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At least 253 records · Page 14Linked to original sources
PubMed2004

Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum.

BACKGROUND: The apicomplexan parasite Cryptosporidium parvum is an emerging pathogen capable of causing illness in humans and other animals and death in immunocompromised individuals. No effective treatment is available and the genome sequence has recently been completed. This parasite differs from other apicomplexans in its lack of a plastid organelle, the apicoplast. Gene transfer, either intracellular from an endosymbiont/donor organelle or horizontal from another organism, can provide evidence of a previous endosymbiotic relationship and/or alter the genetic repertoire of the host organism. Given the importance of gene transfers in eukaryotic evolution and the potential implications for chemotherapy, it is important to identify the complement of transferred genes in Cryptosporidium. RESULTS: We have identified 31 genes of likely plastid/endosymbiont (n = 7) or prokaryotic (n = 24) origin using a phylogenomic approach. The findings support the hypothesis that Cryptosporidium evolved from a plastid-containing lineage and subsequently lost its apicoplast during evolution. Expression analyses of candidate genes of algal and eubacterial origin show that these genes are expressed and developmentally regulated during the life cycle of C. parvum. CONCLUSIONS: Cryptosporidium is the recipient of a large number of transferred genes, many of which are not shared by other apicomplexan parasites. Genes transferred from distant phylogenetic sources, such as eubacteria, may be potential targets for therapeutic drugs owing to their phylogenetic distance or the lack of homologs in the host. The successful integration and expression of the transferred genes in this genome has changed the genetic and metabolic repertoire of the parasite.

1,4-alpha-Glucan Branching Enzyme↗
PubMed2002

Variation in gene expression within and among natural populations.

Evolution may depend more strongly on variation in gene expression than on differences between variant forms of proteins. Regions of DNA that affect gene expression are highly variable, containing 0.6% polymorphic sites. These naturally occurring polymorphic nucleotides can alter in vivo transcription rates. Thus, one might expect substantial variation in gene expression between individuals. But the natural variation in mRNA expression for a large number of genes has not been measured. Here we report microarray studies addressing the variation in gene expression within and between natural populations of teleost fish of the genus Fundulus. We observed statistically significant differences in expression between individuals within the same population for approximately 18% of 907 genes. Expression typically differed by a factor of 1.5, and often more than 2.0. Differences between populations increased the variation. Much of the variation between populations was a positive function of the variation within populations and thus is most parsimoniously described as random. Some genes showed unexpected patterns of expression--changes unrelated to evolutionary distance. These data suggest that substantial natural variation exists in gene expression and that this quantitative variation is important in evolution.

Analysis of Variance↗
PubMed2003

Characterization of hey bHLH genes in teleost fish.

Hairy-related basic helix-loop-helix (bHLH) transcription factors are targets of Delta-Notch signaling and represent essential components for a number of cell fate decisions during vertebrate embryogenesis. Hey genes encode a subfamily of hairy-related proteins that have been implicated in processes like somitogenesis, blood vessel and heart development. We have identified and characterized hey genes in three teleost fish lineages using degenerate PCR and database searches. Phylogenetic analysis of Hey proteins suggests a complex pattern of evolution with high divergence of hey2 in Takifugu rubripes (Fugu, Japanese pufferfish) and possibly loss in the related Tetraodon nigroviridis (the freshwater pufferfish). In addition, duplication of hey1 in both pufferfishes, Fugu and Tetraodon, was observed. Conversely, zebrafish (Danio rerio) has the same complement of three hey genes as known from mammals. All three hey genes show much more restricted gene expression profiles in zebrafish when compared to mouse. Importantly, while all three murine Hey genes are expressed in overlapping patterns in the presomitic mesoderm (PSM) and somites, in zebrafish only hey1 shows PSM and somite expression in a highly dynamic fashion. Therefore, while overlapping expression might account for redundancy of hey function in higher vertebrates, this is unlikely to be the case in zebrafish. In deltaD (dlD) deficient after-eight zebrafish mutants, the dynamic expression of hey1 in the PSM is impaired and completely lost in newly formed somitomeres. Overexpression of dlD on the other hand results in the ectopic expression of hey1 in the axial mesoderm. Hence, hey1 represents a target of Delta-Notch signaling dynamically expressed during somite formation in zebrafish.

Amino Acid Sequence↗
PubMed1975

Gene action in fish of tetraploid origin. II. Cellular and biochemical parameters in clupeoid and salmonoid fish.

By use of cell size, protein and hemoglobin content, and enzyme activities as markers, it becomes apparent that in the course of evolution the gene expression of anciently tetraploid fish of the order Ostariophysi was diploidized, but no such regulatory mechanism has evolved in the phylogenetically tetraploid species of the order Isospondyli. This finding is discussed in terms of possible selective neutrality of tetraploid expression and the phylogenetic age of Isospondyli.

Animals↗
PubMed1999

Retrotransposon 1731 in Drosophila melanogaster changes retrovirus-like expression strategy in host genome.

Earlier related to parasitic elements, retrotransposons of eukaryotes have been demonstrated to participate in general cell processes such as chromosome repair and evolution of gene expression (Teng et al., 1996; McDonald, 1993). Here, we report the existence of two classes of genomic copies of retrotransposon 1731 with different expression strategies, one of which might be driven by natural selection. The first class uses conventional translational frameshifting known to ensure expression of reverse transcriptase (RT) open reading frame (ORF), depending on the efficiency of frameshifting. The bulk of genomic copies are related to the second class where the frameshift is prevented as a result of the substitution of a rare codon recognising rare tRNA by a codon preferred by host genome, whereas the RT ORF is restored by downstream single nucleotide deletion. We suggest that natural selection has driven the switching of 1731 expression strategy from retrovirus-like to the fusion-ORF expression. This observation is in accordance with the detection in testes of fused Gag-RT polypeptide encoded by 1731. The abundance of RT in testes may serve for normal development of host tissue.

Animals↗
PubMedDate not supplied

Both endogenous and environmental factors affect embryo proliferation in the polyembryonic wasp Copidosoma floridanum.

Copidosoma floridanum is a polyembryonic, parasitic wasp of the moth Trichoplusia ni. Following oviposition into a host, the C. floridanum egg initially undergoes complete (holoblastic) cleavage to form a single morula stage embryo. This embryo then undergoes a proliferation phase in which multiple, secondary morulae develop. C. floridanum has also evolved a caste system whereby some secondary morulae develop into soldier larvae whose function is defense whereas others develop into reproductive larvae that become adult wasps. In the current study, we conducted manipulative and candidate gene studies to identify factors affecting the proliferation phase of C. floridanum development. Transplantation of morulae of different ages into different host stages indicated that both embryo age and host environment affected the total number of offspring produced per morula. Morula age and brood size also significantly affected whether offspring of one or both castes were produced in a brood. In contrast, the host environment did not significantly affect caste formation. A putative homolog of the gene hedgehog (Cf-hh) was partially cloned from C. floridanum. In situ hybridization studies indicated that Cf-hh was expressed in secondary morulae during the proliferation phase of development, suggesting a possible role for the Hh signaling pathway in the evolution of polyembryony.

Animals↗
PubMed1993

Polymorphism in the regulatory region of HLA-DRB genes correlating with haplotype evolution.

Class II genes of the human major histocompatibility complex (MHC) are polymorphic. Allelic variation of the coding region of these genes is involved in the antigen presentation and is associated with susceptibility to certain autoimmune diseases. The DR region is unique among human class II regions in that multiple DRB genes are expressed. Differential expression of the different DRB loci has been demonstrated, and we sequenced the proximal promoter region of the HLA-DRB genes, known to be involved in the regulation of these genes. We found locus-specific and allele-specific nucleotide variations in their regulatory regions and we determined the relationship between the regulatory regions of HLA-DRB genes. This polymorphism found in the regulatory conserved boxes could be involved in the observed differential expression of DRB loci. In addition, we found a polymorphism between the regulatory regions of DRB1 alleles which might be involved in an allele-specific regulation and therefore could be considered as an additional factor in susceptibility to autoimmune diseases.

Base Sequence↗
PubMed1993

Macaque salivary proline-rich protein: structure, evolution, and expression.

Proline-rich proteins are a family of proteins that exhibit unique features including an unusual high proline content and salivary-specificity. As a major constituent in the salivary secretion of higher primates, proline-rich proteins may have biological roles in oral lubrication and protection. In this article, the genomic structure and regulation by cAMP of one of the macaque salivary proline-rich protein genes, MnP4, is reviewed. The evolution of this multigene family of proteins is also discussed.

Amino Acid Sequence↗
PubMed1999

Genetic manipulation of Kluyveromyces lactis linear DNA plasmids: gene targeting and plasmid shuffles.

Genetic manipulation of yeast linear DNA plasmids, particularly of k1 and k2 from the non-conventional dairy yeast Kluyveromyces lactis, has been advanced by the recent establishment of DNA transformation-mediated one-step gene disruption and allele replacement techniques. These methods provide the basis for a strategy for the functional analysis of plasmid genes and DNA elements. By use of double selection regimens, these single-gene procedures have been extended to effect disruption of individual genes on plasmid k2 and transplacement of a functional copy onto plasmid k1, resulting in the production of yeast strains with an altered plasmid composition. This cytoplasmic gene shuffle system facilitates the introduction of specifically modified alleles into k1 or k2 in order to study the function, expression (from UCS promoters) and regulation of cytoplasmic linear plasmid genes. Additionally, identification, characterization and localization of plasmid gene products of interest are made possible by shuffling GFP-, epitope- or affinity purification-tagged alleles between k2 and k1. The gene shuffle approach can also be used for vector development and heterologous protein expression in order to exploit the biotechnical potential of the K. lactis k1/k2 system in yeast cell factory research.

Biological Evolution↗
PubMed2005

The complex interplay between plant viruses and host RNA-silencing pathways.

RNA silencing was originally identified as an immune system targeted against transposons and viruses, but is now also recognized as a major regulatory process that affects all layers of host gene expression through the activities of various small RNA species. Recent work in plants and animals indicates that viruses not only suppress, but can also exploit, endogenous RNA silencing pathways to redirect host gene expression. There are also indications that cellular, as opposed to virus-derived small RNAs, might well constitute an unsuspected defense layer against foreign nucleic acids. This complex interplay has implications in the context of disease resistance and evolution of viral genomes.

Biological Evolution↗
PubMed2003

Balancer-Cre transgenic mouse germ cells direct the incomplete resolution of a tri-loxP-targeted Cyp1a1 allele, producing a conditional knockout allele.

To generate conditional alleles, genes are commonly engineered to contain recognition sites for bacteriophage recombinases, such as Cre recombinase. When such motifs (lox sites) flank essential gene sequences, and provided that Cre recombinase is expressed, Cre recombinase will excise the flanked sequence-creating a conditional knockout allele. Targeted conditional alleles contain a minimum of three lox sites. It would be desirable to have Cre recombinase perform partial resolution (i.e., recombination some of the time between only the two lox sites flanking the marker gene). Here we report use of the commercially available Balancer2-Cre transgenic mouse line to carry out this function from a tri-loxP-site-containing cytochrome p450 1A1 (Cyp1a1) targeted allele. Such incomplete resolution of this complex locus occurred progressively with age in germ cells of male mice; the conditional Cyp1a1 gene was recovered in offspring from mice containing the targeted Cyp1a1 allele and the Cre recombinase transgene. Removal of the marker gene resulted in a conditional Cyp1a1 allele whose expression was indistinguishable from that of the wild-type allele.

Alleles↗
PubMed1996

Transcriptional control of Hox genes in the vertebrate nervous system.

The identification, in transgenic mice, of Hox gene DNA regulatory elements that can recapitulate certain aspects of the endogenous gene expression pattern has proceeded with great success. Perfect reproduction of the correct expression pattern, however, is uncommon, even when large genomic fragments spanning neighboring genes are analyzed, suggesting that important regulatory regions may be located at large distances from the genes they control or that their specific context may be important. Four classes of transcriptional regulators have been identified recently that have been shown to directly regulate Hox gene expression in the murine nervous system: retinoic acid receptors, Krox20, the Pbx/exd family, and the Hox genes themselves.

Animals↗
PubMed2006

Widespread adaptive evolution of Drosophila genes with sex-biased expression.

Many genes in higher eukaryotes show sexually dimorphic expression, and these genes tend to be among the most divergent between species. In most cases, however, it is not known whether this rapid divergence is caused by positive selection or if it is due to a relaxation of selective constraint. To distinguish between these two possibilities, we surveyed DNA sequence polymorphism in 91 Drosophila melanogaster genes with male-, female-, or nonsex-biased expression and determined their divergence from the sister species D. simulans. Using several single- and multilocus statistical tests, we estimated the type and strength of selection influencing the evolution of the proteins encoded by genes of each expression class. Adaptive evolution, as indicated by a relative excess of nonsynonymous divergence between species, was common among the sex-biased genes (both male and female). Male-biased genes, in particular, showed a strong and consistent signal of positive selection, while female-biased genes showed more variation in the type of selection they experience. Genes expressed equally in the two sexes, in contrast, showed no evidence for adaptive evolution between D. melanogaster and D. simulans. This suggests that sexual selection and intersexual coevolution are the major forces driving genetic differentiation between species.

Adaptation, Biological↗
PubMed1990

[A concept of limiting genetic factors of expression, organization, and evolution].

Elicitation and analysis of limiting genetic factors represent convenient method for approximate description of complex molecular-genetic systems. In sequential metabolic ways, the limiting is based on the minimum of catalytic activity, in parallel ones--on the maximum activity. In polygenic systems, the expressing polygenes affect always the limiting oligogenes. Limiting genes are only available to selection on the population level, the non-limiting genes being neutrally evolving. This result eliminates the acuteness of the Haldane's dilemma. The complex genetic systems could be quickly evolving by relay-race principle with sequentional change of limiting genes and without violation of Haldane's dilemma. The limiting factors of organization which restrict the possibilities of some special evolutionary directions have the key role in evolution. These limits were historically overcome by acceptance of evolutionary acquirements of wide usage. The sequence of such limits and acquirements was assumed as a basis of "scenario" of Prebiological and Biological Molecular Evolution. The concept is illustrated by some examples and results of theoretical analysis.

Animals↗
PubMed2002

Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene.

Using a combined strategy of random mutagenesis of haloalkane dehalogenase and genetic engineering of a chloropropanol-utilizing bacterium, we constructed an organism that is capable of growth on 1,2,3-trichloropropane (TCP). This highly toxic and recalcitrant compound is a waste product generated from the manufacture of the industrial chemical epichlorohydrin. Attempts to select and enrich bacterial cultures that can degrade TCP from environmental samples have repeatedly been unsuccessful, prohibiting the development of a biological process for groundwater treatment. The critical step in the aerobic degradation of TCP is the initial dehalogenation to 2,3-dichloro-1-propanol. We used random mutagenesis and screening on eosin-methylene blue agar plates to improve the activity on TCP of the haloalkane dehalogenase from Rhodococcus sp. m15-3 (DhaA). A second-generation mutant containing two amino acid substitutions, Cys176Tyr and Tyr273Phe, was nearly eight times more efficient in dehalogenating TCP than wild-type dehalogenase. Molecular modeling of the mutant dehalogenase indicated that the Cys176Tyr mutation has a global effect on the active-site structure, allowing a more productive binding of TCP within the active site, which was further fine tuned by Tyr273Phe. The evolved haloalkane dehalogenase was expressed under control of a constitutive promoter in the 2,3-dichloro-1-propanol-utilizing bacterium Agrobacterium radiobacter AD1, and the resulting strain was able to utilize TCP as the sole carbon and energy source. These results demonstrated that directed evolution of a key catabolic enzyme and its subsequent recruitment by a suitable host organism can be used for the construction of bacteria for the degradation of a toxic and environmentally recalcitrant chemical.

Biodegradation, Environmental↗
PubMed1986

Gene expression and structure of immunoglobulin epsilon chains.

The study of immunoglobulin genes has been an active area of research in recent years. The study of IgE heavy (epsilon) chain gene, in particular, has a significant impact on our understanding of the IgE system. The localization of the epsilon gene in the cluster of mouse heavy chain constant region genes has been determined, and models for gene rearrangements leading to epsilon chain gene expression have been provided. The regulation of IgE antibody production can thus be discussed in the context of these models in combination with knowledge of the cellular basis of IgE production. Comparison of the epsilon chain sequence among human, rat, and mouse has allowed a better understanding of the evolution and structure-function relationship of the epsilon chain. Furthermore, expression of epsilon chain cDNA in Escherichia coli and demonstration of biological activities of expression products have paved the basis for identification of defined peptides representing the structures for recognition by IgE receptors. These studies are discussed in this review.

Amino Acid Sequence↗
PubMed2005

Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution.

MicroRNAs are small noncoding RNAs that serve as posttranscriptional regulators of gene expression in higher eukaryotes. Their widespread and important role in animals is highlighted by recent estimates that 20%-30% of all genes are microRNA targets. Here, we report that a large set of genes involved in basic cellular processes avoid microRNA regulation due to short 3'UTRs that are specifically depleted of microRNA binding sites. For individual microRNAs, we find that coexpressed genes avoid microRNA sites, whereas target genes and microRNAs are preferentially expressed in neighboring tissues. This mutually exclusive expression argues that microRNAs confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions.

3' Untranslated Regions↗
PubMed2004

Evolutionary changes in cis and trans gene regulation.

Differences in gene expression are central to evolution. Such differences can arise from cis-regulatory changes that affect transcription initiation, transcription rate and/or transcript stability in an allele-specific manner, or from trans-regulatory changes that modify the activity or expression of factors that interact with cis-regulatory sequences. Both cis- and trans-regulatory changes contribute to divergent gene expression, but their respective contributions remain largely unknown. Here we examine the distribution of cis- and trans-regulatory changes underlying expression differences between closely related Drosophila species, D. melanogaster and D. simulans, and show functional cis-regulatory differences by comparing the relative abundance of species-specific transcripts in F1 hybrids. Differences in trans-regulatory activity were inferred by comparing the ratio of allelic expression in hybrids with the ratio of gene expression between species. Of 29 genes with interspecific expression differences, 28 had differences in cis-regulation, and these changes were sufficient to explain expression divergence for about half of the genes. Trans-regulatory differences affected 55% (16 of 29) of genes, and were always accompanied by cis-regulatory changes. These data indicate that interspecific expression differences are not caused by select trans-regulatory changes with widespread effects, but rather by many cis-acting changes spread throughout the genome.

Alleles↗