scholarly journals A Replicase Clamp-Binding Dynamin-like Protein Promotes Colocalization of Nascent DNA Strands and Equipartitioning of Chromosomes in E. coli

Cell Reports ◽  
2013 ◽  
Vol 4 (5) ◽  
pp. 985-995 ◽  
Author(s):  
Shogo Ozaki ◽  
Yusaku Matsuda ◽  
Kenji Keyamura ◽  
Hironori Kawakami ◽  
Yasunori Noguchi ◽  
...  
Keyword(s):  
E Coli ◽  
Dna Strands

scholarly journals Regularities in the E. coli promoters composition in connection with the DNA strands interaction and promoter activity

2006 ◽  
Vol 7 (12) ◽  
pp. 969-973
Author(s):  
Andrey Yu Berezhnoy ◽  
Yuriy G. Shckorbatov ◽  
Kiryu Hisanori
Keyword(s):  
Promoter Activity ◽  
E Coli ◽  
Dna Strands

MECHANISM OF IS1 TRANSPOSITION IN E. COLI: CHOICE BETWEEN SIMPLE INSERTION AND COINTEGRATION

Genetics ◽  
1984 ◽  
Vol 108 (2) ◽  
pp. 319-330
Author(s):  
Susan W Biel ◽  
Douglas E Berg
Keyword(s):  
Rolling Circle ◽  
E Coli ◽  
Opposite Result ◽  
F Factor ◽  
Dna Strands ◽  
Resistance Markers ◽  
Vector Sequences ◽  
Circle Model ◽  
Is1 Transposition ◽  
The Way

ABSTRACT nsertion element IS 1 and IS 1-based transposon Tn 9 generate cointegrates (containing vector and target DNAs joined by duplicate copies of IS 1 or Tn 9) and simple insertions (containing IS 1 or Tn 9 detached from vector sequences). Based on studies of transposon Tn 5 we had proposed a conservative (non-replicative) model for simple insertion. Others had proposed that all transposition is replicative, occurring in a rolling circle structure, and that the way DNA strands are joined when replication terminates determines whether a simple insertion or a cointegrate is formed.—We selected for the transposition of amp and cam resistance markers from pBR322::Tn 9 plasmids to an F factor in recA  -  E. coli and identified products containing three and four copies of IS 1, corresponding to true cointegrates (from monomeric plasmids), and simple insertions (from dimeric plasmids). The simple insertions with four copies of IS 1 outnumbered those with three by a ratio of about 3:1, whereas true cointegrates containing three copies of IS 1 were more numerous than those with four.—A straightforward rolling circle model had predicted that the simple insertions containing three copies of IS 1 should be more frequent than those with four. Because we obtained the opposite result we propose that simple insertions only arise when the element fails to replicate or if replication starts but then terminates prematurely. The two classes of products, simple insertions and cointegrates, reflect alternative conservative and replicative fates, respectively, of an early intermediate in transposition.

scholarly journals Endogenous Gene Regulation as a Predicted Main Function of Type I-E CRISPR/Cas System in E. coli

Molecules ◽  
2019 ◽  
Vol 24 (4) ◽  
pp. 784 ◽  
Author(s):  
Bojan Bozic ◽  
Jelena Repac ◽  
Marko Djordjevic
Keyword(s):  
Viral Infections ◽  
Active Regions ◽  
Regulatory Elements ◽  
Functional Enrichment ◽  
Type I ◽  
Main Function ◽  
Endogenous Gene ◽  
E Coli ◽  
Dna Strands ◽  
Turn Over

CRISPR/Cas is an adaptive bacterial immune system, whose CRISPR array can actively change in response to viral infections. However, Type I-E CRISPR/Cas in E. coli (an established model system), appears not to exhibit such active adaptation, which suggests that it might have functions other than immune response. Through computational analysis, we address the involvement of the system in non-canonical functions. To assess targets of CRISPR spacers, we align them against both E. coli genome and an exhaustive (~230) set of E. coli viruses. We systematically investigate the obtained alignments, such as hit distribution with respect to genome annotation, propensity to target mRNA, the target functional enrichment, conservation of CRISPR spacers and putative targets in related bacterial genomes. We find that CRISPR spacers have a statistically highly significant tendency to target i) host compared to phage genomes, ii) one of the two DNA strands, iii) genomic dsDNA rather than mRNA, iv) transcriptionally active regions, and v) sequences (cis-regulatory elements) with slower turn-over rate compared to CRISPR spacers (trans-factors). The results suggest that the Type I-E CRISPR/Cas system has a major role in transcription regulation of endogenous genes, with a potential to rapidly rewire these regulatory interactions, with targets being selected through naïve adaptation.

scholarly journals Epigenetics Theoretical Limits of Synthetic Genomes: The Cases of Artificials Caulobacter (C. eth-2.0), Mycoplasma Mycoides (JCVI-Syn 1.0, JCVI-Syn 3.0 and JCVI_3A), E-coli and YEAST chr XII

2019 ◽  
Author(s):  
Jean-claude Perez
Keyword(s):  
Caulobacter Crescentus ◽  
Fibonacci Numbers ◽  
Three Dimensional ◽  
Craig Venter ◽  
Discussion Section ◽  
Craig Venter Institute ◽  
E Coli ◽  
Synthetic Genome ◽  
Mycoplasma Mycoides ◽  
Dna Strands

In (Venetz et al., 2019), authors rebuilt the essential genome of Caulobacter crescentus through the process of chemical synthesis rewriting and studied the genetic information content at the level of its essential genes. Then, they reduced the native Caulobacter crescentus native Caulobacter NA1000 genome sequence real genome ( 4042929 bp ) to the 785,701-bp reduced synthetic genome. Here we demonstrate the existence of a palindromic-like mirror structure that exists in real genomes and disappears totally in the synthetic genome. This biomathematic meta-organization is based on characteristic proportions of Fibonacci numbers between DNA single strand nucleotides proportions TC / AG on the one hand and TG / AC on the other hand. In both cases, we suggest that this meta-structure enhances the three-dimensional cohesion of the two DNA strands of the genome. We then generalize this study to the different synthetic genomes and synthetic cells published by the Craig Venter Institute on Mycoplasma Mycoides JCVI-syn1.0 (in 2010), JCVI-syn3.0 (in 2016) and JCVI-syn3A (in 2019). Finally, in the discussion section, we extend this study to synthetic genomes of E-Coli and Yeast chromosome XII.

scholarly journals A sister-strand exchange mechanism for recA-independent deletion of repeated DNA sequences in Escherichia coli.

Genetics ◽  
1993 ◽  
Vol 135 (3) ◽  
pp. 631-642 ◽  
Author(s):  
S T Lovett ◽  
P T Drapkin ◽  
V A Sutera ◽  
T J Gluckman-Peskind
Keyword(s):  
Escherichia Coli ◽  
Dna Sequences ◽  
Repeated Sequences ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
E Coli ◽  
Deletion Formation ◽  
Dna Strands

Abstract In the genomes of many organisms, deletions arise between tandemly repeated DNA sequences of lengths ranging from several kilobases to only a few nucleotides. Using a plasmid-based assay for deletion of a 787-bp tandem repeat, we have found that a recA-independent mechanism contributes substantially to the deletion process of even this large region of homology. No Escherichia coli recombination gene tested, including recA, had greater than a fivefold effect on deletion rates. The recA-independence of deletion formation is also observed with constructions present on the chromosome. RecA promotes synapsis and transfer of homologous DNA strands in vitro and is indispensable for intermolecular recombination events in vivo measured after conjugation. Because deletion formation in E. coli shows little or no dependence on recA, it has been assumed that homologous recombination contributes little to the deletion process. However, we have found recA-independent deletion products suggestive of reciprocal crossovers when branch migration in the cell is inhibited by a ruvA mutation. We propose a model for recA-independent crossovers between replicating sister strands, which can also explain deletion or amplification of repeated sequences. We suggest that this process may be initiated as post-replicational DNA repair; subsequent strand misalignment at repeated sequences leads to genetic rearrangements.

Joining of DNA Strands by DNA Ligase of E. coli

1968 ◽  
Vol 33 (0) ◽  
pp. 21-26 ◽  
Author(s):  
M. Gellert ◽  
J. W. Little ◽  
C. K. Oshinsky ◽  
S. B. Zimmerman
Keyword(s):  
Dna Ligase ◽  
E Coli ◽  
Dna Strands

scholarly journals In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Beatriz Álvarez ◽  
Mario Mencía ◽  
Víctor de Lorenzo ◽  
Luis Ángel Fernández
Keyword(s):  
Antibiotic Resistance ◽  
Molecular Evolution ◽  
Protein Evolution ◽  
Antibiotic Resistance Gene ◽  
T7 Rna Polymerase ◽  
Target Sequence ◽  
Transcriptional Elongation ◽  
E Coli ◽  
Dna Strands

AbstractIn vivo mutagenesis systems accelerate directed protein evolution but often show restricted capabilities and deleterious off-site mutations on cells. To overcome these limitations, here we report an in vivo platform to diversify specific DNA segments based on protein fusions between various base deaminases (BD) and the T7 RNA polymerase (T7RNAP) that recognizes a cognate promoter oriented towards the target sequence. Transcriptional elongation of these fusions generates transitions C to T or A to G on both DNA strands and in long DNA segments. To delimit the boundaries of the diversified DNA, the catalytically dead Cas9 (dCas9) is tethered with custom-designed crRNAs as a “roadblock” for BD-T7RNAP elongation. Using this T7-targeted dCas9-limited in vivo mutagenesis (T7-DIVA) system, rapid molecular evolution of the antibiotic resistance gene TEM-1 is achieved. While the efficiency is demonstrated in E. coli, the system can be adapted to a variety of bacterial and eukaryotic hosts.

scholarly journals Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6029 ◽  
Author(s):  
Caroline Zutterling ◽  
Aibek Mursalimov ◽  
Ibtissam Talhaoui ◽  
Zhanat Koshenov ◽  
Zhiger Akishev ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Damage ◽  
Dna Repair ◽  
Uv Irradiation ◽  
Genome Stability ◽  
Dna Duplexes ◽  
E Coli ◽  
Dna Strands ◽  
Induced Mutagenesis

Background DNA repair is essential to counteract damage to DNA induced by endo- and exogenous factors, to maintain genome stability. However, challenges to the faithful discrimination between damaged and non-damaged DNA strands do exist, such as mismatched pairs between two regular bases resulting from spontaneous deamination of 5-methylcytosine or DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved the mismatch-specific DNA glycosylases that can recognize and remove regular DNA bases in the mismatched DNA duplexes. The Escherichia coli adenine-DNA glycosylase (MutY/MicA) protects cells against oxidative stress-induced mutagenesis by removing adenine which is mispaired with 7,8-dihydro-8-oxoguanine (8oxoG) in the base excision repair pathway. However, MutY does not discriminate between template and newly synthesized DNA strands. Therefore the ability to remove A from 8oxoG•A mispair, which is generated via misincorporation of an 8-oxo-2′-deoxyguanosine-5′-triphosphate precursor during DNA replication and in which A is the template base, can induce A•T→C•G transversions. Furthermore, it has been demonstrated that human MUTYH, homologous to the bacterial MutY, might be involved in the aberrant processing of ultraviolet (UV) induced DNA damage. Methods Here, we investigated the role of MutY in UV-induced mutagenesis in E. coli. MutY was probed on DNA duplexes containing cyclobutane pyrimidine dimers (CPD) and pyrimidine (6–4) pyrimidone photoproduct (6–4PP). UV irradiation of E. coli induces Save Our Souls (SOS) response characterized by increased production of DNA repair enzymes and mutagenesis. To study the role of MutY in vivo, the mutation frequencies to rifampicin-resistant (RifR) after UV irradiation of wild type and mutant E. coli strains were measured. Results We demonstrated that MutY does not excise Adenine when it is paired with CPD and 6–4PP adducts in duplex DNA. At the same time, MutY excises Adenine in A•G and A•8oxoG mispairs. Interestingly, E. coli mutY strains, which have elevated spontaneous mutation rate, exhibited low mutational induction after UV exposure as compared to MutY-proficient strains. However, sequence analysis of RifR mutants revealed that the frequencies of C→T transitions dramatically increased after UV irradiation in both MutY-proficient and -deficient E. coli strains. Discussion These findings indicate that the bacterial MutY is not involved in the aberrant DNA repair of UV-induced DNA damage.

scholarly journals Physical and Functional Interactions between Escherichia coli MutY Glycosylase and Mismatch Repair Protein MutS

2006 ◽  
Vol 189 (3) ◽  
pp. 902-910 ◽  
Author(s):  
Haibo Bai ◽  
A-Lien Lu
Keyword(s):  
Escherichia Coli ◽  
Mismatch Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Mutagenic Effect ◽  
Binding Activity ◽  
E Coli ◽  
Repair Protein ◽  
Dna Strands ◽  
Base Excision

ABSTRACT Escherichia coli MutY and MutS increase replication fidelity by removing adenines that were misincorporated opposite 7,8-dihydro-8-oxo-deoxyguanines (8-oxoG), G, or C. MutY DNA glycosylase removes adenines from these mismatches through a short-patch base excision repair pathway and thus prevents G:C-to-T:A and A:T-to-G:C mutations. MutS binds to the mismatches and initiates the long-patch mismatch repair on daughter DNA strands. We have previously reported that the human MutY homolog (hMYH) physically and functionally interacts with the human MutS homolog, hMutSα (Y. Gu et al., J. Biol. Chem. 277:11135-11142, 2002). Here, we show that a similar relationship between MutY and MutS exists in E. coli. The interaction of MutY and MutS involves the Fe-S domain of MutY and the ATPase domain of MutS. MutS, in eightfold molar excess over MutY, can enhance the binding activity of MutY with an A/8-oxoG mismatch by eightfold. The MutY expression level and activity in mutS mutant strains are sixfold and twofold greater, respectively, than those for the wild-type cells. The frequency of A:T-to-G:C mutations is reduced by two- to threefold in a mutS mutY mutant compared to a mutS mutant. Our results suggest that MutY base excision repair and mismatch repair defend against the mutagenic effect of 8-oxoG lesions in a cooperative manner.

scholarly journals In vivo diversification of target genomic sites using processive T7 RNA polymerase-base deaminase fusions blocked by RNA-guided dCas9

2019 ◽  
Author(s):  
Beatriz Álvarez ◽  
Mario Mencía ◽  
Víctor de Lorenzo ◽  
Luis Ángel Fernández
Keyword(s):  
Rna Polymerase ◽  
T7 Rna Polymerase ◽  
Target Sequence ◽  
Transcriptional Elongation ◽  
E Coli ◽  
Dna Strands ◽  
In Cells

AbstractDiversification of specific DNA segments typically involve in vitro generation of large sequence libraries and their introduction in cells for selection. Alternative in vivo mutagenesis systems on cells often show deleterious offsite mutations and restricted capabilities. To overcome these limitations, we have developed an in vivo platform to diversify specific DNA segments based on protein fusions between various base deaminases (BD) and the T7 RNA polymerase (T7RNAP) that recognizes a cognate promoter oriented towards the target sequence. The transcriptional elongation of these fusions generates transitions C to T or A to G on both DNA strands and in long DNA segments. To delimit the boundaries of the diversified DNA, the catalytically dead Cas9 (dCas9) is tethered with custom-designed crRNAs as a “roadblock” for BD-T7RNAP elongation. While the efficiency of this platform is demonstrated in E. coli, the system can be adapted to a variety of bacterial and eukaryotic hosts.

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