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At least 217 records · Page 12Linked to original sources
PubMed2005

Tandem organization of independently duplicated homeobox genes in the basal cnidarian Acropora millepora.

A number of examples of independently duplicated regulatory genes have been identified in cnidarians, but the extent of this phenomenon and organization of these duplicated genes are unknown. Here we describe the identification of three pairs of independently duplicated homeobox genes in the anthozoan cnidarian, Acropora millepora. In each case, the pairs of paralogous genes are tightly linked, but the extent of sequence divergence implies that these do not reflect recent duplication events. The phenomenon is likely to be more general, as the examples reported here represent most of the limited number of Acropora homeobox genes for which genomic data are yet available.

Amino Acid Sequence↗
PubMed2006

Genomic organization and transcript profiling of the bovine toll-like receptor gene cluster TLR6-TLR1-TLR10.

Toll-like receptors (TLRs) are a family of recognition receptors playing a crucial role in the innate immune system. Different combinations of TLRs are thought to be crucial for effective immune response, thus insight into the organization and expression of TLRs is important for understanding disease resistance. Mastitis is the most frequent and costly disease in dairy production, and the innate immune system is considered to be important in the first line defence against this disease. In the present paper we have characterized the genomic organization of TLR6-TLR1-TLR10 in a approximately 50 kb region of bovine chromosome 6, including 5'-untranslated exons not previously described. A method for gene expression analysis was developed and used for transcription profiling of the three paralogous genes in different bovine tissues. The expression analysis showed similar expression profiles for TLR1 and TLR6, which indicate a co-regulation of these two genes in cattle. TLR10 had a different expression profile, pointing toward a stronger functional diversification compared to TLR1 and TLR6. The differences in expression are in accordance with the evolutionary history of this gene cluster, where TLR10 diverged from the common ancestral gene before the duplication event that created TLR1 and TLR6.

5' Untranslated Regions↗
PubMed2004

The altered evolutionary trajectories of gene duplicates.

Gene duplication is widely regarded as the predominant mechanism by which genes with new functions and associated phenotypic novelties arise. However, the mutational events and population-genetic mechanisms that lead to the short-term preservation of duplicate genes are not necessarily the same as those exhibited by well-established paralogs en route to the origin of new beneficial features. Thus, although recent genome-wide analyses have revealed striking patterns of protein-sequence divergence among the members of surviving paralogous gene families, the mechanisms responsible for the historical development of these patterns remain unclear.

Animals↗
PubMed2003

Gene conversion drives GC content evolution in mammalian histones.

To examine the evolutionary influence of gene conversion on DNA base composition, I analysed an exhaustive dataset of histone paralogous genes from human and mouse. I show that those gene copies that belong to subfamilies of very similar sequences (presumably undergoing gene conversion) have a higher GC content than unique gene copies (presumably not undergoing gene conversion). Thus, it seems that gene conversion is a biased process that tends to increase the DNA GC content, a conclusion that has implications for the evolution of isochores in vertebrates.

Animals↗
PubMed2004

Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control.

Rapid rates of evolution can signify either a lack of selective constraint and the consequent accumulation of neutral alleles, or positive Darwinian selection driving the fixation of advantageous alleles. Based on a comparison of 1,350 orthologous gene pairs from human and mouse, we show that the evolution of gene expression profiles is so rapid that it is comparable to that of paralogous gene pairs or randomly paired genes. The expression divergence in the entire set of orthologous pairs neither strongly correlates with sequence divergence, nor focuses in any particular tissue. Moreover, comparing tissue expressions across the orthologous gene pairs, we observe that any human tissue is more similar to any other human tissue examined than to its corresponding mouse tissue. Collectively, these results indicate that, while some differences in expression profiles may be due to adaptive evolution, the levels of divergence are mostly compatible with a neutral mode of evolution, in which a mutation for ectopic expression may rise to fixation by random drift without significantly affecting the fitness. A disturbing corollary of these findings is that knowledge of where the gene is expressed may not carry information about its function.

Animals↗
PubMed1995

Gene products of Escherichia coli: sequence comparisons and common ancestries.

Sequences of 1,862 chromosomally encoded Escherichia coli K12 proteins were examined to identify genes likely to have arisen by duplication of genes in an ancestral chromosome. The criteria for sequence relatedness were an alignment of at least 100 amino acid residues and a PAM distance (number of accepted point mutations per 100 residues separating two sequences) below 250. A total of 971 of the 1,862 proteins examined were found in 2,329 sequence-related pairs that met these criteria. Most proteins of the sequence-related pairs were related in cellular function, as judged by biochemical and/or physiological features. Many of the pairs of proteins could be grouped into sequence-related families. If such groupings were generated from ancestral genes by duplication and divergence events, through these sequence comparisons we can identify putative ancestral sequences of the present-day genes of E. coli and other organisms. The results suggest that the 971 paralogous genes could have been derived from only 204 ancestral genes. We have also shown that the process of duplication and divergence is not the exclusive mechanism of evolution of all E. coli genes. Indeed, the relationships among the sequences of multiple (in the sense of redundant) enzymes indicate that nearly half could have arisen either by convergent evolution or by lateral transfer. Therefore, not all functionally related genes need arise by duplication and divergence.

Bacterial Proteins↗
PubMed2002

Evolution of supergene families associated with insecticide resistance.

The emergence of insecticide resistance in the mosquito poses a serious threat to the efficacy of many malaria control programs. We have searched the Anopheles gambiae genome for members of the three major enzyme families- the carboxylesterases, glutathione transferases, and cytochrome P450s-that are primarily responsible for metabolic resistance to insecticides. A comparative genomic analysis with Drosophila melanogaster reveals that a considerable expansion of these supergene families has occurred in the mosquito. Low gene orthology and little chromosomal synteny paradoxically contrast the easily identified orthologous groups of genes presumably seeded by common ancestors. In A. gambiae, the independent expansion of paralogous genes is mainly a consequence of the formation of clusters among locally duplicated genes. These expansions may reflect the functional diversification of supergene families consistent with major differences in the life history and ecology of these organisms. These data provide a basis for identifying the resistance-associated enzymes within these families. This will enable the resistance status of mosquitoes, flies, and possibly other holometabolous insects to be monitored. The analyses also provide the means for identifying previously unknown molecules involved in fundamental biological processes such as development.

Animals↗
PubMed2002

Analysis of the Bacillus subtilis spoIIIJ gene and its Paralogue gene, yqjG.

The Bacillus subtilis spoIIIJ gene, which has been proven to be vegetatively expressed, has also been implicated as a sporulation gene. Recent genome sequencing information in many organisms reveals that spoIIIJ and its paralogous gene, yqjG, are conserved from prokaryotes to humans. A homologue of SpoIIIJ/YqjG, the Escherichia coli YidC is involved in the insertion of membrane proteins into the lipid bilayer. On the basis of this similarity, it was proposed that the two homologues act as translocase for the membrane proteins. We studied the requirements for spoIIIJ and yqjG during vegetative growth and sporulation. In rich media, the growth of spoIIIJ and yqjG single mutants were the same as that of the wild type, whereas spoIIIJ yqjG double inactivation was lethal, indicating that together these B. subtilis translocase homologues play an important role in maintaining the viability of the cell. This result also suggests that SpoIIIJ and YqjG probably control significantly overlapping functions during vegetative growth. spoIIIJ mutations have already been established to block sporulation at stage III. In contrast, disruption of yqjG did not interfere with sporulation. We further show that high level expression of spoIIIJ during vegetative phase is dispensable for spore formation, but the sporulation-specific expression of spoIIIJ is necessary for efficient sporulation even at the basal level. Using green fluorescent protein reporter to monitor SpoIIIJ and YqjG localization, we found that the proteins localize at the cell membrane in vegetative cells and at the polar and engulfment septa in sporulating cells. This localization of SpoIIIJ at the sporulation-specific septa may be important for the role of spoIIIJ during sporulation.

Bacillus subtilis↗
PubMed1997

Gene dosage-dependent effects of the Hoxa-13 and Hoxd-13 mutations on morphogenesis of the terminal parts of the digestive and urogenital tracts.

Gene targeting experiments have shown that the murine Hoxa-13 and Hoxd-13 paralogous genes control skeletal patterning in the distal region of the developing limbs. However, both genes are also expressed in the terminal part of the digestive and urogenital tracts during embryogenesis and postnatal development. Here, we report the abnormalities occuring in these systems in Hoxa-13(-/-) and Hoxa-13/Hoxd-13 compound mutant mice. Hoxa-13(-/-) mutant fetuses show agenesis of the caudal portion of the Müllerian ducts, lack of development of the presumptive urinary bladder and premature stenosis of the umbilical arteries, which could account for the lethality of this mutation at mid-gestational stages. Due to such lethality, only Hoxa-13(+/-)/Hoxd-13(-/-) compound mutants can reach adulthood. These compound mutants display: (i) agenesis or hypoplasia of some of the male accessory sex glands, (ii) malpositioning of the vaginal, urethral and anal openings, and improper separation of the vagina from the urogenital sinus, (iii) hydronephrosis and (iv) anomalies of the muscular and epithelial layers of the rectum. Thus, Hoxa-13 and Hoxd-13 play important roles in the morphogenesis of the terminal part of the gut and urogenital tract. While Hoxa-13(-/-)/Hoxd-13(+/-) fetuses show severely impaired development of the urogenital sinus, double null (Hoxa-13[-/-]/Hoxd-13[-/-]) fetuses display no separation of the terminal (cloacal) hindgut cavity into a urogenital sinus and presumptive rectum, and no development of the genital bud, thereby demonstrating that both genes act, in a partly redundant manner, during early morphogenesis of posterior trunk structures.

Animals↗
PubMed2006

Natural selection drives extremely rapid evolution in antiviral RNAi genes.

RNA interference (RNAi) is perhaps best known as a laboratory tool. However, RNAi-related pathways represent an antiviral component of innate immunity in both plants and animals. Since viruses can protect themselves by suppressing RNAi, interaction between RNA viruses and host RNAi may represent an ancient coevolutionary "arms race." This could lead to strong directional selection on RNAi genes, but to date their evolution has not been studied. By comparing DNA sequences from different species of Drosophila, we show that the rate of amino acid evolution is substantially elevated in genes related to antiviral RNAi function (Dcr2, R2D2, and Ago2). They are among the fastest evolving 3% of all Drosophila genes; they evolve significantly faster than other components of innate immunity and faster than paralogous genes that mediate "housekeeping" functions. Based on DNA polymorphism data from three species of Drosophila, McDonald-Kreitman tests showed that this rapid evolution is due to strong positive selection. Furthermore, Dcr2 and Ago2 display reduced genetic diversity, indicative of a recent selective sweep in both genes. Together, these data show rapid adaptive evolution of the antiviral RNAi pathway in Drosophila. This is a signature of host-pathogen arms races and implies that the ancient battle between RNA viruses and host antiviral RNAi genes is active and significant in shaping RNAi function.

Amino Acid Sequence↗
PubMed2004

Divergent evolution of the prolactin-inducible protein gene and related genes in the mouse genome.

The prolactin-inducible protein (PIP/GCDFP15) family consists of small secretory polypeptides that are found in various body fluids. In order to study evolutionary events to this family, we cloned member genes and analyzed their sequences. A database search revealed the presence of a novel paralogous gene on mouse chromosome 6q34 and a nonprocessed pseudogene adjacent to PIP on human chromosome 7q34. The mouse PIP and four related genes displayed higher nonsynonymous and synonymous substitution ratios in comparison to other mammalian PIP orthologues; furthermore, these genes exhibited distinct distributions among tissues such as seminal vesicle, colon, and mammary gland. A pair of duplicated genes could have existed prior to radiation to the human and rodents. While only PIP is active in the human lineage, species-specific gene duplications have given rise to functional variants in rodents. Adaptive evolution potentially has occurred among the PIP and its related genes in the mouse genome.

Amino Acid Sequence↗
PubMed2000

Duplication of genes encoding non-clathrin coat protein gamma-COP in vertebrate, insect and plant evolution.

Coatomer is a major component of COPI vesicles and consists of seven subunits. The gamma-COP subunit of the coatomer is believed to mediate the binding to the cytoplasmic dilysine motifs of membrane proteins. We characterized cDNAs for Copg genes encoding gamma-COP from mouse, zebrafish, Drosophila melanogaster and Bombyx mori. Two copies of Copg genes are present in vertebrates and in B. mori. Phylogenetic analysis revealed that two paralogous genes had been derived from a single ancestral gene by duplication independently in vertebrates and in B. mori. Mouse Copg1 showed ubiquitous expression with the highest level in testis. Zebrafish copg2 was biallelically expressed in hybrid larvae in contrast to its mammalian ortholog expressed in a parent-of-origin-specific manner. A phylogenetic analysis with partial plant cDNA sequences suggested that copg gene was also duplicated in the grass family (Poaceae).

Amino Acid Sequence↗
PubMed2004

DNA sequence and analysis of human chromosome 9.

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

Base Composition↗
PubMed2026

Chromosomal-level genome assembly of Trypanosoma carassii, the etiologic agent of a recent outbreak of trypanosomiasis in cage-cultured large yellow croaker (Larimichthys crocea) in China.

Trypanosoma carassii, a typical freshwater fish trypanosome, has recently been identified as the etiological agent of a trypanosomiasis outbreak in cage-cultured large yellow croaker (Larimichthys crocea) in China and has been designated as T. c. larimichthys. To date, publicly available genomic data for trypanosomes have been limited to terrestrial species, particularly those of medical importance. Here, we present a chromosome-level genome assembly of T. carassii, the first genome of an aquatic trypanosome, generated using PacBio HiFi long-read sequencing and Hi-C scaffolding technologies. A preliminary genome survey based on Illumina sequencing data estimated the genome size at 56.38 Mb with a heterozygosity of 1.17%. The final assembled genome spans 48.55 Mb, with contig N50 and scaffold N50 values of 139.15 Kb, and achieves 100.00% BUSCO completeness. Hi-C data resolved the assembly into 34 chromosomes and 9 unanchored scaffolds. Repetitive elements account for 53.29% of the genome (approximately 25.87 Mb). A total of 11,584 protein-coding genes were predicted, 95.36% of which were functionally annotated. Synonymous substitution rates analysis of paralogous genes indicates a recent burst of gene duplication, which likely corresponds to a whole-genome duplications. This high-quality genome assembly provides invaluable resources for understanding the evolution and host adaptation of aquatic trypanosomes.

Animals↗
PubMed2003

Hox genes and kidney patterning.

PURPOSE OF REVIEW: Hox gene activity is essential for proper organization or pattern of the vertebrate body plan and is necessary for organogenesis. Sequence conservation within this family of genes is high yet they are involved in very diverse developmental processes. How this family functions in these processes is a challenging question, but is important for the understanding of renal organogenesis. Multiple Hox genes are expressed in the kidney and mutation in at least one group of paralogous genes results in severe renal defects. RECENT FINDINGS: Recent studies in mice with targeted Hox gene mutations and in kidney cell lines demonstrate that these genes have evolved to control tissue specific functions through their ability to regulate the expression of renal morphogens. The studies also demonstrate that Hox gene activity is not only restricted by the domain of expression but also by the specificity of the DNA binding homeodomain. Interestingly, these conserved homeodomains are not wholly interchangeable for normal renal organogenesis while they do appear to be interchangeable for axial skeleton development. SUMMARY: It is clear that Hox genes regulate important interactions between the ureteric bud and metanephric mesenchyme. Nevertheless, much work remains to define the expression patterns of multiple Hox genes during kidney development, to better determine the functional relationships of the encoded proteins, and to identify additional Hox downstream targets.

Animals↗
PubMed1993

Expression of class I homeobox genes in fetal and adult murine skin.

We examined the expression patterns of several class I homeobox genes in mouse fetal and adult skin. All the genes of the Hox-B locus, except Hoxb-1, are expressed in skin from murine fetuses of 17 and 18 d gestation, at which time the epidermis is undergoing stratification and differentiation. The amount of individual Hox gene message varies considerably, but expression of all genes is detectable by RNase protection except Hoxb-1, which could not be detected even by the reverse transcription-polymerase chain reaction (RT-PCR) assay. Homeobox gene expression in skin is not confined to the Hox-B locus; the paralogous genes Hoxa-4, -b-4, -c-4, and -d-4 are all expressed. The amount of Hoxb-4, -b-2, and -c-4 message in skin is relatively constant from the earliest gestational day examined (day 16) through birth at day 19. Expression of several homeobox genes is also seen in adult skin.

Aging↗
PubMed2006

Regulation and expression of bba66 encoding an immunogenic infection-associated lipoprotein in Borrelia burgdorferi.

When Borrelia burgdorferi (Bb) is transmitted from a tick vector to a mammalian host the spirochaete alters gene expression, allowing for adaptation to the new host. We evaluated the regulation of paralogous gene family (pgf) 54 members in response to environmental cues and focused our efforts on determining the molecular mechanisms influencing bba66 expression. By qRT-PCR, bba65, bba66, bba71 and bba73 displayed regulation similar to ospC under mammalian-like conditions. Of the pgf 54 members, bba66 demonstrated the greatest and second greatest change in expression in response to pH or temperature shift respectively. Furthermore, Bb-infected mice and patients with early disseminated Lyme disease produced detectable antibodies to BBA66. A protein(s) active in Bb at pH 7 was able to interact with the bba66 upstream region and was specific as bba64 and ospC promoters were unable to out-compete for binding. bba66 promoter mapping revealed putative sigma70 and sigmaS consensus sequences, enabling us to narrow the protein binding site to a region within an imperfect inverted repeat upstream of the -35 region. Moreover, BBA66 production is associated with an infectious phenotype, and loss of either sigmaN or sigmaS resulted in loss of BBA66. Promoter-GFP fusion analysis indicated that the sigma70 and/or sigmaS consensus sequences alone were not sufficient to initiate transcription and a portion of the upstream inverted repeat was required. These results suggest a primary role for BBA66 in Bb transmission and infection.

Animals↗
PubMed2001

P13, an integral membrane protein of Borrelia burgdorferi, is C-terminally processed and contains surface-exposed domains.

To elucidate antigens present on the bacterial surface of Borrelia burgdorferi sensu lato that may be involved in pathogenesis, we characterized a protein, P13, with an apparent molecular mass of 13 kDa. The protein was immunogenic and was expressed in large amounts during in vitro cultivation compared to other known antigens. An immunofluorescence assay, immunoelectron microscopy, and protease sensitivity assays indicated that P13 is surface exposed. The deduced sequence of the P13 peptide revealed a possible signal peptidase type I cleavage site, and computer analysis predicted that P13 is an integral membrane protein with three transmembrane-spanning domains. Mass spectrometry, in vitro translation, and N- and C-terminal amino acid sequencing analyses indicated that P13 was posttranslationally processed at both ends and modified by an unknown mechanism. Furthermore, p13 belongs to a gene family with five additional members in B. burgdorferi sensu stricto. The p13 gene is located on the linear chromosome of the bacterium, in contrast to five paralogous genes, which are located on extrachromosomal plasmids. The size of the p13 transcript was consistent with a monocistronic transcript. This new gene family may be involved in functions that are specific for this spirochete and its pathogenesis.

Amino Acid Sequence↗