Mosaic Structure of Plasmids From Natural Populations of Escherichia coli

Abstract The distribution of plasmids related to the fertility factor F was examined in the ECOR reference collection of Escherichia coli. Probes specific for four F-related genes were isolated and used to survey the collection by DNA hybridization. To estimate the genetic diversity of genes in F-like plasmids, DNA sequences were obtained for four plasmid genes. The phylogenetic relationships among the plasmids in the ECOR strains is very different from that of the strains themselves. This finding supports the view that plasmid transfer has been frequent within and between the major groups of ECOR. Furthermore, the sequences indicate that recombination between genes in plasmids takes place at a considerably higher frequency than that observed for chromosomal genes. The plasmid genes, and by inference the plasmids themselves, are mosaic in structure with different regions acquired from different sources. Comparison of gene sequences from a variety of naturally occurring plasmids suggested a plausible donor of some of the recombinant regions as well as implicating a chi site in the mechanism of genetic exchange. The relatively high rate of recombination in F-plasmid genes suggests that conjugational gene transfer may play a greater role in bacterial population structure than previously appreciated.

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JOINT DISTRIBUTION OF INSERTION ELEMENTS IS4 AND IS5 IN NATURAL ISOLATES OF ESCHERICHIA COLI

Genetics ◽

10.1093/genetics/111.2.219 ◽

1985 ◽

Vol 111 (2) ◽

pp. 219-231

Author(s):

Daniel E Dykhuizen ◽

Stanley A Sawyer ◽

Louis Green ◽

Raymond D Miller ◽

Daniel L Hartl

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Significant Negative Correlation ◽

Single Copy ◽

Common Mechanism ◽

Reference Collection ◽

Insertion Elements ◽

Natural Isolates ◽

Dna Insertion ◽

Flanking Sequences

ABSTRACT A reference collection of natural isolates of Escherichia coli has been studied in order to determine the distribution, abundance and joint occurence of DNA insertion elements IS4 and IS5. Among these isolates, 36% were found to contain IS4 and 30% were found to contain IS5. Among strains containing IS4 the mean number of copies per strain was 4.4 ± 0.8; the comparable figure for IS5 was 3.7 ± 1.0. Although the presence of the elements among the isolates was independent, among those isolates containing both IS4 and IS5, there was a significant negative correlation in the number of copies of the elements.— The reference collection was also studied for the presence of the DNA sequences flanking the single copy of IS4 in the chromosome of E. coli K12. Homologous sequences were found in only 26% of the isolates. The sequences flanking the IS4 invariably occur together, and their presence is significantly correlated with the presence of IS4. In eight of the strains that carry these flanking sequences, an IS4 is located between them, and the sequences are present at the homologous position as in the K12 strain. We suggest that IS4 and its flanking sequences share a common mechanism of dissemination, such as plasmids, and we present evidence that they are included in a much larger transposable element.

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The evolution of DNA sequences in Escherichia coli

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1986.0001 ◽

1986 ◽

Vol 312 (1154) ◽

pp. 191-204 ◽

Cited By ~ 18

Keyword(s):

Escherichia Coli ◽

Transposable Elements ◽

Dna Sequences ◽

Insertion Sequence ◽

Horizontal Transmission ◽

Insertion Sequences ◽

Insertion Element ◽

Reference Collection ◽

Natural Isolates ◽

Chromosomal Copy

It is proposed that certain families of transposable elements originally evolved in plasmids and functioned in forming replicon fusions to aid in the horizontal transmission of non-conjugational plasmids. This hypothesis is supported by the finding that the transposable elements Tn 3 and γδ are found almost exclusively in plasmids, and also by the distribution of the unrelated insertion sequences IS4 and IS 5 among a reference collection of 67 natural isolates of Escherichia coli. Each insertion sequence was found to be present in only about one-third of the strains. Among the ten strains found to contain both insertion sequences, the number of copies of the elements was negatively correlated. With respect to IS 5 , approximately half of the strains containing a chromosomal copy of the insertion element also contained copies within the plasmid complement of the strain.

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Deletion between directly repeated DNA sequences measured in extracts of bacteriophage T7-infected Escherichia coli.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)53016-7 ◽

1993 ◽

Vol 268 (11) ◽

pp. 7721-7727

Author(s):

D. Kong ◽

W. Masker

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Bacteriophage T7 ◽

Repeated Dna ◽

Repeated Dna Sequences

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Reproduction in Trypanosomatids: Past and Present

Biology ◽

10.3390/biology10060471 ◽

2021 ◽

Vol 10 (6) ◽

pp. 471

Author(s):

Camino Gutiérrez-Corbo ◽

Bárbara Domínguez-Asenjo ◽

María Martínez-Valladares ◽

Yolanda Pérez-Pertejo ◽

Carlos García-Estrada ◽

...

Keyword(s):

Low Income ◽

Phenotypic Diversity ◽

Natural Populations ◽

Genetic Exchange ◽

Health Concern ◽

Current Debate ◽

Naturally Occurring ◽

Experimental Works ◽

Genomic Recombination ◽

The Impact

Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.

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On the Rate and Linearity of Viability Declines in Drosophila Mutation-Accumulation Experiments: Genomic Mutation Rates and Synergistic Epistasis Revisited

Genetics ◽

10.1093/genetics/166.2.797 ◽

2004 ◽

Vol 166 (2) ◽

pp. 797-806 ◽

Cited By ~ 4

Author(s):

James D Fry

Keyword(s):

Mutation Rate ◽

Average Rate ◽

Natural Populations ◽

Mutation Accumulation ◽

High Rate ◽

Deleterious Mutations ◽

Order Of Magnitude ◽

Contamination Event ◽

Genomic Mutation ◽

The 1960S

Abstract High rates of deleterious mutations could severely reduce the fitness of populations, even endangering their persistence; these effects would be mitigated if mutations synergize each others’ effects. An experiment by Mukai in the 1960s gave evidence that in Drosophila melanogaster, viability-depressing mutations occur at the surprisingly high rate of around one per zygote and that the mutations interact synergistically. A later experiment by Ohnishi seemed to support the high mutation rate, but gave no evidence for synergistic epistasis. Both of these studies, however, were flawed by the lack of suitable controls for assessing viability declines of the mutation-accumulation (MA) lines. By comparing homozygous viability of the MA lines to simultaneously estimated heterozygous viability and using estimates of the dominance of mutations in the experiments, I estimate the viability declines relative to an appropriate control. This approach yields two unexpected conclusions. First, in Ohnishi’s experiment as well as in Mukai’s, MA lines showed faster-than-linear declines in viability, indicative of synergistic epistasis. Second, while Mukai’s estimate of the genomic mutation rate is supported, that from Ohnishi’s experiment is an order of magnitude lower. The different results of the experiments most likely resulted from differences in the starting genotypes; even within Mukai’s experiment, a subset of MA lines, which I argue probably resulted from a contamination event, showed much slower viability declines than did the majority of lines. Because different genotypes may show very different mutational behavior, only studies using many founding genotypes can determine the average rate and distribution of effects of mutations relevant to natural populations.

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INDUCTION OF INTRACHROMOSOMAL RECOMBINATION IN YEAST BY INHIBITION OF THYMIDYLATE BIOSYNTHESIS

Genetics ◽

10.1093/genetics/114.2.375 ◽

1986 ◽

Vol 114 (2) ◽

pp. 375-392

Author(s):

B A Kunz ◽

G R Taylor ◽

R H Haynes

Keyword(s):

Gene Conversion ◽

Dna Sequences ◽

Dna Hybridization ◽

Crossing Over ◽

Repeated Dna ◽

Yeast Saccharomyces Cerevisiae ◽

Haploid Strain ◽

Reciprocal Exchange ◽

Coli Plasmid ◽

Antifolate Drugs

ABSTRACT The biosynthesis of thymidylate in the yeast Saccharomyces cerevisiae can be inhibited by antifolate drugs. We have found that antifolate treatment enhances the formation of leucine prototrophs in a haploid strain of yeast carrying, on the same chromosome, two different mutant leu2 alleles separated by Escherichia coli plasmid sequences. That this effect is a consequence of thymine nucleotide depletion was verified by the finding that provision of exogenous thymidylate eliminates the increased production of Leu+ colonies. DNA hybridization analysis revealed that recombination, including reciprocal exchange, gene conversion and unequal sister-chromatid crossing over, between the duplicated genes gave rise to the induced Leu+ segregants. Although gene conversion unaccompanied by crossing over was responsible for the major fraction of leucine prototrophs, events involving reciprocal exchange exhibited the largest increase in frequency. These data show that recombination is induced between directly repeated DNA sequences under conditions of thymine nucleotide depletion. In addition, the results of this and previous studies are consistent with the possibility that inhibition of thymidylate biosynthesis in yeast may create a metabolic condition that provokes all forms of mitotic recombination.

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