scholarly journals Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence.

Genetics ◽  
1991 ◽  
Vol 129 (4) ◽  
pp. 1021-1032 ◽  
Author(s):  
M J Mahan ◽  
J R Roth
Keyword(s):  
Homologous Recombination ◽  
Parent Strain ◽  
Genetic Material ◽  
Chromosomal Inversion ◽  
Chromosome Segment ◽  
Bacterial Chromosome ◽  
Flanking Sequence ◽  
Flanking Sequences ◽  
Almost All

Abstract Homologous recombination between sequences present in inverse order within the same chromosome can result in inversion formation. We have previously shown that inverse order sequences at some sites (permissive) recombine to generate the expected inversion; no inversions are found when the same inverse order sequences flank other (nonpermissive) regions of the chromosome. In hopes of defining how permissive and nonpermissive intervals are determined, we have constructed a strain that carries a large chromosomal inversion. Using this inversion mutant as the parent strain, we have determined the "permissivity" of a series of chromosomal sites for secondary inversions. For the set of intervals tested, permissivity seems to be dictated by the nature of the genetic material present within the chromosomal interval being tested rather than the flanking sequences or orientation of this material in the chromosome. Almost all permissive intervals include the origin or terminus of replication. We suggest that the rules for recovery of inversions reflect mechanistic restrictions on the occurrence of inversions rather than lethal consequences of the completed rearrangement.

Differentiation between wheat chromosomes 4B and 4D

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1139-1147 ◽  
Author(s):  
Jan Dvořák ◽  
Jorge Dubcovsky ◽  
Ming-Cheng Luo ◽  
Katrien M. Devos ◽  
Michael D. Gale
Keyword(s):  
Homologous Recombination ◽  
Linkage Map ◽  
Segregation Distortion ◽  
Chromosome Pairing ◽  
Genetic Material ◽  
Triticum Aestivum L ◽  
Pseudoautosomal Region ◽  
Homoeologous Recombination ◽  
Consensus Map ◽  
Almost All

A linkage map based on homoeologous recombination, induced by the absence of the Ph1 locus, between chromosome 4D of Triticum aestivum L. (genomes AABBDD) and chromosome 4B of T. turgidum L. (genomes AABB) was compared with a linkage map of chromosome 4Am of T. monococcum L. and a consensus map of chromosomes 4B and 4D of T. aestivum based on homologous recombination. The 4D/4B homoeologous map was only one-third the length of the homologous maps and all intervals were reduced relative to the 4B–4D consensus map. After the homoeologous map was corrected for this overall reduction in recombination, the distribution of recombination in the short arm was similar in both types of maps. In the long arm, homoeologous recombination declined disproportionally in the distal to proximal direction. This gradient was shown to be largely caused by severe segregation distortion reflecting selection against 4D genetic material. The segregation distortion had a maximum that coincided with the centromere and likely had a polygenic cause. Chromosomes 4D and 4B were colinear and recombination between them occurred in almost all intervals where homologous recombination occurred. These findings suggest that these chromosomes are not differentiated structurally and that the differentiation is not segmental. In the presence of Ph1, metaphase I chromosome pairing between chromosomes composed of homologous and differentiated regions correlated with the lengths of the homologous regions. No compensatory allocation of crossovers into the homologous regions was detected. In this respect, the present results are in dramatic contrast with the crossover allocation into the pseudoautosomal region in the mammalian male meiosis.Key words: homoeology, recombination, segregation distortion, chromosome pairing, RFLP, pseudoautosomal region.

Transcriptional insulation of the human keratin 18 gene in transgenic mice

1993 ◽  
Vol 13 (4) ◽  
pp. 2214-2223
Author(s):  
N Neznanov ◽  
I S Thorey ◽  
G Ceceña ◽  
R G Oshima
Keyword(s):  
Transgenic Mice ◽  
Thymidine Kinase ◽  
Copy Number ◽  
Thymidine Kinase Gene ◽  
Flanking Sequence ◽  
Kinase Gene ◽  
Tissue Specific ◽  
Dependent Behavior ◽  
Flanking Sequences ◽  
Keratin 18

Expression of the 10-kb human keratin 18 (K18) gene in transgenic mice results in efficient and appropriate tissue-specific expression in a variety of internal epithelial organs, including liver, lung, intestine, kidney, and the ependymal epithelium of brain, but not in spleen, heart, or skeletal muscle. Expression at the RNA level is directly proportional to the number of integrated K18 transgenes. These results indicate that the K18 gene is able to insulate itself both from the commonly observed cis-acting effects of the sites of integration and from the potential complications of duplicated copies of the gene arranged in head-to-tail fashion. To begin to identify the K18 gene sequences responsible for this property of transcriptional insulation, additional transgenic mouse lines containing deletions of either the 5' or 3' distal end of the K18 gene have been characterized. Deletion of 1.5 kb of the distal 5' flanking sequence has no effect upon either the tissue specificity or the copy number-dependent behavior of the transgene. In contrast, deletion of the 3.5-kb 3' flanking sequence of the gene results in the loss of the copy number-dependent behavior of the gene in liver and intestine. However, expression in kidney, lung, and brain remains efficient and copy number dependent in these transgenic mice. Furthermore, herpes simplex virus thymidine kinase gene expression is copy number dependent in transgenic mice when the gene is located between the distal 5'- and 3'-flanking sequences of the K18 gene. Each adult transgenic male expressed the thymidine kinase gene in testes and brain and proportionally to the number of integrated transgenes. We conclude that the characteristic of copy number-dependent expression of the K18 gene is tissue specific because the sequence requirements for transcriptional insulation in adult liver and intestine are different from those for lung and kidney. In addition, the behavior of the transgenic thymidine kinase gene in testes and brain suggests that the property of transcriptional insulation of the K18 gene may be conferred by the distal flanking sequences of the K18 gene and, additionally, may function for other genes.

scholarly journals Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase

2020 ◽  
Vol 48 (20) ◽  
pp. 11495-11509
Author(s):  
Michael Dukatz ◽  
Sabrina Adam ◽  
Mahamaya Biswal ◽  
Jikui Song ◽  
Pavel Bashtrykov ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Catalytic Mechanism ◽  
Catalytic Domain ◽  
Dna Methyltransferases ◽  
Flanking Sequence ◽  
Cpg Sites ◽  
Binding Interface ◽  
Target Sites ◽  
Flanking Sequences

Abstract DNA methyltransferases interact with their CpG target sites in the context of variable flanking sequences. We investigated DNA methylation by the human DNMT3B catalytic domain using substrate pools containing CpX target sites in randomized flanking context and identified combined effects of CpG recognition and flanking sequence interaction together with complex contact networks involved in balancing the interaction with different flanking sites. DNA methylation rates were more affected by flanking sequences at non-CpG than at CpG sites. We show that T775 has an essential dynamic role in the catalytic mechanism of DNMT3B. Moreover, we identify six amino acid residues in the DNA-binding interface of DNMT3B (N652, N656, N658, K777, N779, and R823), which are involved in the equalization of methylation rates of CpG sites in favored and disfavored sequence contexts by forming compensatory interactions to the flanking residues including a CpG specific contact to an A at the +1 flanking site. Non-CpG flanking preferences of DNMT3B are highly correlated with non-CpG methylation patterns in human cells. Comparison of the flanking sequence preferences of human and mouse DNMT3B revealed subtle differences suggesting a co-evolution of flanking sequence preferences and cellular DNMT targets.

IS1071-mediated recombinational equilibrium in Alcaligenes sp. BR60 carrying the 3-chlorobenzoate catabolic transposon Tn5271

1993 ◽  
Vol 39 (1) ◽  
pp. 92-100 ◽  
Author(s):  
James Ng ◽  
R. Campbell Wyndham
Keyword(s):  
Homologous Recombination ◽  
Parent Strain ◽  
Insertion Sequence ◽  
Class Ii ◽  
Indigenous Plasmid ◽  
Resistant Mutants ◽  
Selection For ◽  
Transposition Mechanism

In experiments designed to Tn5 mutagenize the indigenous plasmid pBRC60 of Alcaligenes sp. BR60, kanamycin-resistant mutants were isolated that were cured of this plasmid and that exhibited recombination of the plasmid-located chlorobenzoate catabolic transposon Tn5271 into the chromosome. These events were independent of the location of Tn5 insertions into the genome of strain BR60. The chromosomal recombinants carried at least two novel copies of IS1071, the class II insertion sequence flanking Tn5271, compared with the parent strain. Recombination of Tn5271 into the chromosome of Alcaligenes sp. BR60 was also detected following mating in of pBRC60-incompatible (IncP1) plasmids, R68 and pGS65. Chromosomal copies of Tn5271 could be mobilized between Alcaligenes strains via plasmids pBRC40 or R68. Conjugation of the incompatible plasmid pGS65 into Alcaligenes strains in the absence of selection for 3-chlorobenzoate catabolism resulted in the recovery of 85% of transconjugants in which the entire pBRC60 plasmid had integrated into the chromosome. These transconjugants exhibited complex rearrangements in chromosomal IS1071 copies. A model of recombinational equilibrium involving homologous recombination between plasmid and chromosomal copies of IS1071 is presented. The results are discussed in terms of the IS1071 (class II) transposition mechanism and the observed products of IS 1071-mediated recombination in natural recipients of pBRC60 in aquatic environments.Key words: transposon, 3-chlorobenzoate catabolism, rearrangement.

Genetical society mendel lecture - Sex factors and viruses

1966 ◽  
Vol 164 (995) ◽  
pp. 230-245 ◽  
Keyword(s):  
Genetic Recombination ◽  
Genetic Material ◽  
Turn Of The Century ◽  
Bacterial Chromosome ◽  
Genetic Determinants ◽  
Physico Chemical ◽  
Biological Discovery ◽  
Tools And Techniques ◽  
Micro Organisms ◽  
First Time

At this Symposium we are remembering and honouring the great and revolutionary discoveries of Gregor Mendel, presented to the world 100 years ago this year, which for the first time expressed the basic phenomena of heredity in a concise, analytical and, above all, numerical form and thus laid the foundation of the science of genetics. However, as the title of this symposium implies, we are not met here merely in adulation of Mendel’s genius but rather to review and discuss the fruits which have now matured on the tree which he planted. I think some of these fruits would seem very strange and incomprehensible to Mendel, for over the last two decades we have witnessed another revolution in genetics as dramatic and as pregnant with new potentialities as that of 100 years ago. The basic ingredients of this revolution were, first, the disclosure of systems of genetic recombination in micro-organisms, and especially in bacteria and their viruses, which enormously increased the resolution of genetic analysis; and, secondly, the elucidation by Watson & Crick, in 1953, of the physico-chemical structure of the genetic material, deoxyribonucleic acid—undoubtedly the most important and provocative biological discovery since Mendel. As a result we are now recapitulating the cytogenetical studies and correlations which marked the turn of the century, but this time the precision and refinement of our tools and techniques have increased more than 1000-fold so that we are looking at genetic behaviour and interaction at the level of molecular structure. In this lecture I would like to discuss what, from the Mendelian viewpoint, must be one of the most bizarre forms of sexual heredity, namely, the process of conjugation and genetic recombination in the bacterium Escherichia coli . My reasons for choosing this rather esoteric topic, apart from personal interest, are three. First, the whole mechanism of sexuality in this organism is mediated and controlled by a new kind of genetic element called the sex factor which, like some temperate bacteriophages, is able to exist in alternative states in the cell, either free in the cytoplasm or as an integral part of the bacterial chromosome, and which can properly be construed as a virus with a novel mode of infectivity, as I hope to show. Secondly, a number of essentially similar elements have recently been discovered in bacteria, masquerading under such different disguises as the genetic determinants of antibiotic substances called colicins or as carriers of transmissible drug resistance, so that the sex factor is far from being a unique entity among the bacteria. Thirdly, genetic interactions occur between the sex factor and the bacterial chromosome which confer great flexibility on this system. Some of the situations which are generated by these interactions mimic those found in the cells of higher organisms so that it is possible to construct plausible, though very speculative, models for the evolution of more stable and highly organized genetic systems.

Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination

2003 ◽  
Vol 36 (4) ◽  
pp. 429-453 ◽  
Author(s):  
Chantal Prévost ◽  
Masayuki Takahashi
Keyword(s):  
Homologous Recombination ◽  
Structural Information ◽  
Double Helix ◽  
Genetic Material ◽  
Strand Exchange ◽  
Double Stranded Dna ◽  
Dna Deformation ◽  
Architectural Proteins ◽  
Dna Strands ◽  
Dna Strand

1. Introduction 4302. Transformations of the RecA filament 4312.1 The different forms of the RecA filament 4312.2 Orientation and position of the RecA monomers in the active filament 4332.3 Transmission of structural information along the filament 4333. RecA-induced DNA deformations 4353.1 Characteristics of RecA-bound DNA 4353.2 Stretching properties of double-stranded DNA 4363.3 DNA bound to architectural proteins 4373.4 Implications for RecA-induced DNA deformations 4383.5 Axial distribution of the DNA stretching deformation 4384. Contacts between RecA and the DNA strands 4404.1 The DNA-binding sites 4404.2 Possible arrangement of loops L1 and L2 and the three bound strands of DNA 4425. Strand arrangement during pairing reorganization 4445.1 Hypotheses for DNA strand association 4445.2 Association via major or minor grooves 4465.3 Post-strand exchange geometries 4466. Conclusion 4477. Acknowledgments 4488. References 448Homologous recombination consists of exchanging DNA strands of identical or almost identical sequence. This process is important for both DNA repair and DNA segregation. In prokaryotes, it involves the formation of long helical filaments of the RecA protein on DNA. These filaments incorporate double-stranded DNA from the cell's genetic material, recognize sequence homology and promote strand exchange between the two DNA segments. DNA processing by these nucleofilaments is characterized by large amplitude deformations of the double helix, which is stretched by 50% and unwound by 40% with respect to B-DNA. In this article, information concerning the structure and interactions of the RecA, DNA and ATP molecules involved in DNA strand exchange is gathered and analyzed to present a view of their possible arrangement within the filament, their behavior during strand exchange and during ATP hydrolysis, the mechanism of RecA-promoted DNA deformation and the role of DNA deformation in the process of homologous recombination. In particular, the unusual characteristics of DNA within the RecA filament are compared to the DNA deformations locally induced by architectural proteins which bind in the DNA minor groove. The possible role and location of two flexible loops of RecA are discussed.

scholarly journals A mechanism for gene conversion in fungi

1964 ◽  
Vol 5 (2) ◽  
pp. 282-304 ◽  
Author(s):  
Robin Holliday
Keyword(s):  
Fine Structure ◽  
Gene Conversion ◽  
Choice Model ◽  
Genetic Material ◽  
Intragenic Recombination ◽  
Heterozygous Site ◽  
Base Sequences ◽  
Repair Mechanisms ◽  
Dna 2 ◽  
Almost All

A mechanism for gene conversion is proposed which overcomes many of the difficulties that any copy choice model encounters. It is suggested that along with general genetic pairing of homologous genomes at meiosis, effective pairing over short regions of the genetic material occurs at the molecular level by the separation of the strands of the DNA double helices, followed by the annealing of strands from two homologous chromatids. If the annealed region happens to span a heterozygous site, mispairing of bases will occur. Such a situation may be analogous to that in DNA which is damaged by mutagens; the same or similar repair mechanisms may operate, and these, by adjusting the base sequences in order to restore normal base pairing, would bring about gene conversion in the absence of any genetic replication. The model indicates how precise breakage and rejoining of chromatids could occur in the vicinity of the conversion, so that conversion would frequently be accompanied by the recombination of outside markers. The model also proposes that the distance between two mutant sites on a fine structure map depends not so much on the frequency of a recombinational event occurring between them, but rather on the degree of inhibition of the processes of genetic pairing by the mutants themselves.The model will explain almost all the data in a formal way, and it has the advantage over copy choice mechanisms for gene conversion in (1) being compatible with semi-conservative replication of DNA, (2) not invoking DNA synthesis during or after genetic pairing, (3) providing a molecular mechanism for close specific pairing, (4) making it unnecessary to postulate sister strand exchange or a process akin to this, (5) suggesting why rates of gene conversion in opposite directions are sometimes unequal and (6) providing an explanation of the clustering of mutant sites, a basis for map expansion and for the apparently capricious departure of fine structure maps from additivity. Although the model proposed is a general rather than a specific one, it suggests that the process of conversion and intragenic recombination is more complex than is usually believed, since it depends on several interacting factors. Nevertheless, it is hoped that the introduction of a model with this complexity will help to stimulate specific experiments, and that these will provide definitive information which would never be obtained if simpler models of conversion and intragenic recombination were believed to explain the genetic data sufficiently well.

scholarly journals Detection of Coxiella burnetii in ticks collected from cattle in several provinces of the Republic of Guinea

2019 ◽  
Vol 24 (5-6) ◽  
pp. 234-239
Author(s):  
Yulia A. Panferova ◽  
Olga A. Freylikhman ◽  
Nikolay K. Tokarevich ◽  
Ekaterina V. Naydenova ◽  
Kirill S. Zakharov ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
Geographical Origin ◽  
Q Fever ◽  
Local Population ◽  
Genetic Material ◽  
Clinical Signs ◽  
Republic Of Guinea ◽  
Plasmid Analysis ◽  
The Republic ◽  
Almost All

Background. Q fever, or coxiellosis, is a natural focal disease characterized by polymorphism of clinical signs and can affect not only humans but also many species of animals. This infection is spread almost all over the world. On the African continent, the foci of coxiellosis infection endanger the local population and people arriving for temporary stay. Given that sick agricultural animals and their ectoparasites are markers of the presence of infection in the region, a study of the latter may be relevant to identify the potential foci of Q fever. This work aimed to identify Coxiella burnetii DNA from ixodic ticks collected from cattle in several provinces of Republic of Guinea and to type isolates using genetic markers (plasmid type) to enable their comparison with strains of different geographical origin. Methods. Using amplification technologies, we investigated the ticks obtained from cattle in the provinces of Boke and Kindia to detect Coxiella DNA. Results. The genetic material of the Q fever causative agent was detected in no more than 5% of the total number of samples studied. For positive samples, typing was performed using plasmid analysis. The isolates with the plasmid type QpH1 circulate in the Republic of Guinea. Conclusion. The findings were analyzed along with data from other researchers on the spread of Q fever in subequatorial Africa. The differences in the levels of prevalence of Coxiella in ticks in the territories of not only different countries but also within the same state can be determined by the prevalence among the hosts within herds. The risk of contamination with Q fever in endemic regions should be considered.

scholarly journals IS6110-Mediated Deletions of Wild-Type Chromosomes of Mycobacterium tuberculosis

1999 ◽  
Vol 181 (3) ◽  
pp. 1014-1020 ◽  
Author(s):  
Z. Fang ◽  
C. Doig ◽  
D. T. Kenna ◽  
N. Smittipat ◽  
P. Palittapongarnpim ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Homologous Recombination ◽  
Insertion Sequence ◽  
Chromosomal Rearrangements ◽  
Genetic Material ◽  
Clinical Isolates ◽  
Induced Mutations ◽  
Base Pairs ◽  
A Site ◽  
Obvious Feature

ABSTRACT The ipl locus is a site for the preferential insertion of IS6110 and has been identified as an insertion sequence, IS1547, in its own right. Various deletions around theipl locus of clinical isolates of Mycobacterium tuberculosis were identified, and these deletions ranged in length from several hundred base pairs up to several kilobase pairs. The most obvious feature shared by these deletions was the presence of an IS6110 copy at the deletion sites, which suggested two possible mechanisms for their occurrence, IS6110transposition and homologous recombination. To clarify the mechanism, an investigation was conducted; the results suggest that although deletion transpositionally mediated by IS6110 was a possibility, homologous recombination was a more likely one. The implications of such chromosomal rearrangements for the evolution ofM. tuberculosis, for IS6110-mediated mutagenesis, and for the development of genetic tools are discussed. The deletion of genomic DNA in isolates of M. tuberculosishas previously been noted at only a few sites. This study examined the deletional loss of genetic material at a new site and suggests that such losses may occur elsewhere too and may be more prevalent than was previously thought. Distinct from the study of laboratory-induced mutations, the detailed analysis of clinical isolates, in combination with knowledge of their evolutionary relationships to each other, gives us the opportunity to study mutational diversity in isolates that have survived in the human host and therefore offers a different perspective on the importance of particular genetic markers in pathogenesis.

scholarly journals Vaccinia virus gene acquisition through non-homologous recombination

2021 ◽  
Author(s):  
Greg Vallee ◽  
Peter Norris ◽  
Patrick Paszkowski ◽  
Ryan Noyce ◽  
David H. Evans
Keyword(s):  
Homologous Recombination ◽  
Vaccinia Virus ◽  
Large Scale ◽  
Virus Evolution ◽  
Flanking Sequence ◽  
Selective Growth Advantage ◽  
Gene Acquisition ◽  
Cellular Genes ◽  
Large Populations ◽  
Infected Cells

Many of the genes encoded by poxviruses are orthologs of cellular genes. These virus genes serve different purposes, but perhaps of most interest is the way some have been repurposed to inhibit the antiviral pathways that their cellular homologs still regulate. What is unclear is how these virus genes were acquired although it is presumed to have been catalyzed by some form(s) of non-homologous recombination (NHR). We used transfection assays and substrates encoding a fluorescent and drug selectable marker to examine the NHR frequency in vaccinia virus (VAC) infected cells. These studies showed that when cells were transfected with linear duplex DNAs bearing VAC N2L gene homology it yielded a recombinant frequency (RF) of 6.7×10−4. In contrast, DNA lacking any VAC homology reduced the yield of recombinants ∼400-fold (RF = 1.6×10−6). DNA·RNA hybrids were also substrates, although homologous molecules yielded fewer recombinants (RF = 2.1×10−5) and non-homologous substrates yielded only rare recombinants (RF ≤ 3×10−8). NHR was associated with genome rearrangements ranging from simple insertions with flanking sequence duplications to large-scale indels that produced helper-dependent viruses. The insert was often also partially duplicated and would rapidly rearrange through homologous recombination. Most of the virus-insert junctions exhibited little or no pre-exiting microhomology, although a few encoded VAC topoisomerase recognition sites (C/T·CCTT). These studies show that VAC can catalyze NHR through a process that may reflect a form of aberrant replication fork repair. Although it is less efficient than classical homologous recombination, the rates of NHR may still be high enough to drive virus evolution. IMPORTANCE Large DNA viruses sometimes interfere in antiviral defenses using repurposed and mutant forms of the cellular proteins that mediate these same reactions. Such virus orthologs of cellular genes were presumably captured through non-homologous recombination, perhaps in the distant past, but nothing is known about the processes that might promote “gene capture” or even how often these events occur over the course of an infectious cycle. This study shows that non-homologous recombination in vaccinia virus infected cells is frequent enough to seed a small but still significant portion of novel recombinants into large populations of newly replicated virus particles. This offers a route by which a pool of virus might survey the host genome for sequences that offer a selective growth advantage and potentially drive discontinuous virus evolution (saltation) through the acquisition of adventitious traits.

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