Mechanism Of Genetic Recombination Research Articles

A structural classification of the variant surface glycoproteins of the African trypanosome.

Long-term immune evasion by the African trypanosome is achieved through repetitive cycles of surface protein replacement with antigenically distinct versions of the dense Variant Surface Glycoprotein (VSG) coat. Thousands of VSG genes and pseudo-genes exist in the parasite genome that, together with genetic recombination mechanisms, allow for essentially unlimited immune escape from the adaptive immune system of the host. The diversity space of the "VSGnome" at the protein level was thought to be limited to a few related folds whose structures were determined more than 30 years ago. However, recent progress has shown that the VSGs possess significantly more architectural variation than had been appreciated. Here we combine experimental X-ray crystallography (presenting structures of N-terminal domains of coat proteins VSG11, VSG21, VSG545, VSG558, and VSG615) with deep-learning prediction using Alphafold to produce models of hundreds of VSG proteins. We classify the VSGnome into groups based on protein architecture and oligomerization state, contextualize recent bioinformatics clustering schemes, and extensively map VSG-diversity space. We demonstrate that in addition to the structural variability and post-translational modifications observed thus far, VSGs are also characterized by variations in oligomerization state and possess inherent flexibility and alternative conformations, lending additional variability to what is exposed to the immune system. Finally, these additional experimental structures and the hundreds of Alphafold predictions confirm that the molecular surfaces of the VSGs remain distinct from variant to variant, supporting the hypothesis that protein surface diversity is central to the process of antigenic variation used by this organism during infection.

Budding of ascospores in Colletotrichum lindemuthianum

AbstractCommon bean anthracnose is one of the main fungal diseases that affect the crop. The disease is caused by the fungus Colletotrichum lindemuthianum, anamorph, which has wide variability as well as its teleomorph. Sexual reproduction is the main mechanism of increasing genetic variability in fungi, therefore the study of morphological characteristics and their sexual structures are important. Homothallic strains of the pathogen have shown the production of new ascospores via mitosis after the sexual cycle. As a result of each mitotic division there are two ascospores with amygdaliform and/or allantoid morphology. In this work the characterization of this phenomenon is described as budding. This is the first report on the occurrence of ascospore budding in the genus Colletotrichum. The homothallic strain UFLA84‐1 was used. Analyses of light microscopy, fluorescence and high‐resolution scanning electron microscopy were used for the description of the budding process. Cytological analyses were carried out to estimate the dimension of ascospores, budding percentage and colony type. The budding cycle is described in six stages, and the complete process develops after the release of all ascospores from an ascus. The ascospores from this process can present both morphologies and bud growth can be apical or lateral. Sexual reproduction is a mechanism of genetic recombination and the budding process increases the number of ascospores generated by meiosis and may therefore represent an adaptive advantage of the pathogen.

Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination.

Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for DNA repair in somatic cells during mitosis while Dmc1 only works during meiosis in germ cells. This spatiotemporal difference is probably due to their distinctive mismatch tolerance during HR: Rad51 does not permit HR in the presence of mismatches, whereas Dmc1 can tolerate certain mismatches. Here, the cryo-EM structures of Rad51–DNA and Dmc1–DNA complexes revealed that the major conformational differences between these two proteins are located in their Loop2 regions, which contain invading single-stranded DNA (ssDNA) binding residues and double-stranded DNA (dsDNA) complementary strand binding residues, stabilizing ssDNA and dsDNA in presynaptic and postsynaptic complexes, respectively. By combining molecular dynamic simulation and single-molecule FRET assays, we identified that V273 and D274 in the Loop2 region of human RAD51 (hRAD51), corresponding to P274 and G275 of human DMC1 (hDMC1), are the key residues regulating mismatch tolerance during strand exchange in HR. This HR accuracy control mechanism provides mechanistic insights into the specific roles of Rad51 and Dmc1 in DNA double-strand break repair and may shed light on the regulatory mechanism of genetic recombination in mitosis and meiosis.

What's in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts.

Mitochondria and plastids evolved from free-living bacteria, but are now considered integral parts of the eukaryotic species in which they live. Therefore, they are implicitly called by the same eukaryotic species name. Historically, mitochondria and plastids were known as “organelles”, even before their bacterial origin became fully established. However, since organelle evolution by endosymbiosis has become an established theory in biology, more and more endosymbiotic systems have been discovered that show various levels of host/symbiont integration. In this context, the distinction between “host/symbiont” and “eukaryote/organelle” systems is currently unclear. The criteria that are commonly considered are genetic integration (via gene transfer from the endosymbiont to the nucleus), cellular integration (synchronization of the cell cycles), and metabolic integration (the mutual dependency of the metabolisms). Here, I suggest that these criteria should be evaluated according to the resulting coupling of genetic recombination between individuals and congruence of effective population sizes, which determines if independent speciation is possible for either of the partners. I would like to call this aspect of integration “sexual symbiont integration”. If the partners lose their independence in speciation, I think that they should be considered one species. The partner who maintains its genetic recombination mechanisms and life cycle should then be the name giving “host”; the other one would be the organelle. Distinguishing between organelles and symbionts according to their sexual symbiont integration is independent of any particular mechanism or structural property of the endosymbiont/host system under investigation.

Neurospora crassa: looking back and looking forward at a model microbe.

Investigation of the red bread mold that contaminated French bakeries nearly two centuries ago has led to a wealth of discoveries that have impacted our understanding of genetic, biochemical, and molecular mechanisms in microbes, from Mendelian genetics and the gene-enzyme relationship to circadian rhythm and plant cell wall degradation. Early Neurospora research focused on elucidating mechanisms of genetic recombination and gene action and later progressed to addressing complex biological questions of eukaryotic microbes. Here we review the evolution of the filamentous fungus Neurospora as a model microbe over the past century. We discuss the origins of Neurospora as a model microbe, the immediate scientific impacts from work in this filamentous fungus, and how the introduction of other model organisms (i.e., Escherichia coli and Saccharomyces cerevisiae) redirected the focus of Neurospora research. Neurospora has and continues to inform our understanding of a myriad of basic scientific concepts and now has the opportunity to forge into the applied biosciences and biotechnology.

基于多信息融合的酵母重组冷热点预测

Meiotic recombination is non-uniformly distributed across the genome, occurring at relatively high frequencies in some genomic regions (hotspots) and at relatively low frequencies in others (coldspots). Recombination depends not only on sequence features, but also on chromatin structure. Accurate identification of recombination hotspots and coldspots would assist our understanding of genetic recombination mechanisms and genome evolution. In this study, 2 kb recombination hot/cold spots were identified in Saccharomyces cerevisiae from experimental data. Using increment diversity with quadratic discriminant (IDQD) and support vector machine (SVM) algorithms, we predicted hot/cold spots from multiple genomic features associated with sequence, structure, thermodynamic stability of DNA and chromatin structure. The predictive model accurately discriminated recombination hotspots from coldspots. IDQD yielded higher overall performance than SVM in terms of sensitivity, specificity and accuracy.

The Function of PRDM9 on Mammalian Recombination Hotspots

PRDM9 (PR domain containing 9) is one kind of histone trimethylase which catalyzes the H3K4 trimethylation, and possesses the activity of transcription factor. PRDM9 transcripts were only expressed in germ cells entering meiotic prophase in female fetal gonads and in postnatal testis, whose deficiency results in sterility. The zinc finger motif of mammalian PRDM9 rapidly evolves, which is respond to the sequences of recombination hotspots. Several researches indicated that PRDM9 was involved in the binding to recombination hotspots and initiation of recombination. These progresses are important for understanding of species evolution and the mechanism of genetic recombination.

Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes

BackgroundMeiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate. Understanding meiosis will not only advance our knowledge of the mechanisms of genetic recombination, but also has substantial applications in crop improvement. Despite the tremendous progress in the past decade in other model organisms (e.g., Saccharomyces cerevisiae and Drosophila melanogaster), the global identification of meiotic genes in flowering plants has remained a challenge due to the lack of efficient methods to collect pure meiocytes for analyzing the temporal and spatial gene expression patterns during meiosis, and for the sensitive identification and quantitation of novel genes.ResultsA high-throughput approach to identify meiosis-specific genes by combining isolated meiocytes, RNA-Seq, bioinformatic and statistical analysis pipelines was developed. By analyzing the studied genes that have a meiosis function, a pipeline for identifying meiosis-specific genes has been defined. More than 1,000 genes that are specifically or preferentially expressed in meiocytes have been identified as candidate meiosis-specific genes. A group of 55 genes that have mitochondrial genome origins and a significant number of transposable element (TE) genes (1,036) were also found to have up-regulated expression levels in meiocytes.ConclusionThese findings advance our understanding of meiotic genes, gene expression and regulation, especially the transcript profiles of MGI genes and TE genes, and provide a framework for functional analysis of genes in meiosis.

Ordered tetrad analysis of two genes in<I>Neurospora</I>

Tetrad analysis helps to determine whether or not two genes are linked by using the four products of meiotic tetrads in Neurospora, yest and Chlamydomonas. This determination, which has been applied in genetic maps of eukaryotes, is critical to understand the mechanisms of heredity. Here, the relationship between ascus types and spore types was analyzed; a logic procedure of ordered tetrad analysis was suggested base on Mendelian laws, mechanisms of genetic recombination and mapping.

Pattern Formation in Mosquitos

IMMUNOLOGY Like the innate immune systems of vertebrates, those of the insect world possess pattern recognition receptors that detect the broad signatures displayed by different classes of pathogens. In contrast, the narrow immune receptor specificity afforded by mechanisms of genetic recombination has been considered a feature unique to adaptive immunity in higher vertebrates. This view has recently undergone some revision, however, with the observation that lower vertebrates and invertebrates are also adept at manufacturing diverse immune receptors. For example, Drosophila use alternative splicing of transcripts from an immunoglobulin domain-containing locus—the Down syndrome cell adhesion molecule gene Dscam —to generate recognition receptors that assist in the phagocytosis of bacteria. Dong et al. observe that in the mosquito Anopheles gambiae (the vector for malaria), the large number of exons in AgDscam could yield as many as 31,000 alternatively spliced products, a range similar to that calculated for Drosophila. Challenging mosquito cell lines with different pathogens resulted in a varied representation of these exons via alternative splicing and AgDscam molecules with distinct specificities. Evidence for alternative splicing of AgDscam was also demonstrated in adult mosquitos, and RNA interference-mediated silencing decreased the resistance of mosquitos to bacterial infection and to oocytes of the malaria parasite carried in the insect midgut. As in Drosophila , the AgDscam forms appeared to enhance phagocytosis of bacteria by hemocytes, although it is likely that the mechanism of Dscam action extends to other modes of immune defense. A further series of experiments revealed that the repertoires of AgDscam molecules could be tailored, in terms of binding affinity, to the infecting pathogens, underscoring the degree to which specificity provided by the Dscam system might help refine pathogen pattern recognition in insects. — SJS PLoS Biol. 4 , e229 (2006).

Induction of natural competence in Streptococcus pneumoniae triggers lysis and DNA release from a subfraction of the cell population.

Naturally competent bacteria have the ability to take up free DNA from the surrounding medium and incorporate this DNA into their genomes by homologous recombination. In naturally competent Streptococcus pneumoniae, and related streptococcal species from the mitis phylogenetic group, the competent state is not a constitutive property but is induced by a peptide pheromone through a quorum-sensing mechanism. Recent studies have shown that natural genetic transformation is an important mechanism for gene exchange between streptococci in nature. A prerequisite for effective gene exchange is the presence of streptococcal donor DNA in the environment. Despite decades of study of the transformation process we still do not know how this donor DNA is released from streptococcal cells to the external milieu. Traditionally, it has been assumed that donor DNA originates from cells that die and fall apart from natural causes. In this study we show that induction of the competent state initiates release of DNA from a subfraction of the bacterial population, probably by cell lysis. The majority of the cells induced to competence take up DNA and act as recipients, whereas the rest release DNA and act as donors. These findings show that natural transformation in streptococci provides a natural mechanism for genetic recombination that resembles sex in higher organisms.

The role of integrons in antibiotic resistance gene capture

AbstractAlthough recently discovered, integrons have played a primordial role in the evolution of bacterial genomes. They are best known as the genetic agents responsible for the capture and spread of antibiotic resistance determinants among diverse Gram-negative clinical isolates, and this activity is at the root of the antibiotic resistance phenomenon that has evolved over the last 60 years. The discovery of the ancestral chromosomal super-integrons, novel integron classes, and the multitude of gene cassettes they propagate solidify the crucial role of this system in adaptive bacterial evolution. Recent evidence suggests that evolutionarily old genetic recombination mechanisms for gene transfer have been adapted to the new antibiotic environment due to the heavy selective pressure of liberal antibiotic use in human medicine and animal husbandry.

Historical overview: searching for replication help in all of the rec places.

For several decades, research into the mechanisms of genetic recombination proceeded without a complete understanding of its cellular function or its place in DNA metabolism. Many lines of research recently have coalesced to reveal a thorough integration of most aspects of DNA metabolism, including recombination. In bacteria, the primary function of homologous genetic recombination is the repair of stalled or collapsed replication forks. Recombinational DNA repair of replication forks is a surprisingly common process, even under normal growth conditions. The new results feature multiple pathways for repair and the involvement of many enzymatic systems. The long-recognized integration of replication and recombination in the DNA metabolism of bacteriophage T4 has moved into the spotlight with its clear mechanistic precedents. In eukaryotes, a similar integration of replication and recombination is seen in meiotic recombination as well as in the repair of replication forks and double-strand breaks generated by environmental abuse. Basic mechanisms for replication fork repair can now inform continued research into other aspects of recombination. This overview attempts to trace the history of the search for recombination function in bacteria and their bacteriophages, as well as some of the parallel paths taken in eukaryotic recombination research.

Phylogenetic relationships within and between Epichloë and Neotyphodium endophytes as estimated by AFLP markers and rDNA sequences

Analysis of Amplified Fragment Length Polymorphisms (AFLP) in a sample population of Epichloe and Neotyphodium was conducted to evaluate the usefulness of this technique in estimating phylogenetic relationships among these fungi. A total of 963 unique restriction fragments were identified with 13 selective primer combinations. Neighbour-joining and parsimony analysis produced phylogenetic trees with high bootstrap support. All Epichloe festucae isolates were monophyletic, and clades of E. festucae were identified that correspond to the host species from which they were isolated. These groups may indicate the importance of coevolution in the development of the fine fescue- E. festucae symbiosis. The grouping of E. festucae isolates from hard fescue and Chewings fescue into one clade conflicts with the current taxonomy of these host grasses. Sequencing of ribosomal DNA spacer regions ITS1 and ITS2 was conducted for comparisons to the phylogenetic relationships estimated by AFLP. Using the maximum likelihood test, a significant difference was detected between AFLP and rDNA trees due to discrepancies in the association of anamorphs ( Neotyphodium ) and teleomorphs ( Epichloe ). This discrepancy may be due to some mechanism of genetic recombination, such as hybridization or parasexual recombination, that occurs in Neotyphodium populations. It is concluded that AFLP markers are useful for producing meaningful phylogenies among a diverse group of fungi and for identifying groups of closely related individuals that are genetically and biologically similar. Further investigation is needed to determine how AFLP markers change over short periods of time in populations and over evolutionary time.

Evolution of a conserved protein module from Archaea to plants

It has been suggested that structurally conserved modules that are found in distantly related proteins are descended from a limited number of ancestral sequence motives1. It is a matter of debate whether exon shuffling2 and/or other mechanisms of genetic recombination can explain their widespread distribution3. Combinatorial rearrangements of prefabricated constituents is a possible mechanism by which the evolution of functionally diverse proteins, often united as a superfamily4, could be accelerated. A common dilemma in the analysis of putative protein families is the distinction between structural convergence and homology by descent5. Based on a highly conserved protein module, we suggest divergent evolutionary pathways of a protein superfamily that led to the plant seed-storage globulins legumin and vicilin, which consist of subunits with two structurally equivalent domains6.

Crystallization of Escherichia coli RuvA complexed with a synthetic Holliday junction.

During homologous recombination in Escherichia coli the RuvA, B and C proteins interact specifically with the Holliday junction formed by the action of RecA to promote the strand-exchange reaction. RuvA, a homotetrameric protein of molecular weight 88 kDa, has been overexpressed in E. coli, purified and co-crystallized with a synthetic Holliday junction substrate made from four 18-base deoxyoligonucleotides. Crystals were grown using the hanging-drop vapour-diffusion method with sodium acetate as the precipitant. The crystals diffract to a resolution of 6 A and belong to the monoclinic system, space group C2, with cell parameters a = 148, b = 148, c = 106 A and beta = 123 degrees. The X-ray analysis of these crystals should reveal the structure of the Holliday junction and its mode of binding to RuvA, providing new insights into the molecular mechanism of genetic recombination.

RNA recombination in brome mosaic virus, a model plus strand RNA virus.

Studies on the molecular mechanism of genetic recombination in RNA viruses have progressed at the time when experimental systems of efficient recombination crossovers were established. The system of brome mosaic virus (BMV) represents one of the most useful and most advanced tools for investigation of the molecular aspects of the mechanism of RNA-RNA recombination events. By using engineered BMV RNA components, the occurrence of both homologous and nonhomologous crosses were demonstrated among the segments of the BMV RNA genome. Studies show that the two types of crossovers require different RNA signal sequences and that both types depend upon the participation of BMV replicase proteins. Mutations in the two BMV-encoded replicase polypeptides (proteins 1a and 2a) reveal that their different regions participate in homologous and in nonhomologous crossovers. Based on all these data, it is most likely that homologous and nonhomologous recombinant crosses do occur via two different types of template switching events (copy-choice mechanism) where viral replicase complex changes RNA templates during viral RNA replication at distinct signal sequences. In this review we discuss various aspects of the mechanism of RNA recombination in BMV and we emphasize future projections of this research.

Genetic instability leads to loss of both p53 alleles in a human glioblastoma.

Little is known about the relationship between genetic recombination mechanisms and loss of tumour suppressor genes in solid tumours. Here, we demonstrate deletion and truncation of both p53 alleles in a primary human glioblastoma and a derived cell line as the combined result of a t(17;20) reciprocal translocation and a 1.1 Mbp genomic deletion on chromosome 17p, starting in intron 4 of the p53 gene and ending at the telomeric CA-repeat marker D17S960. These results (i) suggest that genetic instability can lead to loss of tumour suppressor gene function in solid cancers, (ii) provide mapping of one such recombination event at the nucleotide level, and (iii) establish the orientation of the p53 gene on chromosome 17 as: centromere 5'-3'-telomere.

A new approach to genetic based machine learning for efficient local improvement and its application to a graphic problem

This paper presents a new approach to genetic based machine learning (GBML). The new approach utilizes mechanisms of genetic recombination in bacterial genetics. The new approach is efficient in improving local portions of chromosomes. A simulation of a simple graphic problem using the new approach is done and the effectiveness of the new approach is shown.

Molecular analysis of gene conversion in spermatids from transgenic mice

Investigations into the mechanisms and properties of gene conversion in mammals are greatly restricted by the inability to recover all the products of a meiosis. Additionally, the study of this process has been hampered by the lack of visible markers to detect gene conversion, especially when the events are rare. In previous work, we developed a transgenic system for detection and quantitation of gene conversion events in the germline of mice (Murti, J.R., Bumbulis, M., Schimenti, J.C., 1992. High frequency germline gene conversion in transgenic mice. Mol. Cell. Biol. 12, 2545–2552) that could be exploited as an assay for recombinogenic chemicals (Murti, J.R, Schimenti, K.J., Schimenti, J.C., 1994. A recombination-based transgenic mouse system for genotoxicity testing. Mutat. Res. 307, 583–595). A specific intrachromosomal gene conversion event between two complementarily defective lacZ genes resulted in the production of β-galactosidase in spermatids, enabling a measurement of conversion frequency. Here, we report that the anticancer drug, cisplatin, increased gene conversion in meiotic stage cells in these transgenic mice. Furthermore, a method was developed for direct molecular analysis of transgene conversion events in single or pooled lacZ-positive spermatids. The ability to identify gametes that have undergone a rare gene conversion event, followed by molecular amplification of the recombinant gene, should make it possible to investigate the mechanisms of genetic recombination in mammals in greater detail than previously possible.