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At least 469 records · Page 26Linked to original sources
PubMed2002

Tissue-specific expression of male-transmitted mitochondrial DNA and its implications for rates of molecular evolution in Mytilus mussels (Bivalvia: Mytilidae).

Mytilus and other bivalves exhibit an unusual system of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Specifically, males transmit the mtDNA they have received from their fathers to their sons. Females transmit their mother's mtDNA to both sons and daughters. Males are normally heteroplasmic and females are normally homoplasmic, but not exclusively. This system is associated with an unusual pattern of molecular evolution. Male-transmitted mtDNA (M type) evolves faster than female-transmitted (F type) mtDNA. Relatively relaxed selection on the M type has been proposed as an explanation for this phenomenon. To further evaluate the selective forces acting upon the M-type genome, we used RT-PCR to determine where it is expressed. M-type mtDNA expression was detected in all gonad samples and in 50% of somatic tissues of males, and in a single female tissue. F-type mtDNA expression was detected in all female tissues, all male somatic tissues, and all but one male gonad sample. We argue that the expression of M-type mtDNA in male somatic and male gonad tissues has implications for the strength of selection acting upon it.

Animals↗
PubMed1999

Striking bimodal methylation of the repeat unit of the tandem array encoding human U2 snRNA (the RNU2 locus).

The genes encoding human U2 small nuclear RNA are arrayed in tandem (the RNU2 locus) and have undergone concerted evolution for >35 Myr. Tandem organization of repetitive sequences may facilitate recombination that underlies concerted evolution, but could risk instability. Since DNA methylation plays a crucial role in genome stability, we investigated the methylation status of the RNU2 locus to understand the forces maintaining array stability and homogeneity. We found that a region of approximately 1.5 kb spanning the U2 promoter, U2 gene sequence, and CT microsatellite is completely unmethylated, whereas the rest of the repeat is heavily methylated. Since the U2 transcription enhancer DSE and CT microsatellite mark the boundaries between methylated and unmethylated domains, they might function as cis-acting elements for establishing and maintaining proper methylation at the RNU2 locus. Interestingly, the RNU2 locus in human fibrosarcoma line HT1080 is hypomethylated, and de novo methylation did not occur in an artificial U2 tandem array introduced by stable transfection. The observed bimodal methylation pattern may be important for both efficient transcription of U2 gene and maintenance of nearly perfect tandem arrays in somatic cells.

Cell Line↗
PubMed1999

Rapid structural and epigenetic changes in polyploid and aneuploid genomes.

Recent work with plants has demonstrated that genome instability can be triggered by a change in chromosome number arising from either whole genome duplications (polyploidy) or loss/gain of individual chromosomes (aneuploidy). This genome instability is manifested as rapid structural and epigenetic alterations that can occur somatically or meiotically within a few generations after heteroploid formation. The intrinsic instability of newly formed polyploid and aneuploid genomes has relevance for genome evolution and human carcinogenesis, and points toward recombinational and epigenetic mechanisms that sense and respond to chromosome numerical changes.

Aneuploidy↗
PubMed2006

Molecular mechanism based on self-replicating protein conformation for the inheritance of acquired information in humans.

Recent evidence challenges the paradigmatic view of nucleic acids as the sole mediators of hereditary information. Here I present a molecular mechanism that can explain how acquired information in humans in a DNA independent mode becomes innate and heritable. The model is based on self-replicating protein conformations, a concept derived from prion and amyloid biology. Information is stored in specific beta-sheet protein conformations that can act as cytoplasmic molecular memories. The conformational information can be transmitted to next generations in a non-nucleic acid based inheritance system utilizing the self-perpetuating potential of such beta-rich protein aggregates. Chaperones play a crucial role in the model by regulating and balancing the process of folding and misfolding; they also assist in preventing the development of aggregation-based disease. The protein conformation-mediated information system could represent an evolutionary conserved primordial mechanism: while the main strategy has been to ensure rapid folding of polypeptides into the native, functional conformation, the disfolded, beta-rich amyloidogenic state has provided advantage by providing a cytoplasmic, protease-resistant self-perpetuating DNA-independent adaptive inheritance system. The model offers an explanation for the problematic question of the evolution of complex behavioural traits and has even impact in the context of mammalian cloning: the protein conformation-based information localized in the somatic cytoplasm is lost when transferring nuclei only into enucleated oocytes. The protein conformation-based model presented herein postulates that proteins may contain much more information than determined by the nucleotide-triplet controlled peptide sequence and that there exists cross-talk and information exchange between proteins.

Amyloid↗
PubMed2000

Molecular insights into the immunopathogenesis of follicular lymphoma.

Follicular lymphoma is caused by the transformation of a germinal-center-derived B cell with a t(14;18) chromosomal translocation. The distribution of somatic mutations within immunoglobulin genes indicates that follicular-lymphoma cells can interact with antigen. In addition, nonimmunoglobulin genes such as BCL6 seem to undergo somatic hypermutation. Here, Kostas Stamatopoulos and colleagues relate the molecular data about immunoglobulin genes and the protooncogenes BCL2 and BCL6 to the pathogenesis and evolution of follicular lymphoma.

B-Lymphocyte Subsets↗
PubMed1986

Human inhibitor of the first component of complement, C1: characterization of cDNA clones and localization of the gene to chromosome 11.

C1 inhibitor is a heavily glycosylated plasma protein that regulates the activity of the first component of complement (C1) by inactivation of the serine protease subcomponents, C1r and C1s. C1 inhibitor cDNA clones have been isolated, and one of these (pC1INH1, 950 base pairs) has been partially sequenced. Sequence analysis demonstrates that the C1 inhibitor is a member of the serpin "superfamily" of protease inhibitors. In the region sequenced, C1 inhibitor has 22% identity with antithrombin III, 26% with alpha 1-antitrypsin and alpha 1-antichymotrypsin, and 18% with human angiotensinogen. C1 inhibitor has a larger amino-terminal extension than do the other plasma protease inhibitors. In addition, inspection of residues that are invariant among the other protease inhibitors shows that C1 inhibitor differs at 14 of 41 of these positions. Thus, it appears that C1 inhibitor diverged from the group relatively early in evolution, although probably after the divergence of angiotensinogen. Southern blot analysis of BamHI-digested DNA from normal individuals and from rodent-human somatic cell hybrid cell lines (that contain a limited but varied human chromosome complement) was used to localize the human C1 inhibitor gene to chromosome 11.

Amino Acid Sequence↗
PubMed1981

DNA damage as the primary cause of aging.

DNA damage appears to be ubiquitous in the biological world, as judged by the variety of organisms which have evolved DNA-repair systems. Previously, it was proposed that germ-line DNA of multicellular organisms may be protected from damage, and consequently from aging, by efficient recombinational repair during meiosis. The somatic line, however, may be vulnerable to the accumulation of DNA damage, and hence undergo aging, owing to relatively less repair. Although the DNA lesions most important in aging are not known yet, there is evidence for serveral types of endogenous damage. DNA lesions have been shown to interfere with transcription and replication, and so lead to loss of cell function and death. In mammals, there is a progressive decline of function in many different tissues with increasing age. Deterioration of central nervous system functions appears to be a critical part of the aging process. This may be due to the low DNA repair capacity which is found in postmitotic brain tissue, and which could result in the accumulation of DNA lesions in this tissue. Also reviewed is evidence that species longevity is directly related to tissue DNA-repair capacity and that aging may be accelerated by treatment with DNA-damaging agents, or in individuals with genetically defective repair. Although it has been frequently postulated that somatic mutation may be cause of aging, current evidence suggests that it is probably less important than DNA damage. A prominent theory on the evolution of aging, which attributes special importance to genes that are advantagous in youth but are deleterious later on, is discussed in terms of regulatory genes that reduce DNA repair as cells differentiate to the postmitotic state. Finally, we hypothesize that the factors which determine maximum longevity of individuals in a population are the rate of occurrence of DNA damage, the rate of DNA repair, the degree of cellular redundancy, and the extent of exposure to stress.

Aging↗
PubMed2003

Amplification of repeat-containing transcribed sequences (ARTS): a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer.

Cancer is a genetic disease caused by mutations in somatic cells. Those that carry advantageous mutations are favoured by natural selection. In most cancers, genetic instability increases mutation rate and facilitates cancer cell evolution. Microsatellite instability (MSI), due to defects of the DNA mismatch repair system, affects in particular repeat sequences (microsatellites) scattered throughout the genome. As mutations in expressed genes are more likely to be functional, we developed a procedure for the systematic identification of mutant repeat-containing expressed sequences (amplification of repeat-containing transcribed sequences, ARTS). The entire cell mRNA was converted into short double-stranded cDNA fragments linked to an adapter at both ends. Repeat-containing cDNA fragments were PCR amplified using the adapter-specific primer in combination with different arbitrary primers including the repeat. ARTS yielded discrete PCR products with lengths that were directly correlated to the lengths of the endogenous repeats. Comparison between ARTS products obtained from control cells and cancer cells with microsatellite instability (MSI+) revealed mRNAs carrying insertions or deletions at repeats. The subsequent sequencing allowed the identification of a series of frameshift-mutated mRNAs in MSI+ cancer cells, including the already described mutant BAX transcript. These data show that ARTS provides an unbiased genome-wide approach to the discovery of functionally relevant genes that could be affected by MSI in cancer.

Acyltransferases↗
PubMed2006

Mutant library construction in directed molecular evolution: casting a wider net.

Directed molecular evolution imitates the natural selection process in the laboratory to find mutant proteins with improved properties in the expected aspects by exploring the encoding sequence space. The success of directed molecular evolution experiment depends on the quality of artificially prepared mutant libraries and the availability of convenient high-throughput screening methods. Well-prepared libraries promise the possibility of obtaining desired mutants by screening a library containing a relatively small number of mutants. This article summarizes and reviews the currently available methodologies widely used in directed evolution practices in the hope of providing a general reference for library construction. These methods include error-prone polymerase chain reaction (epPCR), oligonucleotide-based mutagenesis, and genetic recombination exemplified by DNA shuffling and its derivatives. Another designed method is also discussed, in which B-lymphocytes are fooled to mutate nonantibody foreign proteins through somatic hypermutation (SHM).

Animals↗
PubMed2003

[Bacterial aggression].

In all living species, the first line of defence against microbial aggressions is constituted by innate immunity. During Evolution, it appears in invertebrates and plants, long before adaptive immunity, which appears in vertebrate. Adaptive immunity induces acquired resistance against microorganisms through random somatic rearrangements of genes encoding immunoglobulins and T cell receptors, thus generating a high level of diversity of receptors (>10(9)) in response to microbial aggressions. Acquired resistance is not vertically transmitted and reflects the "infectious history" of every individual. In contrast, innate immunity relies on recognition of antigens by a small number of weakly specific receptors (>10(2)) designated Pattern-Recognition Receptors (PRR) and is vertically transmitted by germinal cells. The PRR are expressed on macrophages dendritic cells and B lymphocytes and recognize antigenic structures highly conserved in the living world, termed Pathogen-Associated Molecular Patterns (PAMP), as lipopolysaccharides peptidoglycanes and lipoteichoic acids. PRR are secreted (complement, lectins), or expressed at the cell surface of cells to induce endocytosis or signaling (Toll-like receptors or TLRs). The recognition of antigens induces an immediate inflammatory response and triggers adaptive immunity. Among secreted PRR, the system of complement plays a major role in the immediate inflammatory response, controlling infections by its major role in opsonization, chemotactism and activation of leucocytes. TLRs induce the inflammatory response against microorganisms through NF-kB, a cytoplasmic factor controlling transcription of many genes, including cytokines (TNF, INF, IL-1, IL-2, IL-8, IL-12.) and defensines. So, within few minutes following microbial aggression, the inflammatory response is rapidly triggered to destroy infectious agents and to generate a long-term memory against pathogens.

Animals↗
PubMed1982

Malaria ecology--the Trinidadian aspect.

Triad models serve as reference points for the examination of etiological factors and salient features in Trinidad's malaria control efforts. Adaptive mechanisms and 'role-switching' in biological and cultural evolution are highlighted as are the significance of environment and man-environment forces. A community model is presented which incorporates an inventory of somatic and psychological factors, risk-taking behaviours, and environmental and material resources pertaining to specific diseases which a particular habitat and population group maintain.

Anopheles↗
PubMed1978

Evolution of the 5 S RNA genes in vertebrates.

We have built the phylogenetic tree of Vertebrate 5S RNA using the sequence data of thirteen species belonging to six groups. Evolution of the 5S genes has been very slow in Vertebrates since 90 residues are identical in all 5S RNAs which are presently sequenced. In Amphibians and Teleosts different 5S genes are active in oocytes and in somatic cells. This dual gene system has probably been acquired independently by Amphibians and Teleosts. In Amphibians, the oocyte-type 5S genes have evolved much faster than the somatic-type genes. This is not true in all species since the oocyte-type genes of one Teleost (Tinca tinca) have evolved more slowly than the somatic-type genes. There are in all Vertebrate 5S RNAs five complementary regions which can be base-paired. The sequence data are compatible with the three secondary-structure models that have been proposed for 5S RNA.

Animals↗
PubMed1996

Sex chromatin in lepidoptera.

Like mammals, Lepidoptera possess female-specific sex chromatin. In a compilation of new and published data, 81% of the 238 investigated Lepidoptera species display one or more heterochromatin bodies in female somatic interphase cells, but not in male cells. In contrast with the similar phenomenon in mammals, this sex-specific heterochromatin does not function as a dosage compensation mechanism. Most Lepidoptera have a WZ/ZZ sex chromosome mechanism, and the sex chromatin is derived from the univalent W sex chromosome. Sex chromatin is regarded as an indicator of an advanced stage of W chromosome evolution. In species with a Z/ZZ sex chromosome mechanism, loss of the W chromosome is accompanied by loss of the female-specific heterochromatin. Since sex chromatin can be discerned easily in interphase nuclei, and especially so in the highly polyploid somatic cells, it is a useful marker for diagnosing chromosomal sex of embryos and larvae, and of identifying sex chromosome aberrations in mutagenesis screens. All species with sex chromatin belong to the Ditrysia, the main clade of Lepidoptera that contains more than 98% of all extant species. Sex chromatin has not been reported for clades that branched off earlier. The nonditrysian clades share this character with Trichoptera, a sister group of the Lepidoptera. We propose that Lepidoptera originally had a Z/ZZ sex chromosome mechanism like Trichoptera; the WZ/ZZ sex chromosome mechanism evolved later in the ditrysian branch of Lepidoptera. Secondary losses of the W chromosome account for the sporadically occurring Z/ZZ sex chromosome systems in ditrysian families. The lepidopteran sex chromatin, therefore, appears to mirror the full evolutionary life cycle of a univalent sex chromosome from its birth through heterochromatinization to sporadic loss.

Animals↗
PubMed2002

Coevolution of quasispecies: B-cell mutation rates maximize viral error catastrophes.

Coevolution of two coupled quasispecies is studied, motivated by the competition between viral evolution and adapting immune response. In this coadaptive model, besides the classical error catastrophe for high virus mutation rates, a second "adaptation" catastrophe occurs, when virus mutation rates are too small to escape immune attack. Maximizing both regimes of viral error catastrophes is a possible strategy for an optimal immune response, reducing the range of allowed viral mutation rates to a minimum. From this requirement, one obtains constraints on B-cell mutation rates and receptor lengths, yielding an estimate of somatic hypermutation rates in the germinal center in accordance with observation.

Animals↗
PubMed2026

Mixed Evidence that Dosage Sensitive Genes Drive Global Dosage Compensation in Flour Beetles.

Heteromorphic sex chromosomes create inherent gene dosage differences between males and females because one sex carries a single copy of the X chromosome while the other carries two. Many species have evolved mechanisms that equalize X-linked gene expression between the sexes and, in some cases, restore ancestral autosomal levels, a process known as dosage compensation. Although chromosome-wide compensation is common in male heterogametic (XY) insects, regulatory outcomes vary across taxa and sex chromosome systems, leaving the evolutionary forces shaping sex chromosome regulation unresolved. One hypothesis proposes that the extent to which genes are sensitive to changes in gene dose determines whether complete compensation evolves. We tested predictions of this insensitive sex chromosome hypothesis (ISCH) across five flour beetle species using comparative transcriptomics and genome-wide RNAi-derived measures of gene-by-gene sensitivity. Including an X-autosome fusion in Tribolium confusum allowed direct assessment of expression evolution following a transition from a diploid autosome to a hemizygous Neo-X. Across all five species, we detect complete chromosome-wide dosage compensation and balance between the sexes in somatic tissues, including the Neo-X region. Consistent with ISCH predictions, neither the ancestral Shared-X nor the Neo-X is depleted of genes that are sensitive to RNAi-based expression disruption. However, contrary to expectations, at the level of individual genes, we find little evidence that more sensitive genes exhibit reduced expression divergence. These results suggest that chromosome-wide compensation can be maintained by global regulatory mechanisms that persist through sex chromosome turnover, even when gene-by-gene constraints are weak. Understanding the molecular basis of these mechanisms remains a central challenge in sex chromosome evolution.

Animals↗
PubMed1996

Natural repressors of P-induced hybrid dysgenesis in Drosophila melanogaster: a model for repressor evolution.

Type I repressors control P element transposition and comprise full length elements and elements with small 3' deletions in the final exon. Using a sensitive assay for measuring the strength of repression of P element transposition in somatic and germline tissues, we have isolated and characterized a naturally occurring type I repressor element from a Q population of Drosophila melanogaster. We demonstrate that the almost complete repression of transposition in this population is a mixture of KP elements with intermediate levels of repression, and the strong contribution of a single 2.6 kb P element deletion derivative, which we call SR (Strong Repressor). A deletion in the final intron of SR allows for the constitutive production of a putative 75 kDa repressor protein in germline tissues in addition to the production of the 66 kDa repressor in the soma, which would result in a biparental mode of inheritance of repression. Based on the four observed classes of natural Q populations, we propose a model in which populations containing SR-like elements, capable of producing strong type I repressor constitutively, have a selective advantage over populations which rely either on maternally transmitted P cytotype or on KP-induced weak levels of repression. Such populations may subsequently spread and constitute an evolutionary stable strategy for the repression of hybrid dysgenesis in Drosophila melanogaster.

Amino Acid Sequence↗
PubMed2002

Cell-selfish modes of evolution and mutations directed after transcriptional bypass.

During transcription, prokaryotic and eukaryotic RNA polymerases bypass and misread (transcriptional mutagenesis) several classes of DNA lesions. For example, misreading of 8-OH-dG generates mRNAs containing G to T transversions. After translation, if the mutant protein briefly allowed the cell a growth-DNA replication advantage, then precocious DNA replication would bypass that unrepaired 8-OH-dG and misinsert dA opposite the directing DNA lesion with a higher probability than would be experienced for 8-OH-G lesions at other positions in otherwise identical neighboring cells. Such retromutations would have been tested for their imparted growth advantage as mRNA before they became heritable DNA mutations. The logical properties of a mode of evolution that utilizes directed-retromutagenesis were compared one by one with those of the standard neo-Darwinian mode. The retromutagenesis mode, while minimizing mutational load, is cell-selfish; fitness is for an immediate growth advantage rather than future reproductive potential. In prokaryotes, an evolutionary mode that involves standard Darwinian fitness testing of novel alleles in the genetic background of origin followed by clonal expansion also favors cell-selfish allele combinations when linkage disequilibrium is practiced. For metazoa and plants to have evolved organized tissues, cell-selfish modes of evolution represent systems-poisons that must be totally suppressed. The feedback loops that allow evolution to be cell-serving in prokaryotes are actively blocked in eukaryotes by traits that restrict fitness to future reproductive potential. These traits include (i) delay of fitness testing until after the mutation is made permanently heritable, (ii) diploidy to further delay fitness testing, (iii) segregation of somatic lines from germ lines, (iv) testing of novel alleles against randomized allele combinations constructed by obligate sex, and (v) obligate genetic death to insure that that the most basic systems unit of selfish allele combinatorial uniqueness is the species instead of the cell. The analyses indicate that modes of evolution in addition to our neo-Darwinian one could have existed utilizing known molecular mechanisms. The evolution of multicellularity was as much the discarding of old cell-selfish habits as the acquisition of new altruistic ones.

Alleles↗