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Gene Duplication (gene + duplication)
Terms modified by Gene Duplication Selected AbstractsALLELIC DIVERGENCE PRECEDES AND PROMOTES GENE DUPLICATIONEVOLUTION, Issue 5 2006Stephen R. Proulx Abstract One of the striking observations from recent whole-genome comparisons is that changes in the number of specialized genes in existing gene families, as opposed to novel taxon-specific gene families, are responsible for the majority of the difference in genome composition between major taxa. Previous models of duplicate gene evolution focused primarily on the role that neutral processes can play in evolutionary divergence after the duplicates are already fixed in the population. By instead including the entire cycle of duplication and divergence, we show that specialized functions are most likely to evolve through strong selection acting on segregating alleles at a single locus, even before the duplicate arises. We show that the fitness relationships that allow divergent alleles to evolve at a single locus largely overlap with the conditions that allow divergence of previously duplicated genes. Thus, a solution to the paradox of the origin of organismal complexity via the expansion of gene families exists in the form of the deterministic spread of novel duplicates via natural selection. [source] Simulating evolution by gene duplication of protein features that require multiple amino acid residuesPROTEIN SCIENCE, Issue 10 2004Michael J. Behe MR, multiresidue Abstract Gene duplication is thought to be a major source of evolutionary innovation because it allows one copy of a gene to mutate and explore genetic space while the other copy continues to fulfill the original function. Models of the process often implicitly assume that a single mutation to the duplicated gene can confer a new selectable property. Yet some protein features, such as disulfide bonds or ligand binding sites, require the participation of two or more amino acid residues, which could require several mutations. Here we model the evolution of such protein features by what we consider to be the conceptually simplest route,point mutation in duplicated genes. We show that for very large population sizes N, where at steady state in the absence of selection the population would be expected to contain one or more duplicated alleles coding for the feature, the time to fixation in the population hovers near the inverse of the point mutation rate, and varies sluggishly with the ,th root of 1/N, where , is the number of nucleotide positions that must be mutated to produce the feature. At smaller population sizes, the time to fixation varies linearly with 1/N and exceeds the inverse of the point mutation rate. We conclude that, in general, to be fixed in 108 generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 109. [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] Dinoflagellate mitochondrial genomes: stretching the rules of molecular biologyBIOESSAYS, Issue 2 2009Ross F. Waller Abstract Mitochondrial genomes represent relict bacterial genomes derived from a progenitor ,-proteobacterium that gave rise to all mitochondria through an ancient endosymbiosis. Evolution has massively reduced these genomes, yet despite relative simplicity their organization and expression has developed considerable novelty throughout eukaryotic evolution. Few organisms have reengineered their mitochondrial genomes as thoroughly as the protist lineage of dinoflagellates. Recent work reveals dinoflagellate mitochondrial genomes as likely the most gene-impoverished of any free-living eukaryote, encoding only two to three proteins. The organization and expression of these genomes, however, is far from the simplicity their gene content would suggest. Gene duplication, fragmentation, and scrambling have resulted in an inflated and complex genome organization. Extensive RNA editing then recodes gene transcripts, and trans-splicing is required to assemble full-length transcripts for at least one fragmented gene. Even after these processes, messenger RNAs (mRNAs) lack canonical start codons and most transcripts have abandoned stop codons altogether. [source] Gene duplications and the time thereafter , examples from plant secondary metabolismPLANT BIOLOGY, Issue 4 2010D. Ober Abstract Gene duplications are regarded as one of the central mechanisms for the origin of new genes. Recent studies in plant secondary metabolism have provided several examples of genes that originated by duplication with successive diversification. In this review, the mechanisms of gene duplication are explained and several models discussed that suggest the way that gene duplicates develop into genes with new functions. Signatures of gene duplication and diversification processes are discussed using the biosynthesis of benzoxazinones and of pyrrolizidine alkaloids as examples. [source] THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATIONEVOLUTION, Issue 5 2007Hopi E. Hoekstra An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis -regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis -regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis -regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis -regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis -regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis -regulatory and structural mutations, with a substantial contribution of the latter. [source] Ontogeny of sexual dimorphism via tissue duplication in an ostracod (Crustacea)EVOLUTION AND DEVELOPMENT, Issue 2 2009Ajna S. Rivera SUMMARY The adaptive significance of specific sexual dimorphism is well studied. However, the evolutionary history and ontogenic origins of the dimorphism are often unknown. As dimorphism represents two phenotypes generated from relatively similar genotypes, it is of interest to understand both its evolutionary and developmental/genetic underpinnings. Here, we present the first ontogenetic examination of the eyes of philomedid ostracods (Crustacea), which exhibit extremely sexually dimorphic lateral eyes. Adult male philomedids have large compound lateral eyes, whereas females have rudimentary lateral eyes. First, we show that eye dimorphism is unlikely to be due to additional genes present on a male-specific chromosome because karyotype analysis suggests philomedids are XX/XO. We then examine the ontogeny of eye development and find that in at least two species of Euphilomedes, this dimorphism is not generated solely by differences in tissue growth rates, as has been commonly shown for sexually dimorphic characters of other species. Instead, the dimorphism appears to arise during development via tissue duplication, where a single tissue becomes two, perhaps with different developmental potentials. The second eye field is only observed in male Euphilomedes, producing most of the adult eye tissue. We point out that tissue duplication is a developmental process with evolutionary implications because novel characters could evolve via alternative modification of the duplicated fields, analogous to the origin of new genes by gene duplication and alternative modification. Depending on the evolutionary history of the duplicated field, it may have either facilitated or directly caused the observed sexual dimorphism of philomedid ostracods. [source] Platypus Pou5f1 reveals the first steps in the evolution of trophectoderm differentiation and pluripotency in mammalsEVOLUTION AND DEVELOPMENT, Issue 6 2008Hitoshi Niwa SUMMARY Uterine nourishment of embryos by the placenta is a key feature of mammals. Although a variety of placenta types exist, they are all derived from the trophectoderm (TE) cell layer of the developing embryo. Egg-laying mammals (platypus and echidnas) are distinguished by a very short intrauterine embryo development, in which a simple placenta forms from TE-like cells. The Pou5f1 gene encodes a class V POU family transcription factor Oct3/4. In mice, Oct3/4 together with the highly conserved caudal -related homeobox transcription factor Cdx2, determines TE fate in pre-implantation development. In contrast to Cdx2, Pou5f1 has only been identified in eutherian mammals and marsupials, whereas, in other vertebrates, pou2 is considered to be the Pou5f1 ortholog. Here, we show that platypus and opossum genomes contain a Pou5f1 and pou2 homolog, pou2-related, indicating that these two genes are paralogues and arose by gene duplication in early mammalian evolution. In a complementation assay, we found that platypus or human Pou5f1, but not opossum or zebrafish pou2, restores self-renewal in Pou5f1 -null mouse ES cells, showing that platypus possess a fully functional Pou5f1 gene. Interestingly, we discovered that parts of one of the conserved regions (CR4) is missing from the platypus Pou5f1 promoter, suggesting that the autoregulation and reciprocal inhibition between Pou5f1 and Cdx2 evolved after the divergence of monotremes and may be linked to the development of more elaborate placental types in marsupial and eutherian mammals. [source] Today's multiple choice exam: (a) gene duplication; (b) structural mutation; (c) co-option; (d) regulatory mutation; (e) all of the aboveEVOLUTION AND DEVELOPMENT, Issue 6 2007Todd H. Oakley No abstract is available for this article. [source] A gene duplication led to specialized ,-aminobutyrate and ,-alanine aminotransferase in yeastFEBS JOURNAL, Issue 7 2007Gorm Andersen In humans, ,-alanine (BAL) and the neurotransmitter ,-aminobutyrate (GABA) are transaminated by a single aminotransferase enzyme. Apparently, yeast originally also had a single enzyme, but the corresponding gene was duplicated in the Saccharomyces kluyveri lineage. SkUGA1 encodes a homologue of Saccharomyces cerevisiae GABA aminotransferase, and SkPYD4 encodes an enzyme involved in both BAL and GABA transamination. SkPYD4 and SkUGA1 as well as S. cerevisiaeUGA1 and Schizosaccharomyces pombeUGA1 were subcloned, over-expressed and purified. One discontinuous and two continuous coupled assays were used to characterize the substrate specificity and kinetic parameters of the four enzymes. It was found that the cofactor pyridoxal 5,-phosphate is needed for enzymatic activity and ,-ketoglutarate, and not pyruvate, as the amino group acceptor. SkPyd4p preferentially uses BAL as the amino group donor (Vmax/Km = 0.78 U·mg,1·mm,1), but can also use GABA (Vmax/Km = 0.42 U·mg,1·mm,1), while SkUga1p only uses GABA (Vmax/Km = 4.01 U·mg,1·mm,1). SpUga1p and ScUga1p transaminate only GABA and not BAL. While mammals degrade BAL and GABA with only one enzyme, but in different tissues, S. kluyveri and related yeasts have two different genes/enzymes to apparently ,distinguish' between the two reactions in a single cell. It is likely that upon duplication ,200 million years ago, a specialized Uga1p evolved into a ,novel' transaminase enzyme with broader substrate specificity. [source] Evaluating low level sequence identitiesFEBS JOURNAL, Issue 2 2001AROM homologous?, Are Aspergillus QUTA A review published several years ago [Hawkins, A.R. & Lamb, H.K. (1995) Eur. J. Biochem. 232, 7,18] proposed that genetic, biochemical and physiological data can override sequence comparison in the determination of homology in instances where structural information is unavailable. Their lead example was the hypothesis that the transcriptional activator protein for quinate catabolism in Aspergillus nidulans, QUTA, is derived from the pentafunctional AROM protein by a gene duplication followed by cleavage [Hawkins, A.R., Lamb, H.K., Moore, J.D. & Roberts, C.F. (1993) Gene136, 49,54]. We tested this hypothesis by a sensitive combination of position-specific log-odds scoring matrix methods. The position-specific log-odds scoring matrices were derived from a large number of 3-dehydroquinate synthase and 5- enolpyruvylshikimate-3-phosphate synthase domains that were proposed to be the domains from the AROM protein that gave rise to the transcriptional activator protein for quinate metabolism. We show that the degree and pattern of similarity between these position-specific log-odds scoring matrices and the transcriptional activator protein for quinate catabolism in A. nidulans is that expected for random sequences of the same composition. This level of similarity provides no support for the suggested gene duplication and cleavage. The lack of any trace of evidence for homology following a comprehensive sequence analysis indicates that the homology hypothesis is without foundation, underlining the necessity to accept only similarity of sequence and/or structure as evidence of evolutionary relatedness. Further, QUTA is homologous throughout its entire length to an extended family of fungal transcriptional regulatory proteins, rendering the hypothesized QUTA,AROM homology even more problematic. [source] Genetic polymorphisms of drug-metabolizing enzymes CYP2D6, CYP2C9, CYP2C19 and CYP3A5 in the Greek populationFUNDAMENTAL & CLINICAL PHARMACOLOGY, Issue 4 2007Kostas Arvanitidis Abstract The aim of the present study was to determine the prevalence of the most common allelic variants of the polymorphic cytochrome P450 (CYP) enzymes CYP2D6, CYP2C9, CYP2C19 and CYP3A5 and to predict the genotype frequency for each polymorphism in the Greek population. DNA isolated from peripheral blood samples derived from 283 non-related Greek ethnic subjects was used to determine the frequency of CYP2D6*3, CYP2D6*4, CYP2C9*2, CYP2C9*3 and CYP3A5*3 allelic variants by the polymerase chain reaction (PCR)-restriction fragment length polymorphism method, CYP2C19*2 and CYP2C19*3 with allelic specific amplification (PCR-ASA), and CYP2D6*2 (gene duplications) by long PCR analysis. The allelic frequencies (out of a total of 566 alleles) for CYP2D6*3 and CYP2D6*4, were 2.3% and 17.8%, respectively, while gene duplications (CYP2D6*2) were found in 7.4% of the subjects tested. For CYP2C9*2 and CYP2C9*3 polymorphisms the allelic frequencies were 12.9% and 8.13% respectively. For CYP2C19, the *2 polymorphism was present at an allelic frequency of 13.1%, while no subjects were found carrying the CYP2C19*3 allele. Finally, the CYP3A5*3 allele was abundantly present in the Greek population with an allelic frequency of 94.4%. Overall our results show that the frequencies of the common defective allelic variants of CYP2C9, CYP2C19 and CYP3A5 in Greek subjects are similar to those reported for several other Caucasian populations. Finally, a high prevalence of CYP2D6 gene duplication among Greeks was found, a finding that strengthens the idea that a South/North gradient exists in the occurrence of CYP2D6 ultrarapid metabolizers in European populations. [source] Genes encoding a group of related small secreted proteins from the gut of Hessian fly larvae [Mayetiola destructor (Say)]INSECT SCIENCE, Issue 5 2006MING-SHUN CHEN Abstract A group of related genes has been isolated and characterized from the gut of Hessian fly larvae [Mayetiola destructor (Say)]. Members in this group appear to encode proteins with secretary signal pep tides at the N-terminals. The mature putative proteins are small, acidic proteins with calculated molecular masses of 14.5 to 15.3 kDa, and isoelectric points from 4.56 to 4.88. Northern blot analysis revealed that these genes are expressed predominantly in the gut of Hessian fly larvae and pupae. Two related genes, G10K1 and G10K2, were isolated as tandem repeats. Both genes contain three exons and two introns. The intron/exon boundaries were conserved in terms of amino acid encoding, suggesting that they arose by gene duplication. The fact that the frequency of this group of clones in a gut cDNA library higher than that of total cDNA clones encoding digestive enzymes suggested that this group of proteins may perform an important function in the gut physiology of this insect. However, the exact functions of these proteins are as yet known since no sequence similarity could be identified between these proteins and any known sequences in public databases using standard methods. [source] Heterotachy and Functional Shift in Protein EvolutionIUBMB LIFE, Issue 4-5 2003Hervé Philippe Abstract Study of structure/function relationships constitutes an important field of research, especially for modification of protein function and drug design. However, the fact that rational design (i.e. the modification of amino acid sequences by means of directed mutagenesis, based on knowledge of the three-dimensional structure) appears to be much less efficient than irrational design (i.e. random mutagenesis followed by in vitro selection) clearly indicates that we understand little about the relationships between primary sequence, three-dimensional structure and function. The use of evolutionary approaches and concepts will bring insights to this difficult question. The increasing availability of multigene family sequences that has resulted from genome projects has inspired the creation of novel in silico evolutionary methods to predict details of protein function in duplicated (paralogous) proteins. The underlying principle of all such approaches is to compare the evolutionary properties of homologous sequence positions in paralogs. It has been proposed that the positions that show switches in substitution rate over time--i.e., 'heterotachous sites'--are good indicators of functional divergence. However, it appears that heterotachy is a much more general process, since most variable sites of homologous proteins with no evidence of functional shift are heterotachous. Similarly, it appears that switches in substitution rate are as frequent when paralogous sequences are compared as when orthologous sequences are compared. Heterotachy, instead of being indicative of functional shift, may more generally reflect a less specific process related to the many intra- and inter-molecular interactions compatible with a range of more or less equally viable protein conformations. These interactions will lead to different constraints on the nature of the primary sequences, consistently with theories suggesting the non-independence of substitutions in proteins. However, a specific type of amino acid variation might constitute a good indicator of functional divergence: substitutions occurring at positions that are generally slowly evolving. Such substitutions at constrained sites are indeed much more frequent soon after gene duplication. The identification and analysis of these sites by complementing structural information with evolutionary data may represent a promising direction to future studies dealing with the functional characterization of an ever increasing number of multi-gene families identified by complete genome analysis. IUBMB Life, 55: 257-265, 2003 [source] Exclusive expression of a membrane-bound Spink3-interacting serine protease-like protein TESPL in mouse testisJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2010Chung-Mao Ou Abstract We identified a testis-specific protease-like protein tentatively named TESPL and a pancreatic trypsinogen Prss2 from the clones of a yeast two-hybrid screen against a mouse testicular cDNA library using the trypsin inhibitor Spink3 from male accessory sexual glands as bait. The enzymatic motifs and the cysteine patterns in serine proteases are highly conserved in these two proteins. Based on the phylogenetic analysis, Prss2 duplicated recently and TESPL underwent distant evolution without gene duplication from the progenitor of trypsin-like and chymotrypsin-like proteases. We found that TESPL transcription was restricted to the testis and that the level of transcription was positively correlated with animal maturation. In contrast, Prss2 was constitutively expressed in many tissues including testis. Alignment of the cDNA-deduced sequences of serine proteases showed the replacement of an essential serine residue in the catalytic triad of serine proteases by a proline residue in TESPL, which was demonstrated to be a membrane-bound protein devoid of proteolytic activity. The immunohistochemical staining patterns of seminiferous tubules in the testis revealed TESPL mainly on postmeiotic cells such as spermatids and spermatozoa. On the mouse sperm from caudal epididymis, TESPL was localized mainly on the plasma membrane overlaying the acrosomal region. Further, orthology group for mouse TESPL was identified in the conserved gene family of eutherian testis serine protease 5. J. Cell. Biochem. 110: 620,629, 2010. © 2010 Wiley-Liss, Inc. [source] Mitochondrial DNA in Atherina (Teleostei, Atheriniformes): differential distribution of an intergenic spacer in lagoon and marine forms of Atherina boyeriJOURNAL OF FISH BIOLOGY, Issue 5 2008V. MILANA The big-scale sand smelt Atherina boyeri lives in fresh water, brackish water and sea water of the western Atlantic Ocean and Mediterranean Sea. Previous studies concerning distribution, biometric characters and genetic molecular markers have suggested the possible existence of two or even three different groups or species of sand smelt, one ,lagoon' type and one (or two , punctuated and non-punctuated on the flanks) ,marine' type. In this study, the presence and the localization of an insertion was described, c. 200 bp in length, in the mtDNA of the lagoon and marine punctuated specimens of A. boyeri and its absence in the marine non-punctuated specimens, as well as in other two congeneric species, Atherina hepsetus and Atherina presbyter, and in the atheriniform Menidia menidia. The intergenic spacer is located between the tRNAGlu and cytochrome b (cyt b) genes and shares a c. 50% sequence similarity with cyt b. The distribution and the features of the intergenic spacer suggest that it might have originated from an event of gene duplication, which involved the cyt b gene (or, more likely, a part of it) and which took place in the common ancestor of the lagoon and the marine punctuated specimens. The data obtained therefore support the hypothesis of the existence of three cryptic and, or sibling species within the A. boyeri taxon and provide a genetic molecular marker to distinguish them. [source] Polymorphism and signature of selection in the MHC class I genes of the three-spined stickleback Gasterosteus aculeatusJOURNAL OF FISH BIOLOGY, Issue 2006H. Schaschl The role and intensity of positive selection maintaining the polymorphism of major histocompatibility complex (MHC) class I genes in the three-spined stickleback Gasterosteus aculeatus was investigated. The highly polymorphic set of MHC class I genes found was organized in a single linkage group. Between 5 and 14 sequence variants per individual were identified by single-stranded conformation polymorphism (SSCP) analysis. Segregation analysis studied in 10 three-spined stickleback families followed the expected pattern of Mendelian inheritance. The gamete fusion in three-spined stickleback thus seems to be random with respect to the MHC class I genes. The DNA sequence analyses showed that the expressed MHC class I loci are under strong selection pressure, possibly mediated by parasites. Codons that were revealed to be under positive selection are potentially important in antigen binding. MHC class I sequences did not form significant supported clusters within a phylogenetic tree. Analogous to MHC class II genes, it was not possible to assign the class I sequences to a specific locus, suggesting that the class I genes may have been generated by recent gene duplication. [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] THE , SUBUNITS OF PHYCOERYTHRIN FROM A RED ALGA: POSITION IN PHYCOBILISOMES AND SEQUENCE CHARACTERIZATIONJOURNAL OF PHYCOLOGY, Issue 1 2001Kirk E. Apt Aglaothamnion neglectum Feldman-Mazoyer has two , subunits, ,31 and ,33, that are associated with phycoerythrin in the light-harvesting phycobilisomes. We demonstrate that these subunits are spatially separated within the phycobilisome, with the ,31 subunit present at the distal end of phycobilisome rods and the ,33 subunit present on the proximal end. These subunits are thought to link phycoerythrin hexamers together in the rod substructure, serving a role analogous to that of linker polypeptides of cyanobacteria (although unlike the cyanobacterial linker polypeptides they are chromophorylated). The sequencing of tryptic polypeptides of the , subunits enabled us to prepare oligonucleotides encoding different regions of ,31. These oligonucleotides were used as primers to generate a probe for isolating a ,31 cDNA clone. Characterization of the cDNA clone predicts a polypeptide of 280 amino acids with a 42 amino acid presequence that is characteristic of a transit peptide, the peptide that targets proteins to chloroplasts of vascular plants. The ,31 subunit has 50% similarity to the previously characterized ,33 subunit but has no identifiable similarity to functionally related polypeptides present in cyanobacterial phycobilisomes or to any other polypeptides in the databases. A repeat of 95 amino acids is present in the red algal , subunit sequences, suggesting that these proteins were generated by a gene duplication followed by fusion of the duplicate sequences. [source] Role of Potassium Channel Gene Kcnj10 in Ethanol Preference in C57bl/6J and DBA/2J MiceALCOHOLISM, Issue 3 2009Shicong B. Zou Background:, Inwardly-rectifying potassium channel protein Kir4.1 is encoded by Kcnj10 which maps to a quantitative trait locus on chromosome 1 for the voluntary alcohol consumption phenotype in mice. Kcnj10 brain expression differences have been established between ethanol-preferring C57Bl/6J and ethanol-avoiding BALB/cJ mice, but its differential expression in other tissues and strains have largely been overlooked. A nonsynonymous single nucleotide polymorphism exists between C57Bl/6J and ethanol-avoiding DBA/2J mice which changes amino acid 262 from threonine (C57Bl/6J) to serine (DBA/2J). This Kcnj10 SNP and its expression may serve as valuable markers in predicting the ethanol preference phenotype in mice. Methods:, The evolutionary divergence of the Kir gene family was characterized using phylogenetic analysis involving the 16 mouse Kir channels. Kcnj10 expression differences in the brain, liver, lung, heart, spleen, kidney, testes, and muscle of male C57Bl/6J and DBA/2J mice at different developmental stages were examined using semiquantitative RT-PCR analysis. A SNP analysis was conducted to assess the association of Kcnj10 Thr262Ser SNP and the ethanol preference phenotype in F2 mice derived from the reciprocal crosses of the C57Bl/6J and DBA/2J strains. Results:, Evolutionary analysis supports gene duplication and genetic recombination as likely sources of diversity within the Kir gene family. Semiquantitative RT-PCR analysis revealed significantly higher Kcnj10 expression in the brain, spleen, and kidney of both strains when compared to other tissues from the same strain. There were no significant differences in tissue-specific mRNA levels between strains except in the testes. Genotype distributions of the Kcnj10 Thr262Ser SNP were different between low- and high-drinkers. A significant difference in the average ethanol preference level of each genotype was also observed. Conclusion:, Our results suggest a role for Kcnj10 in ethanol preference determination in mice. However, further experiments are needed to establish if this association is due to the nonsynonymous SNP or other additional factors associated with Kcnj10. [source] TBP domain symmetry in basal and activated archaeal transcriptionMOLECULAR MICROBIOLOGY, Issue 1 2009Mohamed Ouhammouch Summary The TATA box binding protein (TBP) is the platform for assembly of archaeal and eukaryotic transcription preinitiation complexes. Ancestral gene duplication and fusion events have produced the saddle-shaped TBP molecule, with its two direct-repeat subdomains and pseudo-two-fold symmetry. Collectively, eukaryotic TBPs have diverged from their present-day archaeal counterparts, which remain highly symmetrical. The similarity of the N- and C-halves of archaeal TBPs is especially pronounced in the Methanococcales and Thermoplasmatales, including complete conservation of their N- and C-terminal stirrups; along with helix H,1, the C-terminal stirrup of TBP forms the main interface with TFB/TFIIB. Here, we show that, in stark contrast to its eukaryotic counterparts, multiple substitutions in the C-terminal stirrup of Methanocaldococcus jannaschii (Mja) TBP do not completely abrogate basal transcription. Using DNA affinity cleavage, we show that, by assembling TFB through its conserved N-terminal stirrup, Mja TBP is in effect ambidextrous with regard to basal transcription. In contrast, substitutions in either its N- or the C-terminal stirrup abrogate activated transcription in response to the Lrp-family transcriptional activator Ptr2. [source] Adapting a diet from sugar to meat: double-dealing genes of Streptococcus pyogenesMOLECULAR MICROBIOLOGY, Issue 2 2007Jason W. Rosch Summary Intuitively, paralogues created by gene duplication should retain related functions. However, a study of the two lactose metabolic operons of Streptococcus pyogenes, reported in this issue of Molecular Microbiology, indicates that paralogues might evolve very different functions, in this case changing from a metabolic enzyme to a regulator of virulence. Divergence of paralogues could be a newly recognized theme in the metamorphosis of a bacteria from innocuous to pathogenic. [source] Analysis of Campylobacter jejuni capsular loci reveals multiple mechanisms for the generation of structural diversity and the ability to form complex heptosesMOLECULAR MICROBIOLOGY, Issue 1 2005Andrey V. Karlyshev Summary We recently demonstrated that Campylobacter jejuni produces a capsular polysaccharide (CPS) that is the major antigenic component of the classical Penner serotyping system distinguishing Campylobacter into >60 groups. Although the wide variety of C. jejuni serotypes are suggestive of structural differences in CPS, the genetic mechanisms of such differences are unknown. In this study we sequenced biosynthetic cps regions, ranging in size from 15 to 34 kb, from selected C. jejuni strains of HS:1, HS:19, HS:23, HS:36, HS:23/36 and HS:41 serotypes. Comparison of the determined cps sequences of the HS:1, HS:19 and HS:41 strains with the sequenced strain, NCTC11168 (HS:2), provides evidence for multiple mechanisms of structural variation including exchange of capsular genes and entire clusters by horizontal transfer, gene duplication, deletion, fusion and contingency gene variation. In contrast, the HS:23, HS:36 and HS:23/36 cps sequences were highly conserved. We report the first detailed structural analysis of 81-176 (HS:23/36) and G1 (HS:1) and refine the previous structural interpretations of the HS:19, HS:23, HS:36 and HS:41 serostrains. For the first time, we demonstrate the commonality and function of a second heptose biosynthetic pathway for Campylobacter CPS independent of the pathway for lipooligosaccharide (LOS) biosynthesis and identify a novel heptosyltransferase utilized by this alternate pathway. Furthermore, we show the retention of two functional heptose isomerases in Campylobacter and the sharing of a phosphatase for both LOS and CPS heptose biosynthesis. [source] Origin of the murine implantation serine proteinase subfamily,MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 2 2004Colleen M. O'Sullivan Abstract The S1 serine protease family is one of the largest gene families known. Within this family there are several subfamilies that have been grouped together as a result of sequence comparisons and substrate identification. The grouping of related genes allows for the speculation of function for newly found members by comparison and for novel subfamilies by contrast. Analysis of the evolutionary patterns of genes indicates whether or not orthologs are likely to be identified in other species as well as potentially indicating that hypothesized orthologs are in fact not. Looking at subtle differences between subfamily members can reveal intricacies about function and expression. Previously, we have described genes encoding two novel serine proteinases, ISP1 and ISP2, which are most closely related to tryptases. The ISP1 gene encodes the embryo-derived enzyme strypsin, which is necessary for blastocyst hatching and invasion in vitro. Additionally both ISP1 and ISP2 are co-expressed in the endometrial gland during the time of hatching, suggesting that they may also both participate in zona lysis from within the uterine lumen. Here, we demonstrate that the ISPs are tandemly linked within the tryptase cluster on 17A3.3. We suggest that remarkable similarities within the 5,-untranslated and first intron regions of ISP1 and ISP2 may explain their intimate co-regulation in uterus. We also suggest that ISP genes have evolved through gene duplication and that the ISP1 gene has also begun to adopt an additional new function in the murine preimplantation embryo. Mol. Reprod. Dev. 69: 126,136, 2004. © 2004 Wiley-Liss, Inc. [source] Conservation and diversification of the symmetry developmental program among close relatives of snapdragon with divergent floral morphologiesNEW PHYTOLOGIST, Issue 3 2009Jill C. Preston Summary ,,Multiple evolutionary shifts in floral symmetry and stamen number have occurred in the snapdragon (Antirrhinum majus) family Veronicaceae. In Mohavea, Veronica and Gratiola there have been independent evolutionary reductions in stamen number and modifications to corolla shape. It is hypothesized that changes in the regulation of homologs of snapdragon dorsal flower identity genes CYCLOIDEA (CYC) and RADIALIS (RAD) underlie these floral transitions. ,,CYC -like and RAD -like genes from Veronica montana and Gratiola officinalis were cloned and sequenced, compared with homologs from other Veronicaceae species using phylogenetic analysis, and their expression was investigated by reverse transcriptase-polymerase chain reaction (RT-PCR) and in situ hybridization. ,,VmCYC1, GoCYC1, GoCYC2 and RAD -like genes are expressed exclusively in the dorsal region of floral meristems and developing flowers. Their expression patterns do not correlate with patterns of stamen arrest. VmCYC2 and GoCYC3 are expressed in both vegetative and floral tissues, with VmCYC2 being most abundant in all regions of the floral meristem and all petals. ,,These results support conservation of the floral symmetry gene network for Veronicaceae RAD -like and some CYC -like paralogs, suggest regulatory evolution of other CYC -like genes following gene duplication and implicate different genetic mechanisms underlying dorsal versus ventral stamen abortion within Veronica and Gratiola. [source] Evolutionary history of the ancient cutinase family in five filamentous Ascomycetes reveals differential gene duplications and losses and in Magnaporthe grisea shows evidence of sub- and neo-functionalizationNEW PHYTOLOGIST, Issue 3 2008Pari Skamnioti Summary ,,The cuticle is the first barrier for fungi that parasitize plants systematically or opportunistically. Here, the evolutionary history is reported of the multimembered cutinase families of the plant pathogenic Ascomycetes Magnaporthe grisea, Fusarium graminearum and Botrytis cinerea and the saprotrophic Ascomycetes Aspergillus nidulans and Neurospora crassa. ,,Molecular taxonomy of all fungal cutinases demonstrates a clear division into two ancient subfamilies. No evidence was found for lateral gene transfer from prokaryotes. The cutinases in the five Ascomycetes show significant copy number variation, they form six clades and their extreme sequence diversity is highlighted by the lack of consensus intron. The average ratio of gene duplication to loss is 2 : 3, with the exception of M. grisea and N. crassa, which exhibit extreme family expansion and contraction, respectively. ,,Detailed transcript profiling in vivo, categorizes the M. grisea cutinases into four regulatory patterns. Symmetric or asymmetric expression profiles of phylogenetically related cutinase genes suggest subfunctionalization and neofunctionalization, respectively. ,,The cutinase family-size per fungal species is discussed in relation to genome characteristics and lifestyle. The ancestry of the cutinase gene family, together with the expression divergence of its individual members provides a first insight into the drivers for niche differentiation in fungi. [source] Combating plant diseases,the Darwin connectionPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 11 2009Derek W Hollomon Abstract Although Darwin knew of plant diseases, he did not study them as part of his analysis of natural selection. Effective plant disease control has only been developed after his death. This article explores the relevance of Darwin's ideas to three problem areas with respect to diseases caused by fungi: emergence of new diseases, loss of disease resistance bred into plants and development of fungicide resistance. Darwin's concept of change through natural or artificial selection relied on selection of many small changes, but subsequent genetic research has shown that change can also occur through large steps. Appearance of new diseases can involve gene duplication, transfer or recombination, but all evidence points to both host plant resistance and fungicide susceptibility being overcome through point mutations. Because the population size of diseases such as rusts and powdery and downy mildews is so large, all possible point mutations are likely to occur daily, even during moderate epidemics. Overcoming control measures therefore reflects the overall fitness of these mutants, and much resource effort is being directed towards assessment of their fitness, both in the presence and in the absence of selection. While recent developments in comparative genomics have caused some revision of Darwin's ideas, experience in managing plant disease control measures clearly demonstrates the relevance of concepts he introduced 150 years ago. It also reveals the remarkable speed and the practical impact of adaptation in wild microorganism populations to changes in their environment, and the difficulty of stopping or delaying such adaptation. Copyright © 2009 Society of Chemical Industry [source] Gene duplications and the time thereafter , examples from plant secondary metabolismPLANT BIOLOGY, Issue 4 2010D. Ober Abstract Gene duplications are regarded as one of the central mechanisms for the origin of new genes. Recent studies in plant secondary metabolism have provided several examples of genes that originated by duplication with successive diversification. In this review, the mechanisms of gene duplication are explained and several models discussed that suggest the way that gene duplicates develop into genes with new functions. Signatures of gene duplication and diversification processes are discussed using the biosynthesis of benzoxazinones and of pyrrolizidine alkaloids as examples. [source] Simulating evolution by gene duplication of protein features that require multiple amino acid residuesPROTEIN SCIENCE, Issue 10 2004Michael J. Behe MR, multiresidue Abstract Gene duplication is thought to be a major source of evolutionary innovation because it allows one copy of a gene to mutate and explore genetic space while the other copy continues to fulfill the original function. Models of the process often implicitly assume that a single mutation to the duplicated gene can confer a new selectable property. Yet some protein features, such as disulfide bonds or ligand binding sites, require the participation of two or more amino acid residues, which could require several mutations. Here we model the evolution of such protein features by what we consider to be the conceptually simplest route,point mutation in duplicated genes. We show that for very large population sizes N, where at steady state in the absence of selection the population would be expected to contain one or more duplicated alleles coding for the feature, the time to fixation in the population hovers near the inverse of the point mutation rate, and varies sluggishly with the ,th root of 1/N, where , is the number of nucleotide positions that must be mutated to produce the feature. At smaller population sizes, the time to fixation varies linearly with 1/N and exceeds the inverse of the point mutation rate. We conclude that, in general, to be fixed in 108 generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 109. [source] REVIEW ARTICLE: Evolution and Function of the Uterine Serpins (SERPINA14)AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, Issue 4 2010Maria B. Padua Citation Padua MB, Hansen PJ. Evolution and function of the uterine serpins (SERPINA14). Am J Reprod Immunol 2010 Uterine serpins (recently designated as SERPINA14) are hormonally induced proteins secreted in large quantities by the endometrial epithelium during pregnancy. The SERPINA14 proteins belong to the serine proteinase inhibitor (serpin) superfamily, but their apparent lack of inhibitory activity toward serine proteinases suggests that these proteins evolved a different function from the anti-proteinase activity typically found in most members of the serpin superfamily. The gene is present in a limited group of mammals in the Laurasiatheria superorder (ruminants, horses, pigs, dolphins and some carnivores) while being absent in primates, rodents, lagomorphs and marsupials. Thus, the gene is likely to have evolved by gene duplication after divergence of Laurasiatheria and to play an important role in pregnancy. That role may vary between species. In sheep, SERPINA14 probably serves an immunoregulatory role to prevent rejection of the fetal allograft. It is inhibitory to lymphocyte proliferation and natural killer cell function. In the pig, SERPINA14 is involved in iron transport to the fetus by binding to and stabilizing the iron-binding protein uteroferrin. It is possible that SERPINA14 has undergone divergence in function since the original emergence of the gene in a common ancestor of species possessing SERPINA14. [source] | |||||||||||||||||||||||||||||||