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PubMed2004

Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group.

BACKGROUND: DNA repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. The importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes. RESULTS: The genome sequences of two Xanthomonas species were used as the basis for phylogenetic analyses of genes related to DNA repair that were found duplicated. Although 16S rRNA phylogenetic analyses confirm their classification at the basis of the gamma proteobacteria subdivision, differences were found in the origin of the various genes investigated. Except for lexA, detected as a recent duplication, most of the genes in more than one copy are represented by two highly divergent orthologs. Basically, one of such duplications is frequently positioned close to other gamma proteobacteria, but the second is often positioned close to unrelated bacteria. These orthologs may have occurred from old duplication events, followed by extensive gene loss, or were originated from lateral gene transfer (LGT), as is the case of the uvrD homolog. CONCLUSIONS: Duplications of DNA repair related genes may result in redundancy and also improve the organisms' responses to environmental challenges. Most of such duplications, in Xanthomonas, seem to have arisen from old events and possibly enlarge both functional and evolutionary genome potentiality.

DNA Repair↗
PubMed2006

Adaptive evolution of Hox-gene homeodomains after cluster duplications.

BACKGROUND: Hox genes code for homeodomain-containing transcription factors that function in cell fate determination and embryonic development. Hox genes are arranged in clusters with up to 14 genes. This archetypical chordate cluster has duplicated several times in vertebrates, once at the origin of vertebrates and once at the origin of gnathostoms, an additional duplication event is associated with the origin of teleosts and the agnanths, suggesting that duplicated Hox cluster genes are involved in the genetic mechanisms behind the diversification of vertebrate body plans, and the origin of morphological novelties. Preservation of duplicate genes is promoted by functional divergence of paralogs, either by subfunction partitioning among paralogs or the acquisition of a novel function by one paralog. But for Hox genes the mechanisms of paralog divergence is unknown, leaving open the role of Hox gene duplication in morphological evolution. RESULTS: Here, we use several complementary methods, including branch-specific dN/dS ratio tests, branch-site dN/dS ratio tests, clade level amino acid conservation/variation patterns, and relative rate ratio tests, to show that the homeodomain of Hox genes was under positive Darwinian selection after cluster duplications. CONCLUSION: Our results suggest that positive selection acted on the homeodomain immediately after Hox clusters duplications. The location of sites under positive selection in the homeodomain suggests that they are involved in protein-protein interactions. These results further suggest that adaptive evolution actively contributed to Hox-gene homeodomain functions.

Adaptation, Biological↗
PubMed2003

Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster.

BACKGROUND: Pericentric inversions are the most common euchromatic chromosomal differences among humans and the great apes. The human and chimpanzee karyotype differs by nine such events, in addition to several constitutive heterochromatic increases and one chromosomal fusion event. Reproductive isolation and subsequent speciation are thought to be the potential result of pericentric inversions, as reproductive boundaries form as a result of hybrid sterility. RESULTS: Here we employed a comparative fluorescence in situ hybridization approach, using probes selected from a combination of physical mapping, genomic sequence, and segmental duplication analyses to narrow the breakpoint interval of a pericentric inversion in chimpanzee involving the orthologous human 15q11-q13 region. We have refined the inversion breakpoint of this chimpanzee-specific rearrangement to a 600 kilobase (kb) interval of the human genome consisting of entirely duplicated material. Detailed analysis of the underlying sequence indicated that this region comprises multiple segmental duplications, including a previously characterized duplication of the alpha7 neuronal nicotinic acetylcholine receptor subunit gene (CHRNA7) in 15q13.3 and several Golgin-linked-to-PML, or LCR15, duplications. CONCLUSIONS: We conclude that, on the basis of experimental data excluding the CHRNA7 duplicon as the site of inversion, and sequence analysis of regional duplications, the most likely rearrangement site is within a GLP/LCR15 duplicon. This study further exemplifies the genomic plasticity due to the presence of segmental duplications and highlights their importance for a complete understanding of genome evolution.

Animals↗
PubMed2003

Different evolutionary patterns between young duplicate genes in the human genome.

BACKGROUND: Following gene duplication, two duplicate genes may experience relaxed functional constraints or acquire different mutations, and may also diverge in function. Whether the two copies will evolve in different patterns remains unclear, however, because previous studies have reached conflicting conclusions. In order to resolve this issue, by providing a general picture, we studied 250 independent pairs of young duplicate genes from the whole human genome. RESULTS: We showed that nearly 60% of the young duplicate gene pairs have evolved at the amino-acid level at significantly different rates from each other. More than 25% of these gene pairs also showed significantly different ratios of nonsynonymous to synonymous rates (Ka/Ks ratios). Moreover, duplicate pairs with different rates of amino-acid substitution also tend to differ in the Ka/Ks ratio, with the fast-evolving copy tending to have a slightly higher Ks than the slow-evolving one. Lastly, a substantial portion of fast-evolving copies have accumulated amino-acid substitutions evenly across the protein sequences, whereas most of the slow-evolving copies exhibit uneven substitution patterns. CONCLUSIONS: Our results suggest that duplicate genes tend to evolve in different patterns following the duplication event. One copy evolves faster than the other and accumulates amino-acid substitutions evenly across the sequence, whereas the other copy evolves more slowly and accumulates amino-acid substitutions unevenly across the sequence. Such different evolutionary patterns may be largely due to different functional constraints on the two copies.

Amino Acid Substitution↗
PubMed2006

Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution.

BACKGROUND: Systematic analyses of loss-of-function phenotypes have been carried out for most genes in Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster. Although such studies vastly expand our knowledge of single gene function, they do not address redundancy in genetic networks. Developing tools for the systematic mapping of genetic interactions is thus a key step in exploring the relationship between genotype and phenotype. RESULTS: We established conditions for RNA interference (RNAi) in C. elegans to target multiple genes simultaneously in a high-throughput setting. Using this approach, we can detect the great majority of previously known synthetic genetic interactions. We used this assay to examine the redundancy of duplicated genes in the genome of C. elegans that correspond to single orthologs in S. cerevisiae or D. melanogaster and identified 16 pairs of duplicated genes that have redundant functions. Remarkably, 14 of these redundant gene pairs were duplicated before the divergence of C. elegans and C. briggsae 80-110 million years ago, suggesting that there has been selective pressure to maintain the overlap in function between some gene duplicates. CONCLUSION: We established a high throughput method for examining genetic interactions using combinatorial RNAi in C. elegans. Using this technique, we demonstrated that many duplicated genes can retain redundant functions for more than 80 million years of evolution. This provides strong support for evolutionary models that predict that genetic redundancy between duplicated genes can be actively maintained by natural selection and is not just a transient side effect of recent gene duplication events.

Animals↗
PubMed2005

Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution.

Gene duplication is the primary source of new genes. Duplicate genes that are stably preserved in genomes usually have divergent functions. The general rules governing the functional divergence, however, are not well understood and are controversial. The neofunctionalization (NF) hypothesis asserts that after duplication one daughter gene retains the ancestral function while the other acquires new functions. In contrast, the subfunctionalization (SF) hypothesis argues that duplicate genes experience degenerate mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We here show that neither NF nor SF alone adequately explains the genome-wide patterns of yeast protein interaction and human gene expression for duplicate genes. Instead, our analysis reveals rapid SF, accompanied by prolonged and substantial NF in a large proportion of duplicate genes, suggesting a new model termed subneofunctionalization (SNF). Our results demonstrate that enormous numbers of new functions have originated via gene duplication.

Amino Acid Sequence↗
PubMed2005

Chromosome segment duplications in Neurospora crassa and their effects on repeat-induced point mutation and meiotic silencing by unpaired DNA.

The size and extent of four Neurospora crassa duplications, Dp(AR17), Dp(IBj5), Dp(OY329), and Dp(B362i), was determined by testing the coverage of RFLP markers. The first three duplications were all > approximately 350 kb and have been shown in earlier studies to act as dominant suppressors of repeat-induced point mutation (RIP) in gene-sized duplications, possibly via titration of the RIP machinery. Dp(B362i), which is only approximately 117 kb long, failed to suppress RIP. RIP suppression in gene-sized duplications by large duplications was demonstrated using another test gene, dow, and supposedly applies generally. Crosses homozygous for Dp(AR17) or Dp(IBj5) were as barren as heterozygous crosses. Barrenness of the heterozygous but not the homozygous crosses was suppressible by Sad-1, a semidominant suppressor of RNAi-dependent meiotic silencing by unpaired DNA. A model is proposed in which large duplications recessively suppress semidominant Sad-1 mutations. The wild-isolated Sugartown strain is hypothesized to contain a duplication that confers not only dominant suppression of RIP but also a barren phenotype, which is linked (9%) to supercontig 7.118 in LG VII.

Chromosome Mapping↗
PubMed2006

The pro-opiomelanocortin genes in rainbow trout (Oncorhynchus mykiss): duplications, splice variants, and differential expression.

Pro-opiomelanocortin (POMC) is a precursor for several important peptide hormones involved in a variety of functions ranging from stress response to energy homeostasis. In mammals and fish, the POMC-derived peptide alpha-melanocyte stimulating hormone (MSH) is known to be involved in appetite suppression through its interaction with melanocortin-4 receptors. The details of energy homeostasis in fishes are beginning to be elucidated and many of the genes involved in mammalian neuroendocrine signaling pathways are being discovered in fish. In salmonid fishes such as the rainbow trout, genome duplication adds another degree of complexity when trying to compare gene function and homology with other vertebrates. This is true of the POMC gene. Two copies of the POMC gene were previously identified, A and B, presumably resulting from the salmonid duplication. However, while investigating POMC involvement in the feeding response of rainbow trout, a second copy of POMC-A was discovered which is more likely the result of the salmonid duplication and suggests that POMC-B is a duplicate resulting from the earlier teleost duplication prior to tetrapod divergence. The duplicated POMC-A had five deleted amino acids, five inserted amino acids, and 39 amino acid differences from the published POMC-A. In addition to the duplicate POMC-A, a splice variant of the published POMC-A sequence was also identified. Quantitative real-time PCR assays were developed for the different POMC transcripts, and expression was examined in a variety of tissues. Expression of POMC transcripts was highest in the pituitary for all POMC genes, but varied among other tissues for POMC-A1, POMC-A2, POMC-A2s, and POMC-B. POMC-A1 was the only transcript to respond significantly to food deprivation.

Amino Acid Sequence↗
PubMed1998

Ultrarapid metabolism of sparteine: frequency of alleles with duplicated CYP2D6 genes in a Danish population as determined by restriction fragment length polymorphism and long polymerase chain reaction.

CYP2D6 is a polymorphically expressed enzyme with two phenotypes. Poor metabolizers lack the enzyme caused by inactivating mutations in the CYP2D6 gene and extensive metabolizers have at least one active CYP2D6 gene. Extensive metabolizers with very high capacity for CYP2D6 dependent drug metabolisms are termed ultrarapid metabolizers and carry alleles with duplicated, multi duplicated or amplified CYP2D6 genes. In the present study, we examined the frequency of CYP2D6 gene duplications in a Danish population and validated a long polymerase chain reaction method for identification of ultrarapid metabolizers. Sixty individuals having a metabolic ratio for sparteine at or below 0.15 were selected and a control group of 53 individuals with a metabolic ratio between 0.16 and 12.4 was used. Based on EcoRI restriction fragment length polymorphism analysis, eight individuals were found with a duplicated CYP2D6 gene, whereas using a long polymerase chain reaction method, nine individuals with a 3.6 kb fragment indicative of two CYP2D6 genes in tandem were found among the 60 individuals with a low metabolic ratio. No gene duplication was found in the control group or in any individuals with a metabolic ratio > 0.14. Based on these results, we estimate the frequency of individuals with CYP2D6 duplication in the Danish population to be 0.8%, which is comparable to the frequency in the Swedish and the German populations, but considerably lower than in Spanish or African populations. We conclude that the long polymerase chain reaction assay is simple and reliable for detection of duplications of the CYP2D6 gene.

Alleles↗
PubMed1999

The effect of gene duplication on homology.

Genes related by gene duplication within an organism's evolutionary lineage are termed paralogues; genes related by speciation are orthologues. It is generally agreed that orthologous genes must be compared when using DNA sequences to reconstruct the evolutionary history of organisms. There is an important exception: information from paralogous genes can reveal the root position of a phylogenetic tree. The duplicated rDNA genes of arrow worms provide an example. Gene duplication is also relevant when comparing gene expression between taxa; for example, when trying to identify homologous roles of genes. When gene duplication occurred after lineage divergence, single orthologues no longer exist, and comparison is complicated. This is a particular problem when comparing roles of vertebrate and invertebrate genes. Amphioxus and ascidian genes can be useful in such situations, since they diverged before extensive gene duplication in the vertebrate lineage. Using Otx and Pax as examples, I show how examination of amphioxus or ascidian genes reveals patterns of gene divergence after duplication, assisting the identification of homologous gene functions. Given the problems of comparing duplicated genes between species, the time is ripe for the introduction of additional terminology to elaborate on the concepts of paralogy and orthology.

Animals↗
PubMedDate not supplied

MR-revealed myelination in the cerebral corticospinal tract as a marker for Pelizaeus-Merzbacher's disease with proteolipid protein gene duplication.

BACKGROUND AND PURPOSE: Pelizaeus-Merzbacher's disease (PMD) is caused by mutations in the proteolipid protein (PLP) gene. Recent studies have shown that an increased PLP dosage, resulting from total duplication of the PLP gene, invariably causes the classic form of PMD. The purpose of this study was to compare the MR findings of PMD attributable to PLP duplication with those of PMD arising from a missense mutation. METHODS: Seven patients with PMD, three with a PLP missense mutation in either exon 2 or 5 (patients 1-3), and four with PLP duplication (patient 4 having larger PLP duplication than patients 5-7) were clinically classified as having either the classic or connatal form of PMD. Cerebral MR images were obtained to analyze the presence of myelination and T1 and T2 shortening in the deep gray matter. Multiple MR studies were performed in six of the seven patients to analyze longitudinal changes. RESULTS: Four patients (patients 1-4) were classified as having connatal PMD, whereas the other three (patients 5-7) were classified as having classic PMD. Myelination in the cerebral corticospinal tract, optic radiation, and corpus callosum was observed in three cases of classic PMD with PLP duplication. In patient 4, myelination extended to the internal capsule, corona radiata, and centrum semiovale over a 3-year period. No myelination was observed in three PMD cases with a PLP point mutation. T2 shortening in the deep gray matter was recognized in all patients with PMD. CONCLUSION: The presence of myelination in the cerebral corticospinal tract with diffuse white matter hypomyelination on MR images could be a marker for PMD with PLP duplication. It is suggested that progression of myelination may be present in connatal PMD with large PLP duplication.

Adolescent↗
PubMed2005

Evidence for an ancient whole-genome duplication event in rice and other cereals.

Gene duplication has been proposed as an accelerator of evolution. Ancient genome duplication events have been identified in diverse organisms, such as yeast, vertebrates, and Arabidopsis. Here, we have identified a whole genome duplication event (WGD) in the rice genome, which took place prior to the divergence of grasses about 70 million years ago (mya). A total of 117 duplicated blocks were detected, which are distributed on all 12 chromosomes and cover about 60% of the rice genome. About 20% genes on these duplicated segments are retained as duplicate pairs. In contrast, 60% of the transcription factor genes are retained as duplicates. The identification of a WGD in the ancestral grass genome will impact the study of grass genome evolution, and suggest that polyploidization and subsequent gene losses and chromosomal rearrangements have played an important role in the diversification of grasses.

Edible Grain↗
PubMed2000

A subset of centrosomal proteins are arranged in a tubular conformation that is reproduced during centrosome duplication.

The centrosome plays a fundamental role in organizing the interphase cytoskeleton and the mitotic spindle, and its protein complexity is modulated to support these functions. The centrosome must also duplicate itself once during each cell cycle, thus ensuring the formation of a bipolar spindle and its continuity through successive cell divisions. In this study, we have used a battery of antibodies directed against centrosomal components to study the general organization of the centrosome during the cell cycle and during the centrosome duplication process. We demonstrate that a subset of centrosomal proteins are arranged together to form a tubular pattern within the centrosome. The tubular conformation defined by these proteins has a polarity and is closed at one end. The centriole complement of the centrosome is normally placed near this end. We show that the "wall" of the tube is enriched in proteins such as CDC2, ninein, and pericentrin as well as gamma-tubulin. In addition, a subset of gamma-tubulin is localized to the "lumen" of the tube. We also demonstrate, for the first time, that antibody staining can be used to detect centrosome duplication allowing the identification of duplication intermediates. We show that one product of centrosome duplication is the replication of the tubular structure found within the centrosome. The position of the centriole duplexes prior to and during centrosome duplication is documented and a model of the morphogenesis of the centrosome during the duplication process is proposed.

Animals↗
PubMed2002

Two cases of the caudal duplication anomaly including a discordant monozygotic twin.

We present two unrelated patients with various duplications in the caudal region. One patient presented with a duplication of the distal spine from L4, left double ureter, duplication of the vagina and cervix, and duplication of the distal colon. The second patient was diagnosed with a duplication of the colon, bladder, vagina and uterus. The first patient had an unaffected monozygotic twin sister. Dominguez et al. [1993: Am J Dis Child 147:1048-1052] presented six similar cases, and introduced the name "caudal duplication syndrome." The pathogenesis of the caudal duplication anomaly is unclear. The possibility of a polytopic primary developmental field defect or a disruptive sequence are discussed. On the other hand, somatic or germline mutations in certain developmental genes could be involved, as illustrated by the mouse mutations disorganisation and fused. DNA-analysis of the AXIN1 gene, the human homologue of the gene responsible for fused, performed in our first patient, did not show any apparent pathogenic mutation.

Abnormalities, Multiple↗
PubMed1993

Inverted duplication of 8p: ten new patients and review of the literature.

We evaluated 10 patients with an inverted tandem duplication of 8p. Inverted duplications of chromosome 8 have been reported infrequently, and no syndrome has been previously identified. All 8 patients on whom birth histories were available were hypotonic at birth, and had feeding difficulties in the neonatal period. All patients have significant developmental delay. Manifestations present in 5 or more patients were prominent forehead, high arched palate, large mouth with a thin upper lip, malformed and/or apparently low-set ears, broad nasal bridge, dental and skeletal abnormalities, and joint laxity or hyperextensibility. Variation in the phenotype may, in part, be explained by the different breakpoints. Recurrence risks of de novo rearrangements are probably very low, but for the recombinants the risk may be significant. The duplication appeared to be de novo in 6 patients (both parental karyotypes were normal); maternal karyotypes were normal in 2 patients, and both parents of 1 patient were not available. One propositus had a monocentric recombinant of a paracentric inv(8) (p12p23.3) carried by the mother, and is one of only 6 known cases of duplication associated with a balanced paracentric inversion in a parent. The carrier parent was the mother in 5 of those 6 cases. Each case involved a different chromosome, and each probably was created by an unusual meiotic recombination event. Inverted duplication 8p is one of the most common duplications observed in our laboratories, and ranks in frequency with the classical deletions, such as Wolf-Hirschhorn and cri-du-chat syndromes and duplication or secondary trisomy 15q1.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗
PubMed2004

Clinical, cytogenetic, and molecular characterization of a patient with a de novo interstitial 22q12 duplication.

We report a 19-year-old woman with minor craniofacial anomalies, mild mental retardation, and foramina parietalia permagna (FPP) (OMIM 168500). Cytogenetic analysis showed a de novo interstitial chromosome 22 long arm duplication. FISH with a panel of chromosome 22q12-q13 bands-specific BAC clones refined the cytogenetic investigation, and restricted the duplicated segment to the q12 region. Mutation analysis of FPP genes identified an insertion mutation in the ALX4 gene (344insC) in the proband and her father with loss of function of the gene. The patient's phenotype is considered in the light of the results of the cytogenetic, FISH, and molecular investigations, and her features are compared with those of other patients with similar duplications. Finally, variable phenotypic findings due to different 22q duplicated chromosomal segments are discussed. Our report indicates that 22q12 interstitial duplications are associated with craniofacial anomalies and mild mental retardation, while life threatening malformations are usually not present. Although these phenotypic changes are common and non-specific, molecular study of our patient established more precise relationships between clinical findings and 22q duplicated region(s). This approach fosters better counseling of the families of patients with newly diagnosed, similar duplications.

Abnormalities, Multiple↗
PubMed1992

Duplication of part of chromosome 17 is commonly associated with hereditary motor and sensory neuropathy type I (Charcot-Marie-Tooth disease type 1).

Hereditary motor and sensory neuropathy type I (HMSNI), also known as Charcot-Marie-Tooth disease type 1 (CMT1), has been shown to be genetically heterogeneous. A major gene maps to chromosome 17 (CMT1A). A set of loci, D17S122, D17S125, and D17S124, show tight linkage to the CMT1A locus, and a duplication of D17S122 has been detected in some families. We show that the locus D17S122 is duplicated in affected individuals from 7 informative families with HMSNI. The duplication was demonstrated either by differences in hybridization densities between two bands of a restriction fragment length polymorphism or by the presence of all three alleles. No normal individual had the duplication. A single recombinant exists between the MspI polymorphism of D17S122 and the duplicated band, suggesting that the duplication is of considerable size. Patients with HMSN type II do not show the duplication. These findings will have considerable impact on the diagnosis of chronic demyelinating neuropathies, in patients with or without similarly affected relatives.

Charcot-Marie-Tooth Disease↗
PubMed1997

A common duplication in the lysyl hydroxylase gene of patients with Ehlers Danlos syndrome type VI results in preferential stimulation of lysyl hydroxylase activity and mRNA by hydralazine.

Patients with Ehlers Danlos Syndrome type VI (EDS VI) are biochemically characterized by a deficiency of lysyl hydroxylase (LH), an enzyme that hydroxylates lysine residues required in the formation of stable crosslinks in collagen biosynthesis. Recently, in 19% of 35 EDS VI families, a duplication of seven exons in the LH gene has been identified as a common cause of EDS VI. We have observed that in fibroblasts from patients with this duplication mutation, administration of hydralazine, an iron-chelating agent, and ascorbate, a cofactor for LH activity, stimulates LH activity and its mRNA significantly more than in other EDS VI patients who do not have this duplication. Administration of these reagents, either singly or in combination, to fibroblasts from five patients homozygous for the duplication stimulated the low basal level of LH activity (<20% of normal) by five- to sixfold (hydralazine +/- ascorbate) and by twofold (ascorbate alone) at 72 h. This paralleled the increase in the steady-state level of mRNA for LH measured in similarly treated fibroblasts from four of these patients. In contrast, the activity of LH in fibroblasts from six other EDS VI patients and the mRNA from four of these patients who did not have the duplication were increased only three- to fourfold by hydralazine +/- ascorbate. The mechanism for the preferential stimulation of LH activity and mRNA by hydralazine in the EDS VI cells carrying the duplication is unknown, but it could be attributed to the presence of, for example, an enhancer sequence within the duplicated region of the LH gene.

2,2'-Dipyridyl↗