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Duplication Events (duplication + event)
Kinds of Duplication Events Selected AbstractsChromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomesEVOLUTION AND DEVELOPMENT, Issue 5 2003L. F. C. Castro Summary Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and AmphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis -duplication events of genes early in animal evolution. A trans -duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes. [source] Analyses of the CYP11B gene family in the guinea pig suggest the existence of a primordial CYP11B gene with aldosterone synthase activityFEBS JOURNAL, Issue 15 2002Hannes E. Bülow In this study we describe the isolation of three genes of the CYP11B family of the guinea pig. CYP11B1 codes for the previously described 11,-hydroxylase [Bülow, H.E.,Möbius, K., Bähr, V. & Bernhardt, R. (1996) Biochem. Biophys. Res. Commun. 221, 304,312] while CYP11B2 represents the aldosterone synthase gene. As no expression for CYP11B3 was detected this gene might represent a pseudogene. Transient transfection assays show higher substrate specificity for its proper substrate for CYP11B1 as compared to CYP11B2, which could account for the zone-specific synthesis of mineralocorticoids and glucocorticoids, respectively. Thus, CYP11B2 displayed a fourfold higher ability to perform 11,-hydroxylation of androstenedione than CYP11B1, while this difference is diminished with the size of the C17 substituent of the substrate. Furthermore, analyses with the electron transfer protein adrenodoxin indicate differential sensitivity of CYP11B1 and CYP11B2 as well as the three hydroxylation steps catalysed by CYP11B2 to the availability of reducing equivalents. Together, both mechanisms point to novel protein intrinsic modalities to achieve tissue-specific production of mineralocorticoids and glucocorticoids in the guinea pig. In addition, we conducted phylogenetic analyses. These experiments suggest that a common CYP11B ancestor gene that possessed both 11,-hydroxylase and aldosterone synthase activity underwent a gene duplication event before or shortly after the mammalian radiation with subsequent independent evolution of the system in different lines. Thus, a differential mineralocorticoid and glucocorticoid synthesis might be an exclusive achievement of mammals. [source] Characterization of novel GPCR gene coding locus in amphioxus genome: Gene structure, expression, and phylogenetic analysis with implications for its involvement in chemoreceptionGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 2 2005Gouki Satoh Abstract Chemosensation is the primary sensory modality in almost all metazoans. The vertebrate olfactory receptor genes exist as tandem clusters in the genome, so that identifying their evolutionary origin would be useful for understanding the expansion of the sensory world in relation to a large-scale genomic duplication event in a lineage leading to the vertebrates. In this study, I characterized a novel GPCR (G-protein-coupled receptor) gene-coding locus from the amphioxus genome. The genomic DNA contains an intronless ORF whose deduced amino acid sequence encodes a seven-transmembrane protein with some amino acid residues characteristic of vertebrate olfactory receptors (ORs). Surveying counterparts in the Ciona intestinalis (Asidiacea, Urochordata) genome by querying BLAST programs against the Ciona genomic DNA sequence database resulted in the identification of a remotely related gene. In situ hybridization analysis labeled primary sensory neurons in the rostral epithelium of amphioxus adults. Based on these findings, together with comparison of the developmental gene expression between amphioxus and vertebrates, I postulate that chemoreceptive primary sensory neurons in the rostrum are an ancient cell population traceable at least as far back in phylogeny as the common ancestor of amphioxus and vertebrates. genesis 41:47,57, 2005. © 2005 Wiley-Liss, Inc. [source] Gene duplication, exon gain and neofunctionalization of OEP16 -related genes in land plantsTHE PLANT JOURNAL, Issue 5 2006Sinéad C. Drea Summary OEP16, a channel protein of the outer membrane of chloroplasts, has been implicated in amino acid transport and in the substrate-dependent import of protochlorophyllide oxidoreductase A. Two major clades of OEP16-related sequences were identified in land plants (OEP16-L and OEP16-S), which arose by a gene duplication event predating the divergence of seed plants and bryophytes. Remarkably, in angiosperms, OEP16-S genes evolved by gaining an additional exon that extends an interhelical loop domain in the pore-forming region of the protein. We analysed the sequence, structure and expression of the corresponding Arabidopsis genes (atOEP16-S and atOEP16-L) and demonstrated that following duplication, both genes diverged in terms of expression patterns and coding sequence. AtOEP16-S, which contains multiple G-box ABA-responsive elements (ABREs) in the promoter region, is regulated by ABI3 and ABI5 and is strongly expressed during the maturation phase in seeds and pollen grains, both desiccation-tolerant tissues. In contrast, atOEP-L, which lacks promoter ABREs, is expressed predominantly in leaves, is induced strongly by low-temperature stress and shows weak induction in response to osmotic stress, salicylic acid and exogenous ABA. Our results indicate that gene duplication, exon gain and regulatory sequence evolution each played a role in the divergence of OEP16 homologues in plants. [source] Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomesEVOLUTION AND DEVELOPMENT, Issue 5 2003L. F. C. Castro Summary Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and AmphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis -duplication events of genes early in animal evolution. A trans -duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes. [source] Expression of a homologue of the fushi tarazu (ftz) gene in a cirripede crustaceanEVOLUTION AND DEVELOPMENT, Issue 2 2002Emmanuèle Mouchel-Vielh SUMMARY In Metazoa, Hox genes control the identity of the body parts along the anteroposterior axis. In addition to this homeotic function, these genes are characterized by two conserved features: They are clustered in the genome, and they contain a particular sequence, the homeobox, encoding a DNA-binding domain. Analysis of Hox homeobox sequences suggests that the Hox cluster emerged early in Metazoa and then underwent gene duplication events. In arthropods, the Hox cluster contains eight genes with a homeotic function and two other Hox -like genes, zerknullt (zen)/Hox3 and fushi tarazu (ftz). In insects, these two genes have lost their homeotic function but have acquired new functions in embryogenesis. In contrast, in chelicerates, these genes are expressed in a Hox -like pattern, which suggests that they have conserved their ancestral homeotic function. We describe here the characterization of Diva, the homologue of ftz in the cirripede crustacean Sacculina carcini. Diva is located in the Hox cluster, in the same position as the ftz genes of insects, and is not expressed in a Hox -like pattern. Instead, it is expressed exclusively in the central nervous system. Such a neurogenic expression of ftz has been also described in insects. This study, which provides the first information about the Hox cluster in Crustacea, reveals that it may not be much smaller than the insect cluster. Study of the Diva expression pattern suggests that the arthropod ftz gene has lost its ancestral homeotic function after the divergence of the Crustacea/Hexapoda clade from other arthropod clades. In contrast, the function of ftz during neurogenesis is well conserved in insects and crustaceans. [source] Organization of six functional mouse alcohol dehydrogenase genes on two overlapping bacterial artificial chromosomesFEBS JOURNAL, Issue 1 2002Gabor Szalai Mammalian alcohol dehydrogenases (ADH) form a complex enzyme system based on amino-acid sequence, functional properties, and gene expression pattern. At least four mouse Adh genes are known to encode different enzyme classes that share less than 60% amino-acid sequence identity. Two ADH-containing and overlapping C57BL/6 bacterial artificial chromosome clones, RP23-393J8 and -463H24, were identified in a library screen, physically mapped, and sequenced. The gene order in the complex and two new mouse genes, Adh5a and Adh5b, and a pseudogene, Adh5ps, were obtained from the physical map and sequence. The mouse genes are all in the same transcriptional orientation in the order Adh4 - Adh1 - Adh5a - Adh5b - Adh5ps - Adh2 - Adh3. A phylogenetic tree analysis shows that adjacent genes are most closely related suggesting a series of duplication events resulted in the gene complex. Although mouse and human ADH gene clusters contain at least one gene for ADH classes I,V, the human cluster contains 3 class I genes while the mouse cluster has two class V genes plus a class V pseudogene. [source] Evolution and phylogenetic relationships of APSES proteins from HemiascomycetesFEMS YEAST RESEARCH, Issue 4 2008Bernardo Ramírez-Zavala Abstract Available complete genomic sequences of hemiascomycetous yeast species were analysed in order to identify the APSES protein family, which belongs to transcriptional factors of the basic helix,loop,helix (bHLH) class. Phylogenetic analyses of the amino acid sequences revealed that a similar set of proteins were present in all yeast species studied. The genome duplication event of Saccharomycetales allows the acquisition of complementary functions between the APSES proteins. Putative ancestors, such as Ashbya gossypii, the Kluyveromyces group and filamentous fungi, only have one APSES protein. Conserved gene order relationships allow the possibility of tracing the evolution of this family and the detection of duplication events. Multiple alignments revealed strict conservation of the APSES motif, although other regions of the APSES proteins were diversified. This review focuses on the evolution of the gene family of APSES proteins in related Hemiascomycetes species; the comparisons could shed light on the functional overlap of these proteins with regard to the regulation of morphogenetic processes and their involvement in the virulence of pathogenic microorganisms. [source] Object-oriented approach to drug design enabled by NMR SOLVE: First real-time structural tool for characterizing protein,ligand interactionsJOURNAL OF CELLULAR BIOCHEMISTRY, Issue S37 2001Daniel S. Sem Abstract As a result of genomics efforts, the number of protein drug targets is expected to increase by an order of magnitude. Functional genomics efforts are identifying these targets, while structural genomics efforts are determining structures for many of them. However, there is a significant gap in going from structural information for a protein target to a high affinity (Kd,<,100 nM) inhibitor, and the problem is multiplied by the sheer number of new targets now available. nature frequently designs proteins in classes that are related by the reuse, through gene duplication events, of cofactor binding domains. This reuse of functional domains is an efficient way to build related proteins in that it is object-oriented. There is a growing realization that the most efficient drug design strategies for attacking the mass of targets coming from genomics efforts will be systems-based approaches that attack groups of related proteins in parallel. We propose that the most effective drug design strategy will be one that parallels the object-oriented manner by which nature designed the gene families themselves. IOPE (Integrated Object-Oriented PharmacoEngineering) is such an approach. It is a three-step technology to build focused combinatorial libraries of potential inhibitors for major families and sub-families of enzymes, using cogent NMR data derived from representatives of these protein families. The NMR SOLVE (Structurally Oriented Library Valency Engineering) data used to design these libraries are gathered in days, and data can be obtained for large proteins (>,170 kDa). Furthermore, the process is fully object-oriented in that once a given bi-ligand is identified for a target, potency is retained if different cofactor mimics are swapped. This gives the drug design process maximum flexibility, allowing for the more facile transition from in vitro potency to in vivo efficacy. J. Cell. Biochem. Suppl. 37: 99,105, 2001. © 2002 Wiley-Liss, Inc. [source] A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and OryzaJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 6 2007Chuanzhu Fan Abstract To systematically estimate the gene duplication events in closely related species, we have to use comparative genomic approaches, either through genomic sequence comparison or comparative genomic hybridization (CGH). Given the scarcity of complete genomic sequences of plant species, in the present study we adopted an array based CGH to investigate gene duplications in the genus Arabidopsis. Fragment genomic DNA from four species, namely Arabidopsis thaliana, A. lyrata subsp. lyrata, A. lyrata subsp. petraea, and A. halleri, was hybridized to Affymetrix (Santa Clara, CA, USA) tiling arrays that are designed from the genomic sequences of A. thaliana. Pairwise comparisons of signal intensity were made to infer the potential duplicated candidates along each phylo-genetic branch. Ninety-four potential candidates of gene duplication along the genus were identified. Among them, the majority (69 of 94) were A. thaliana lineage specific. This result indicates that the array based CGH approach may be used to identify candidates of duplication in other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. sativa and A. thaliana and found a strikingly higher number of chimera retroposed genes in rice. The higher rate of gene duplication through retroposition and other mechanisms may indicate that the grass species is able to adapt to more diverse environments. [source] Similar gene structure of two Sox9a genes and their expression patterns during gonadal differentiation in a teleost fish, rice field eel (Monopterus albus)MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 3 2003Rongjia Zhou Abstract The Sox9 gene encodes a transcription factor that is critical for testis determination and chondrogenesis in vertebrates. Mutations in human SOX9 cause campomelic dysplasia, a dominant skeletal dysmorphology syndrome often associated with male to female sex reversal. Here we show that the Sox9a gene was duplicated during evolution of the rice field eel, Monopterus albus, a freshwater fish which undergoes natural sex reversal from female to male during its life, and has a haploid genome size (0.6,0.8 pg) that is among the smallest of the vertebrates. The duplicated copies of the gene (named Sox9al and Sox9a2) fit within the Sox9 clade of vertebrates, especially in the Sox9a subfamily, not in the Sox9b subfamily. They have similar structures as revealed by both genomic and cDNA analysis. Furthermore, both Sox9al and Sox9a2 are expressed in testis, ovary, and ovotestis; and specifically in the outer layer (mainly gonocytes) of gonadal epithelium with bipotential capacity to form testis or ovary, suggesting that they have similar roles in gonadal differentiation during sex reversal in this species. The closely related gene structure and expression patterns of the two sox9a genes in the rice field eel also suggest that they arose in recent gene duplication events during evolution of this fish lineage. Mol. Reprod. Dev. 66: 211,217, 2003. © 2003 Wiley-Liss, Inc. [source] Two sunflower 17.6HSP genes, arranged in tandem and highly homologous, are induced differently by various elicitorsPLANT BIOLOGY, Issue 1 2010P. Rampino Abstract Plants respond to environmental stimuli, such as heat shock, by re-programming cellular activity through differential gene expression, mainly controlled at the transcription level. The current study refers to two sunflower small heat shock protein (sHSP) genes arranged in tandem in head-to-head orientation and linked by a 3809 bp region. These genes exhibit only slight structural differences in the coding portion. They code for cytosolic class I sHSPs and are named HaHSP17.6a and HaHSP17.6b according to the molecular weight of the putative proteins. The genomic organization of these genes is consistent with the idea that many HSP genes originate from duplication events; in this case, probably an inversion and duplication occurred. The HaHSP17.6a and HaHSP17.6b genes are characterized by different expression levels under various heat stress conditions; moreover, their expression is differently induced by various elicitors. The differential regulation observed for HaHSP17.6a and HaHSP17.6b genes differs from previous observations on duplicated sHSP genes in plants. [source] Functionally redundant SHI family genes regulate Arabidopsis gynoecium development in a dose-dependent mannerTHE PLANT JOURNAL, Issue 1 2006Sandra Kuusk Summary Gene duplication events, and the subsequent functional divergence of duplicates, are believed to be important evolutionary agents, driving morphological diversification. We have studied the structural and functional diversification of members of a plant-specific gene family in Arabidopsis thaliana by analysing mutant phenotypes, expression patterns and phylogeny. The SHI gene family comprises ten members that encode proteins with a RING finger-like zinc finger motif. We show that, despite being highly divergent in sequence, except in two conserved regions, many of the SHI -related genes are partially redundant in function and synergistically promote gynoecium, stamen and leaf development in Arabidopsis. Gynoecia of the loss-of-function sty1-1 mutant display subtle morphological defects, and, although mutations in the related STY2, SHI, SRS3, SRS4, SRS5, SRS7 and LRP1 genes have no apparent effect on gynoecium development, the sty1-1 mutant phenotype is gradually enhanced in double, triple, quadruple and quintuple mutant combinations, suggesting a remarkably extensive functional conservation within the family, which appears to be based on dosage dependency and protection against dominant negative mutations. In multiple mutant lines, all marginal tissues in the apical part of the gynoecium are dramatically reduced or missing, and our data indicate that SHI family members may promote formation of these tissues downstream of the transcriptional co-repressor LEUNIG (LUG). [source] New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genomeTHE PLANT JOURNAL, Issue 3 2004Jérôme Salse Summary A unigene set of 1411 contigs was constructed from 2629 redundant maize expressed sequence tags (ESTs) mapped on the maizeDB genetic map. Rice orthologous sequences were identified by blast alignment against the rice genomic sequence. A total of 1046 (74%) maize contigs were associated with their corresponding homologues in the rice genome and 656 (47%) defined as potential orthologous relationships. One hundred and seventeen (8%) maize EST contigs mapped to two distinct loci on the maize genetic map, reflecting the tetraploid nature of the maize genome. Among 492 mono-locus contigs, 344 (484 redundant ESTs) identify collinear blocks between maize chromosomes 2 and 4 and a single rice chromosome, defining six new collinear regions. Fine-scale analysis of collinearity between rice chromosomes 1 and 5 with maize chromosomes 3, 6 and 8 shows the presence of internal rearrangements within collinear regions. Mapping of maize contigs to two distinct loci on the rice sequence identifies five new duplication events in rice. Detailed analysis of a duplication between rice chromosomes 1 and 5 shows that 11% of the annotated genes from the chromosome 1 locus are found duplicated on the chromosome 5 paralogous counterpart, indicating a high degree of re-organisations. The implications of these findings for map-based cloning in collinear regions are discussed. [source] | ||||||||||||||||||||||