutamine occurs at this position. We have investigated basic enzymological parameters and the dependence to chloride of Amyrel of both species, produced in yeast, and in mutants substituting arginine to glutamine or glutamine to arginine. We found that the amylolytic activity of Amyrel is about thirty times weaker than the classical Drosophila α-amylase, and that the substitution of the arginine by a glutamine in D. melanogaster suppressed the chloride-dependence but was detrimental to activity. In contrast, changing the glutamine into an arginine rendered D. virilis Amyrel chloride-dependent, and interestingly, significantly increased its catalytic efficiency. These results show that the chloride ion is not mandatory for Amyrel but stimulates the reaction rate. The possible phylogenetic origin of the arginine/glutamine substitution is also discussed.     

Evolution of a multigene family that encodes the Kunitz chymotrypsin inhibitor in winged bean: a possible intermediate in the generation of a new gene with a distinct pattern of expression

Winged bean Kunitz chymotrypsin inhibitor (WCI) accumulates in an organ-specific and temporally regulated manner. The protein is encoded by a multigene family that includes at least four putative inhibitor-coding genes and three pseudogenes. The structure of the WCI genes indicates that an insertion at a 5′ proximal site occurred after duplication of the ancestral WCI gene and that several gene conversion events subsequently contributed to the evolution of this gene family. Analysis of the promoter activity of the 5′ regions of the WCI genes in transgenic tobacco showed that only the 5′ regions of the WCI-3a and WCI-3b genes, which encode the major WCI protein in winged bean, promoted the organ-specific and temporally regulated expression of a reporter gene. The 5′ region of a pseudogene, the WCI-P1 gene which contains frameshift mutations, exhibited constitutive promoter activity in tobacco, an indication that the 5′ region of the WCI-P1 gene might spontaneously have acquired new regulatory sequences during evolution. Since gene conversion is a relatively frequent event and since the homology between the WCI-P1 and WCI-3a/b genes is disrupted at a 5′ proximal site by remnants of an inserted sequence, the WCI-P1 gene appears to be a possible intermediate that could be converted into a new functional gene with a distinct pattern of expression by a single gene-conversion event. Received: 17 April 1996 / Accepted: 23 October 1996     

Heterochromatin markers: Arrangement of obligatory heterochromatin,histone genes and multisite gene families in the interphase nucleus of D. melanogaster

Localization, as detected by in situ hybridization, of major heterochromatic blocks in interphase nuclei of larval brain and imaginal discs is reported. We conclude that the position of heterochromatic regions in interphase nuclei is correlated with their respective position in metaphase chromosomes and hence, independent of sequence recognition. Furthermore, chromocentral associations of X-, Y- or autosomal-based heterochromatin are not formed in these cells. Homologues do align in close proximity, but heterochromatin plays no role in this arrangement. Heterochromatin, and probably nucleoli, establish their membrane links in situ, and have no prefixed recognition sites. The most intimate association between homologous repetitive sequences was found in the histone locus, but no tendency for clustering was found among loci of multisite euchromatic gene families.     

Quantitative comparison of foliage development amongDryopteris monticola,D. tokyoensis and a putative hybrid,D. kominatoensis in Northern Japan

Developmental leaf architecture was quantitatively described in terms of measurements of various parameters on leaf blade from different size of sporophytes inDryopteris monticola, D. tokyoensis and a putative hybrid,D. kominatoensis in the natural site of Hokkaido, to compare the ontogenetic differentiation in foliage structure among allied ferns. The morphological stage of leaf and sporophyte was tentatively quantified by the number of midrib branches of the leaf (NV, number of veins), which exhibited a significant correlation to the leaf-shape complexity from a circle (DI=marginal length/2×(3.14×square)^1/2) of leaf blade. D. kominatoensis showed intermediate values between others in following characters; DI increase, maximum NV (also blade length), maximum number of costa branches of pinnae (NVMP), number of costa branches of the lowest pinna (NVLP), difference between NVMP and NVLP (NVMP-NVLP), during heteroblastic leaf development. A larger number of leaves per sporophyte was found inD. kominatoensis than in others. The fertility rate (%) and initiation of fertility (IF) in the relative developmental stage (RDS) ofD. kominatoensis shifted to that ofD. tokyoensis, while the order of pinnae with NVMP shifted to that ofD. monticola. Even in the intermediate characters inD. kominatoensis, slight shifts in characters to those of putative parents were found during heteroblastic leaf development. Contribution No. 3145 from the Institute of Low Temperature Science, Hokkaido University.