Rearrangement Of DNA Sequences Research Articles

Epigenetics and the improvement of crop plants

Epigenetics is a term that refers to the changes in gene expression that are heritable and induced by DNA methylation, histones post-translational modifications, or sncRNA, not resulting from the DNA sequence rearrangements. Epigenetic modifications influence gene expression, and thus, the plasticity of plants' development and phenotype in response to external and internal factors. Until recently, the only known epigenetic modification of the DNA in eukaryotic organisms was 5-methylcytosine. The growing interest in epigenetics and the development of sensitive detection methods enabled the discovery of other modifications of the DNA nitrogenous bases, i.e., 4-methylcytosine and 6-methyladenine. However, whilst research on the 5mC distribution and role in eukaryotic organisms is widespread, analyses regarding 6mA are scarced. Nevertheless, there are indications of a potential epigenetic role of 6-methyladenine in eukaryotic genomes. Understanding epigenetic mechanisms, which are triggered in response to environmental changes, is crucial for agriculture. This review shows epigenetic mechanisms, with particular emphasis on adenine methylation in plants, as well as the role of epigenetic variation in epibreeding, affecting the improvement of agronomic traits.

Distinguishing between monozygotic twins' blood samples through immune repertoire sequencing.

Monozygotic (MZ) twins with highly similar genomic DNA sequences can not be distinguished by conventional forensic DNA testing. The immune repertoire (IR) reflects an individual's immune history, which is unique between individuals, has been applied to individualized treatment in precision medicine. However, the application of IR in forensic genetics has not been reported to date. In this study, the diversity in the complementary determining region 3 (CDR3) of both the T-cell receptor β chain (TCRβ) and B-cell receptor heavy chain (also known as immunoglobulin heavy chain, IGH) in four pairs of MZ twins were analyzed. The results showed that the amino acid sequences length distribution frequency of TCRβ CDR3 had 4-10 differences, and the nucleic acid sequences length distribution frequency of TCRβ CDR3 had 2-7 differences between MZ twins. The shared difference of four pairs of MZ twins focused on the length distribution frequency of 34bp nucleotide sequences in TCRβ. By analyzing the usage frequency of V and J genes in TCRβ and IGH CDR3 DNA sequence rearrangements, we also found that there were biases between each pair of MZ twins, and the usage frequency of TRBJ2-3 showed common differences between each pair of MZ twins. Furthermore, each pair of MZ twins had its own unique V-J genes combination mode in TCRβ and IGH CDR3 DNA sequences. This study, for the first time, suggested that IR can be used as a potential biological marker to distinguish MZ twins.

Regulation of topoisomerase II stability and activity by ubiquitination and SUMOylation: clinical implications for cancer chemotherapy.

DNA topoisomerases II (TOP2) are peculiar enzymes (TOP2α and TOP2β) that modulate the conformation of DNA by momentarily breaking double-stranded DNA to allow another strand to pass through, and then rejoins the DNA phosphodiester backbone. TOP2α and TOP2β play vital roles in nearly all events involving DNA metabolism, including DNA transcription, replication, repair, and chromatin remodeling. Beyond these vital functions, TOP2 enzymes are therapeutic targets for various anticancer drugs, termed TOP2 poisons, such as teniposide, etoposide, and doxorubicin. These drugs exert their antitumor activity by inhibiting the activity of TOP2-DNA cleavage complexes (TOP2ccs) containing DNA double-strand breaks (DSBs), subsequently leading to the degradation of TOP2 by the 26S proteasome, thereby exposing the DSBs and eliciting a DNA damage response. Failure of the DSBs to be appropriately repaired leads to genomic instability. Due to this mechanism, patients treated with TOP2-based drugs have a high incidence of secondary malignancies and cardiotoxicity. While the cytotoxicity associated with TOP2 poisons appears to be TOP2α-dependent, the DNA sequence rearrangements and formation of DSBs appear to be mediated primarily through TOP2β inhibition, likely due to the differential degradation patterns of TOP2α and TOP2β. Research over the past few decades has shown that under various conditions, the ubiquitin-proteasome system (UPS) and the SUMOylation pathway are primarily responsible for regulating the stability and activity of TOP2 and are therefore critical regulators of the therapeutic effect of TOP2-targeting drugs. In this review, we summarize the current progress on the regulation of TOP2α and TOP2β by ubiquitination and SUMOylation. By fully elucidating the basic biology of these essential and complex molecular mechanisms, better strategies may be developed to improve the therapeutic efficacy of TOP2 poisons and minimize the risks of therapy-related secondary malignancy.

Application of Graph Theory in DNA similarity analysis of Evolutionary Closed Species.

DNA is a complex molecule that consists of biological information that is passed down from generation to generation. With the evolution over time, there are different kinds of species that evolved from a common ancestor because of the occurrence of DNA sequence rearrangements. DNA sequence similarity analysis is a major challenge since the number of sequences is rapidly increasing in the DNA database. In this research, we based a mathematical method to analyze the similarity of two DNA sequences using Graph Theory. This mathematical method started by modeling a weighted directed graph for each DNA sequence, constructing its adjacency matrix, and converting it to the representative vector for each graph. From these vectors, the similarity was determined by distance measurements such as Euclidean, Cosine, and Correlation. By keeping this method as the based method, we will check whether it is applicable for any DNA fragments in considered genomes and molecular similarity coefficients can be used as distance measurements. We will obtain similarities using the graph spectrum instead of the representative vector. Then we will compare the results from the representative vector and that of the graph spectrum. The modified method is tested by using the mitochondrial DNA of Human, Gorilla, and Orangutan. It gives the same result when the number of nucleotides in DNA fragments is increased.

An Evolutionary View of Trypanosoma Cruzi Telomeres.

Like in most eukaryotes, the linear chromosomes of Trypanosoma cruzi end in a nucleoprotein structure called the telomere, which is preceded by regions of variable length called subtelomeres. Together telomeres and subtelomeres are dynamic sites where DNA sequence rearrangements can occur without compromising essential interstitial genes or chromosomal synteny. Good examples of subtelomeres involvement are the expansion of human olfactory receptors genes, variant surface antigens in Trypanosoma brucei, and Saccharomyces cerevisiae mating types. T. cruzi telomeres are made of long stretches of the hexameric repeat 5′-TTAGGG-OH-3′, and its subtelomeres are enriched in genes and pseudogenes from the large gene families RHS, TS and DGF1, DEAD/H-RNA helicase and N-acetyltransferase, intermingled with sequences of retrotransposons elements. In particular, members of the Trans-sialidase type II family appear to have played a role in shaping the current T. cruzi telomere structure. Although the structure and function of T. cruzi telomeric and subtelomeric regions have been documented, recent experiments are providing new insights into T. cruzi's telomere-subtelomere dynamics. In this review, I discuss the co-evolution of telomere, subtelomeres and the TS gene family, and the role that these regions may have played in shaping T. cruzi's genome.

Rapid and efficient in vitro excision of BAC sequences from herpesvirus genomes using Cre-mediated recombination

Cre-mediated recombination is a widely used technique for the re-arrangement of DNA sequences that are bracketed by loxP recognition sites. This bacteriophage P1 enzyme is commonly used to excise the bacterial artificial chromosome (BAC) sequence, a vector sequence used for large herpesvirus genomes for the purposes of propagation and manipulation in Escherichia coli. Most methods utilize cell lines that can be induced for the expression of Cre enzyme to facilitate this excision. In addition, methods have been developed that express Cre from the virus genome and enable auto-excision of the BAC plasmid. We report a versatile and rapid in vitro method based on purified Cre enzyme to carry out the same process in a test tube and does not require cell line generation or cloning into the virus genome. This method greatly increases the repertoire of methods available to modify the genome prior to reconstitution of virus infectivity in a mammalian host.

Control of serine integrase recombination directionality by fusion with the directionality factor.

Bacteriophage serine integrases are extensively used in biotechnology and synthetic biology for assembly and rearrangement of DNA sequences. Serine integrases promote recombination between two different DNA sites, attP and attB, to form recombinant attL and attR sites. The ‘reverse’ reaction requires another phage-encoded protein called the recombination directionality factor (RDF) in addition to integrase; RDF activates attL × attR recombination and inhibits attP × attB recombination. We show here that serine integrases can be fused to their cognate RDFs to create single proteins that catalyse efficient attL × attR recombination in vivo and in vitro, whereas attP × attB recombination efficiency is reduced. We provide evidence that activation of attL × attR recombination involves intra-subunit contacts between the integrase and RDF moieties of the fusion protein. Minor changes in the length and sequence of the integrase–RDF linker peptide did not affect fusion protein recombination activity. The efficiency and single-protein convenience of integrase–RDF fusion proteins make them potentially very advantageous for biotechnology/synthetic biology applications. Here, we demonstrate efficient gene cassette replacement in a synthetic metabolic pathway gene array as a proof of principle.

Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains

Background Plasmodium vivax is the most prevalent human malaria parasite, causing serious public health problems in malaria-endemic countries. Until recently the Duffy-negative blood group phenotype was considered to confer resistance to vivax malaria for most African ethnicities. We and others have reported that P. vivax strains in African countries from Madagascar to Mauritania display capacity to cause clinical vivax malaria in Duffy-negative people. New insights must now explain Duffy-independent P. vivax invasion of human erythrocytes.Methods/Principal FindingsThrough recent whole genome sequencing we obtained ≥70× coverage of the P. vivax genome from five field-isolates, resulting in ≥93% of the Sal I reference sequenced at coverage greater than 20×. Combined with sequences from one additional Malagasy field isolate and from five monkey-adapted strains, we describe here identification of DNA sequence rearrangements in the P. vivax genome, including discovery of a duplication of the P. vivax Duffy binding protein (PvDBP) gene. A survey of Malagasy patients infected with P. vivax showed that the PvDBP duplication was present in numerous locations in Madagascar and found in over 50% of infected patients evaluated. Extended geographic surveys showed that the PvDBP duplication was detected frequently in vivax patients living in East Africa and in some residents of non-African P. vivax-endemic countries. Additionally, the PvDBP duplication was observed in travelers seeking treatment of vivax malaria upon returning home. PvDBP duplication prevalence was highest in west-central Madagascar sites where the highest frequencies of P. vivax-infected, Duffy-negative people were reported.Conclusions/SignificanceThe highly conserved nature of the sequence involved in the PvDBP duplication suggests that it has occurred in a recent evolutionary time frame. These data suggest that PvDBP, a merozoite surface protein involved in red cell adhesion is rapidly evolving, possibly in response to constraints imposed by erythrocyte Duffy negativity in some human populations.

Topoisomerase II-Mediated DNA Cleavage and Mutagenesis Activated by Nitric Oxide Underlie the Inflammation-Associated Tumorigenesis

Both cancer-suppressing and cancer-promoting properties of reactive nitrogen and oxygen species (RNOS) have been suggested to play a role in tumor pathology, particularly those activities associated with chronic inflammation. Here, we address the impact of nitric oxide (NO) on the induction of DNA damage and genome instability with a specific focus on the involvement of topoisomerase II (TOP2). We also investigate the contribution of NO to the formation of skin melanoma in mice. Similar to the TOP2-targeting drug, etoposide (VP-16), the NO-donor, S-nitrosoglutathione (GSNO), induces skin melanomas formation in 7,12-dimethyl- benz[a]anthracene (DMBA)-initiated mice. To explore the mechanism(s) underlying this NO-induced tumorigenesis, we use a co-culture model system to demonstrate that inflamed macrophages with inducible NO synthase (iNOS) expression cause γ-H2AX activation, p53 phosphorylation, and chromosome DNA breaks in the target cells. Inhibitor experiments revealed that NO and TOP2 isozymes are responsible for the above described cellular phenotypes. Notably, NO, unlike VP-16, preferentially induces the formation of TOP2β cleavable complexes (TOP2βcc) in cells. Moreover, GSNO induced TOP2-dependent DNA sequence rearrangements and cytotoxicity. Furthermore, the incidences of GSNO- and VP-16-induced skin melanomas were also observed to be lower in the skin-specific top2β-knockout mice. Our results suggest that TOP2 isozymes contribute to NO-induced mutagenesis and subsequent cancer development during chronic inflammation. We provide the first experimental evidence for the functional role of TOP2 in NO-caused DNA damage, mutagenesis, and carcinogenesis. Notably, these studies contribute to our molecular understanding of the cancer-promoting actions of RNOS during chronic inflammation.

A Reevaluation of Rice Mitochondrial Evolution Based on the Complete Sequence of Male-Fertile and Male-Sterile Mitochondrial Genomes

Plant mitochondrial genomes have features that distinguish them radically from their animal counterparts: a high rate of rearrangement, of uptake and loss of DNA sequences, and an extremely low point mutation rate. Perhaps the most unique structural feature of plant mitochondrial DNAs is the presence of large repeated sequences involved in intramolecular and intermolecular recombination. In addition, rare recombination events can occur across shorter repeats, creating rearrangements that result in aberrant phenotypes, including pollen abortion, which is known as cytoplasmic male sterility (CMS). Using next-generation sequencing, we pyrosequenced two rice (Oryza sativa) mitochondrial genomes that belong to the indica subspecies. One genome is normal, while the other carries the wild abortive-CMS. We find that numerous rearrangements in the rice mitochondrial genome occur even between close cytotypes during rice evolution. Unlike maize (Zea mays), a closely related species also belonging to the grass family, integration of plastid sequences did not play a role in the sequence divergence between rice cytotypes. This study also uncovered an excellent candidate for the wild abortive-CMS-encoding gene; like most of the CMS-associated open reading frames that are known in other species, this candidate was created via a rearrangement, is chimeric in structure, possesses predicted transmembrane domains, and coopted the promoter of a genuine mitochondrial gene. Our data give new insights into rice mitochondrial evolution, correcting previous reports.

Intermediates in serine recombinase-mediated site-specific recombination

Site-specific recombinases are enzymes that promote precise rearrangements of DNA sequences. They do this by cutting and rejoining the DNA strands at specific positions within a pair of target sites recognized and bound by the recombinase. One group of these enzymes, the serine recombinases, initiates strand exchange by making double-strand breaks in the DNA of the two sites, in an intermediate built around a catalytic tetramer of recombinase subunits. However, these catalytic steps are only the culmination of a complex pathway that begins when recombinase subunits recognize and bind to their target sites as dimers. To form the tetramer-containing reaction intermediate, two dimer-bound sites are brought together by protein dimer-dimer interactions. During or after this initial synapsis step, the recombinase subunit and tetramer conformations change dramatically by repositioning of component subdomains, bringing about a transformation of the enzyme from an inactive to an active configuration. In natural serine recombinase systems, these steps are subject to elaborate regulatory mechanisms in order to ensure that cleavage and rejoining of DNA strands only happen when and where they should, but we and others have identified recombinase mutants that have lost dependence on this regulation, thus facilitating the study of the basic steps leading to catalysis. We describe how our studies on activated mutants of two serine recombinases, Tn3 resolvase and Sin, are providing us with insights into the structural changes that occur before catalysis of strand exchange, and how these steps in the reaction pathway are regulated.

Genistein induces topoisomerase IIbeta- and proteasome-mediated DNA sequence rearrangements: Implications in infant leukemia

Genistein is a bioflavonoid enriched in soy products. However, high levels of maternal soy consumption have been linked to the development of infant leukemia ALL and AML. The majority of infant leukemia is linked to mixed lineage leukemia gene (MLL) translocations. Previous studies have implicated topoisomerase II (Top2) in genistein-induced infant leukemia. In order to understand the roles of the two Top2 isozymes in and the molecular mechanism for genistein-induced infant leukemia, we carried out studies in vitro using purified recombinant human Top2 isozymes, as well as studies in cultured mouse myeloid progenitor cells (32Dc13) and Top2β knockout mouse embryonic fibroblasts (MEFs). First, we showed that genistein efficiently induced both Top2α and Top2β cleavage complexes in the purified system as well as in cultured mouse cells. Second, genistein induced proteasomal degradation of Top2β in 32Dc13 cells. Third, the genistein-induced DNA double-strand break (DSB) signal, γ-H2AX, was dependent on the Top2β isozyme and proteasome activity. Fourth, the requirement for Top2β and proteasome activity was mirrored in genistein-induced DNA sequence rearrangements, as monitored by a DNA integration assay. Together, our results suggest a model in which genistein-induced Top2β cleavage complexes are processed by proteasome, leading to the exposure of otherwise Top2β-concealed DSBs and subsequent chromosome rearrangements, and implicate a major role of Top2β and proteasome in genistein-induced infant leukemia.

Newly synthesized wheat allohexaploids display progenitor‐dependent meiotic stability and aneuploidy but structural genomic additivity

To understand key mechanisms leading to stabilized allopolyploid species, we characterized the meiotic behaviour of wheat allohexaploids in relation to structural and genetic changes. For that purpose, we analysed first generations of synthetic allohexaploids obtained through interspecific hybridization, followed by spontaneous chromosome doubling, between several genotypes of Triticum turgidum and Aegilops tauschii wheat species, donors of AB and D genomes, respectively. As expected for these Ph1 (Pairing homoeologous 1) gene-carrying allopolyploids, chromosome pairing at metaphase I of meiosis essentially occurs between homologous chromosomes. However, the different synthetic allohexaploids exhibited progenitor-dependent meiotic irregularities, such as incomplete homologous pairing, resulting in univalent formation and leading to aneuploidy in the subsequent generation. Stability of the synthetic allohexaploids was shown to depend on the considered genotypes of both AB and D genome progenitors, where few combinations compare to the natural wheat allohexaploid in terms of regularity of meiosis and euploidy. Aneuploidy represents the only structural change observed in these synthetic allohexaploids, as no apparent DNA sequence elimination or rearrangement was observed when analysing euploid plants with molecular markers, developed from expressed sequence tags (ESTs) as well as simple sequence repeat (SSR) and transposable element sequences.

Uncoupling of Satellite DNA and Centromeric Function in the Genus Equus

In a previous study, we showed that centromere repositioning, that is the shift along the chromosome of the centromeric function without DNA sequence rearrangement, has occurred frequently during the evolution of the genus Equus. In this work, the analysis of the chromosomal distribution of satellite tandem repeats in Equus caballus, E. asinus, E. grevyi, and E. burchelli highlighted two atypical features: 1) several centromeres, including the previously described evolutionary new centromeres (ENCs), seem to be devoid of satellite DNA, and 2) satellite repeats are often present at non-centromeric termini, probably corresponding to relics of ancestral now inactive centromeres. Immuno-FISH experiments using satellite DNA and antibodies against the kinetochore protein CENP-A demonstrated that satellite-less primary constrictions are actually endowed with centromeric function. The phylogenetic reconstruction of centromere repositioning events demonstrates that the acquisition of satellite DNA occurs after the formation of the centromere during evolution and that centromeres can function over millions of years and many generations without detectable satellite DNA. The rapidly evolving Equus species gave us the opportunity to identify different intermediate steps along the full maturation of ENCs.

Progress in the detection of human genome structural variations

The emerging of high-throughput and high-resolution genomic technologies led to the detection of submicroscopic variants ranging from 1 kb to 3 Mb in the human genome. These variants include copy number variations (CNVs), inversions, insertions, deletions and other complex rearrangements of DNA sequences. This paper briefly reviews the commonly used technologies to discover both genomic structural variants and their potential influences. Particularly, we highlight the array-based, PCR-based and sequencing-based assays, including array-based comparative genomic hybridization (aCGH), representational oligonucleotide microarray analysis (ROMA), multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), paired-end mapping (PEM), and next-generation DNA sequencing technologies. Furthermore, we discuss the limitations and challenges of current assays and give advices on how to make the database of genomic variations more reliable.

In silico, biologically-inspired modelling of genomic variation generation in surface proteins of Trypanosoma cruzi.

BackgroundProtozoan parasites improve the likelihood of invading or adapting to the host through their capacity to present a large repertoire of surface molecules. The understanding of the mechanisms underlying the generation of antigenic diversity is crucial to aid in the development of therapies and the study of evolution. Despite advances driven by molecular biology and genomics, there is a need to gain a deeper understanding of key properties that may facilitate variation generation, models for explaining the role of genomic re-arrangements and the characterisation of surface protein families on the basis of their capacity to generate variation. Computer models may be implemented to explore, visualise and estimate the variation generation capacity of gene families in a dynamic fashion. In this paper we report the dynamic simulation of genomic variation using real T. cruzi coding sequences as inputs to a computational simulation system. The effects of random, multiple-point mutations and gene conversions on genomic variation generation were quantitatively estimated and visualised. Simulations were also implemented to investigate the potential role of pseudogenes as a source of antigenic variation in T. cruzi.ResultsComputational models of variation generation were applied to real coding sequences from surface proteins in T. cruzi: trans-sialidase-like proteins and putative surface protein dispersed gene family-1. In the simulations the sequences self-replicated, mutated and re-arranged during thousands of generations. Simulations were implemented for different mutation rates to estimate the relative robustness of the protein families in the face of DNA multiple-point mutations and sequence re-arrangements. The gene super-families and families showed distinguishing evolutionary responses, which may be used to characterise them on the basis of their capacity to generate variability. The simulations showed that sequences from T. cruzi nuclear genes tend to be relatively more robust against random, multiple-point mutations than those obtained from surface protein genes. Simulations also showed that a gene conversion model may act as an effective variation generation mechanism. Differential variation responses can be used to characterise the sequence groups under study. For example, unlike other families, sequences from the DGF1 family have the capacity to maximise variation at the amino acid level under relatively low mutation rates and through gene conversion. However, in relation to the other protein families, they exhibit more robust behaviour in response to more severe modifications through intra-family genomic sequence exchange. Independent simulations indicate that DGF1 pseudogenes might play a role in the generation of greater genomic variation in the DFG1 gene family through gene conversion under different experimental conditions.ConclusionDigital, dynamic simulations may be implemented to characterise gene families on the basis of their capacity to generate variation in the face of genomic perturbations. Such simulations may be useful to explore antigenic variation mechanisms and hypotheses about robustness at the genomic level. This investigation illustrated how sequences derived from surface protein genes and computer simulations can be used to investigate variation generation mechanisms. Such in silico experiments of self-replicating sequences undergoing random mutations and genomic re-arrangements can offer insights into the diversity generation potential of the genes under study. Biologically-inspired simulations may support the study of genomic variation mechanisms in pathogens whose genomes have been recently sequenced.

Roles of DNA topoisomerase II isozymes in chemotherapy and secondary malignancies

Drugs that target DNA topoisomerase II (Top2), including etoposide (VP-16), doxorubicin, and mitoxantrone, are among the most effective anticancer drugs in clinical use. However, Top2-based chemotherapy has been associated with higher incidences of secondary malignancies, notably the development of acute myeloid leukemia in VP-16-treated patients. This association is suggestive of a link between carcinogenesis and Top2-mediated DNA damage. We show here that VP-16-induced carcinogenesis involves mainly the beta rather than the alpha isozyme of Top2. In a mouse skin carcinogenesis model, the incidence of VP-16-induced melanomas in the skin of 7,12-dimethylbenz[a]anthracene-treated mice is found to be significantly higher in TOP2beta(+) than in skin-specific top2beta-knockout mice. Furthermore, VP-16-induced DNA sequence rearrangements and double-strand breaks (DSBs) are found to be Top2beta-dependent and preventable by cotreatment with a proteasome inhibitor, suggesting the importance of proteasomal degradation of the Top2beta-DNA cleavage complexes in VP-16-induced DNA sequence rearrangements. VP-16 cytotoxicity in transformed cells expressing both Top2 isozymes is, however, found to be primarily Top2alpha-dependent. These results point to the importance of developing Top2alpha-specific anticancer drugs for effective chemotherapy without the development of treatment-related secondary malignancies.

Delineation of the Chemical Pathways Underlying Nitric Oxide-Induced Homologous Recombination in Mammalian Cells

Inflammation is an important risk factor for cancer. During inflammation, macrophages secrete nitric oxide (NO*), which reacts with superoxide or oxygen to create ONOO- or N2O3, respectively. Although homologous recombination causes DNA sequence rearrangements that promote cancer, little was known about the ability of ONOO- and N2O3 to induce recombination in mammalian cells. Here, we show that ONOO- is a potent inducer of homologous recombination at an integrated direct repeat substrate, whereas N2O3 is relatively weakly recombinogenic. Furthermore, on a per lesion basis, ONOO(-)-induced oxidative base lesions and single-strand breaks are significantly more recombinogenic than N2O3-induced base deamination products, which did not induce detectable recombination between plasmids. Similar results were observed in mammalian cells from two different species. These results suggest that ONOO(-)-induced recombination may be an important mechanism underlying inflammation-induced cancer.

Genome plasticity: insertion sequence elements, transposons and integrons, and DNA rearrangement.

Living organisms are defined by the genes they possess. Control of expression of this gene set, both temporally and in response to the environment, determines whether an organism can survive changing conditions and can compete for the resources it needs to reproduce. Bacteria are no exception; changes to the genome will, in general, threaten the ability of the microbe to survive, but acquisition of new genes may enhance its chances of survival by allowing growth in a previously hostile environment. For example, acquisition of an antibiotic resistance gene by a bacterial pathogen can permit it to thrive in the presence of an antibiotic that would otherwise kill it; this may compromise clinical treatments. Many forces, chemical and genetic, can alter the genetic content of DNA by locally changing its nucleotide sequence. Notable for genetic change in bacteria are transposable elements and site-specific recombination systems such as integrons. Many of the former can mobilize genes from one replicon to another, including chromosome-plasmid translocation, thus establishing conditions for interspecies gene transfer. Balancing this, transposition activity can result in loss or rearrangement of DNA sequences. This chapter discusses bacterial DNA transfer systems, transposable elements and integrons, and the contributions each makes towards the evolution of bacterial genomes, particularly in relation to bacterial pathogenesis. It highlights the variety of phylogenetically distinct transposable elements, the variety of transposition mechanisms, and some of the implications of rearranging DNA, and addresses the effects of genetic change on the fitness of the microbe.

Relationship between nucleotide sequence and 3D protein structure of six genes in Escherichia coli, by analysis of DNA sequence using a Markov model

We speculate that structures of genes might have been produced not only by the origination of the gene by itself, but also by the combination of several parts of structures from other species, through events, such as gene transfer, fusion of DNA sequences, and rearrangement of DNA sequences, to create new functions in evolution. To study the relationship between the 3D structure and DNA sequence of proteins comprised of multi-domains, six genes in Escherichia coli, including those coding for Flavodoxin (ferredoxin) reductase, Flavin oxidoreductase, Integrase/recombinase xerD, Endonuclease III, Heat shock protein (grpE), and Elongation Factor Tu (tufB), were chosen, since the 3D structures of these proteins had been determined by X-ray crystallography. The DNA sequences were analyzed by probability as calculated by using a species-specific inhomogeneous Markov model and divided into regions. The probability was calculated by the GeneMark program from the third-order matrix of Class III genes (Escherichia coli horizontally transferred genes) produced with the Markov model by Borodovsky M. et al.. The probability indicates the degree of similarity to the DNA sequence of the genes that were used for producing the matrix with the Markov model. Moreover, the probability indicates whether the origin of the divided DNA sequence would be different from that of the Class III genes. The divided regions, except for those of Flavin oxidoreductase, corresponded to the structural domains classified by CATH. Namely, the divided regions, suggested to be of different origins by analysis with the Markov model, showed correspondence to the domains and the gross content of the 3D structure. We can ascertain which DNA sequences would have been incorporated into the structure of a gene as parts of the structure in evolution. We propose a hypothesis that in evolution, the structure of genes might have been arisen by the incorporation of DNA sequences from other species. Key Words: DNA sequence analysis, Markov model, evolution, structural evolution Area of Interest: Bioinformatics and Bio Computing