scholarly journals Opposing Roles of the Holliday Junction Processing Systems of Escherichia coli in Recombination-Dependent Adaptive Mutation

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 681-691 ◽  
Author(s):  
Reuben S Harris ◽  
Kimberly J Ross ◽  
Susan M Rosenberg
Keyword(s):  
Escherichia Coli ◽  
Homologous Recombination ◽  
Frameshift Mutation ◽  
Experimental System ◽  
The Other ◽  
Conjugative Plasmid ◽  
Holliday Junction ◽  
Adaptive Mutation ◽  
Replication Error ◽  
Resolution System

Abstract Aspects of the molecular mechanism of “adaptive” mutation are emerging from one experimental system: reversion of an Escherichia coli lac frameshift mutation carried on a conjugative plasmid. Homologous recombination is required and the mutations resemble polymerase errors. Reports implicating a role for conjugal transfer proteins suggested that the mutation mechanism is ordinary replication error occurring during transfer synthesis, followed by conjugation-like recombination, to capture the replicated fragment into an intact replicon. Whereas conjugational recombination uses either of two systems of Holliday junction resolution, we find that the adaptive lac reversions are inhibited by one resolution system and promoted by the other. Moreover, temporary absence of both resolution systems promotes mutation. These results imply that recombination intermediates themselves promote the mutations.

scholarly journals Chi-Dependent Intramolecular Recombination in Escherichia coli

Genetics ◽  
1998 ◽  
Vol 148 (2) ◽  
pp. 545-557
Author(s):  
Rachel Friedman-Ohana ◽  
Iris Karunker ◽  
Amikam Cohen
Keyword(s):  
Escherichia Coli ◽  
Homologous Recombination ◽  
Experimental System ◽  
Cis Acting ◽  
Enzymes Activity ◽  
Intramolecular Recombination ◽  
Insight Into

Abstract Homologous recombination in Escherichia coli is enhanced by a cis-acting octamer sequence named Chi (5′-GCTGGTGG-3′) that interacts with RecBCD. To gain insight into the mechanism of Chi-enhanced recombination, we recruited an experimental system that permits physical monitoring of intramolecular recombination by linear substrates released by in vivo restriction from infecting chimera phage. Recombination of the released substrates depended on recA, recBCD and cis-acting Chi octamers. Recombination proficiency was lowered by a xonA mutation and by mutations that inactivated the RuvABC and RecG resolution enzymes. Activity of Chi sites was influenced by their locations and by the number of Chi octamers at each site. A single Chi site stimulated recombination, but a combination of Chi sites on the two homologs was synergistic. These data suggest a role for Chi at both ends of the linear substrate. Chi was lost in all recombinational exchanges stimulated by a single Chi site. Exchanges in substrates with Chi sites on both homologs occurred in the interval between the sites as well as in the flanking interval. These observations suggest that the generation of circular products by intramolecular recombination involves Chi-dependent processing of one end by RecBCD and pairing of the processed end with its duplex homolog.

scholarly journals Formation of Chromosomal Tandem Arrays of the SXT Element and R391, Two Conjugative Chromosomally Integrating Elements That Share an Attachment Site

2001 ◽  
Vol 183 (4) ◽  
pp. 1124-1132 ◽  
Author(s):  
Bianca Hochhut ◽  
John W. Beaber ◽  
Roger Woodgate ◽  
Matthew K. Waldor
Keyword(s):  
Escherichia Coli ◽  
Homologous Recombination ◽  
Vibrio Cholerae ◽  
South African ◽  
Recipient Cell ◽  
Attachment Site ◽  
The Other ◽  
Chromosomal Integration ◽  
Providencia Rettgeri ◽  
Surface Exclusion

ABSTRACT The SXT element, a conjugative, self-transmissible, integrating element (a constin) originally derived from a Vibrio cholerae O139 isolate from India, and IncJ element R391, originally derived from a South African Providencia rettgeri isolate, were found to be genetically and functionally related. Both of these constins integrate site specifically into the Escherichia coli chromosome at an identical attachment site within the 5′ end of prfC. They encode nearly identical integrases, which are required for chromosomal integration, excision, and extrachromosomal circularization of these elements, and they have similar tra genes. Therefore, these closely related constins have virtually identical mechanisms for chromosomal integration and dissemination. The presence of either element in a recipient cell did not significantly reduce its ability to acquire the other element, indicating that R391 and SXT do not encode surface exclusion determinants. In cells harboring both elements, SXT and R391 were integrated in tandem fashion on the chromosome, and homologous recombination appeared to play little or no role in the formation of these arrays. Interference between R391 and SXT was detected by measuring the frequency of loss of an unselected resident element upon introduction of a second selected element. In these assays, R391 was found to have a stronger effect on SXT stability than vice versa. The level of expression and/or activity of the donor and recipient integrases may play a role in the interference between these two related constins.

scholarly journals Large inversion in Escherichia coli K-12 1485IN between inversely oriented IS3 elements near lac and cdd.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 639-645 ◽  
Author(s):  
Y Komoda ◽  
M Enomoto ◽  
A Tominaga
Keyword(s):  
Escherichia Coli ◽  
Homologous Recombination ◽  
The Other ◽  
Normal Strain ◽  
Restriction Maps ◽  
Mapping Data ◽  
F Factor ◽  
K 12 ◽  
And Inversion

Abstract A companion study has shown that the inversion carried by strain 1485IN has one terminus between lac and proC and the other between his and cdd of the normal strain. Starting with this mapping data, we have done molecular work demonstrating that the inversion occurred by recombination between inversely oriented two IS3 elements, one present near lac and the other near the cdd locus; i.e., the inversion is IN(is3B-is3E). Evidence supporting this conclusion includes: (i) Normal and inversion strains share two short regions with identical restriction maps. One of these regions is near lac and the other near cdd. (ii) IS3 homology was detected in each of the terminus regions of both the normal and inversion strains. (iii) The sequence on one side of the original IS3 element near lac has been exchanged with the sequence on one side of the IS3 near cdd. Whether the inversion has occurred by one event of homologous recombination between the two IS3 elements or has been caused by involvement of IS3 elements on an F factor is discussed. Another rearrangement, probably related to inversion and deletion, was detected between the IS3 and cdd of the inversion strain.

scholarly journals Increased Episomal Replication Accounts for the High Rate of Adaptive Mutation in recD Mutants of Escherichia coli

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 15-30 ◽  
Author(s):  
Patricia L Foster ◽  
William A Rosche
Keyword(s):  
Escherichia Coli ◽  
Mutation Rate ◽  
Copy Number ◽  
Frameshift Mutation ◽  
High Rate ◽  
Adaptive Mutation ◽  
Lacz Gene ◽  
Exonuclease Activity ◽  
Wild Type ◽  
Mutant Cells

Abstract Adaptive mutation has been studied extensively in FC40, a strain of Escherichia coli that cannot metabolize lactose (Lac-) because of a frameshift mutation affecting the lacZ gene on its episome. recD mutants of FC40, in which the exonuclease activity of RecBCD (ExoV) is abolished but its helicase activity is retained, have an increased rate of adaptive mutation. The results presented here show that, in several respects, adaptive mutation to Lac+ involves different mechanisms in recD mutant cells than in wild-type cells. About half of the apparent increase in the adaptive mutation rate of recD mutant cells is due to a RecA-dependent increase in episomal copy number and to growth of the Lac- cells on the lactose plates. The remaining increase appears to be due to continued replication of the episome, with the extra copies being degraded or passed to recD+ recipients. In addition, the increase in adaptive mutation rate in recD mutant cells is (i) dependent on activities of the single-stranded exonucleases, RecJ and ExoI, which are not required for (in fact, slightly inhibit) adaptive mutation in wild-type cells, and (ii) enhanced by RecG, which opposes adaptive mutation in wild-type cells.

scholarly journals The distribution of plasmids determining citrate utilization in citratè-positive variants ofEscherichia colifrom humans, domestic animals, feral birds and environments

1979 ◽  
Vol 83 (2) ◽  
pp. 331-344 ◽  
Author(s):  
Naotaka Ishiguro ◽  
Gihei Sato
Keyword(s):  
Escherichia Coli ◽  
Domestic Animals ◽  
Domestic Animal ◽  
The Other ◽  
Conjugative Plasmid ◽  
E Coli ◽  
Resistance Determinants ◽  
Sucrose Fermentation ◽  
R Plasmids ◽  
K 12

summarySixty-seven isolates of citrate-positive variants ofEscherichia coliwere isolated from human, domestic animal, feral bird and environmental sources. With the exception of citrate utilization, all isolates were identified as typicalE. coliby their biochemical reactions. The transmission of the ability to utilize citrate on Simmons' citrate agar was demonstrated in 53 (79·1%) out of the 67 citratepositiveE. colivariants obtained from various sources. Drug resistance determinants and citrate utilizing character were co-transmitted intoE. coliK-12 by conjugation among citrate-positiveE. coliisolates carrying R plasmids except for that isolated from horses. The other characters (haemolysin or colicin production, raffinose or sucrose fermentation) were not transmitted together with the citrate utilizing character. These facts suggested that the structural gene responsible for citrate utilizing ability in citrate-positive variants ofE. coliwas located on a conjugative plasmid.

scholarly journals Selective Inbreeding: Genetic Crosses Drive Apparent Adaptive Mutation in the Cairns-Foster System of Escherichia coli

Genetics ◽  
2019 ◽  
Vol 214 (2) ◽  
pp. 333-354 ◽  
Author(s):  
Amanda Nguyen ◽  
Sophie Maisnier-Patin ◽  
Itsugo Yamayoshi ◽  
Eric Kofoid ◽  
John R. Roth
Keyword(s):  
Escherichia Coli ◽  
Natural Selection ◽  
Alternative Model ◽  
Replication Origin ◽  
Frameshift Mutation ◽  
Adaptive Mutation ◽  
Genome Sequences ◽  
Rolling Circle ◽  
Induced Mutagenesis ◽  
Chromosomal Mutations

The Escherichia coli system of Cairns and Foster employs a lac frameshift mutation that reverts rarely (10−9/cell/division) during unrestricted growth. However, when 108 cells are plated on lactose medium, the nongrowing lawn produces ∼50 Lac+ revertant colonies that accumulate linearly with time over 5 days. Revertants carry very few associated mutations. This behavior has been attributed to an evolved mechanism (“adaptive mutation” or “stress-induced mutagenesis”) that responds to starvation by preferentially creating mutations that improve growth. We describe an alternative model, “selective inbreeding,” in which natural selection acts during intercellular transfer of the plasmid that carries the mutant lac allele and the dinB gene for an error-prone polymerase. Revertant genome sequences show that the plasmid is more intensely mutagenized than the chromosome. Revertants vary widely in their number of plasmid and chromosomal mutations. Plasmid mutations are distributed evenly, but chromosomal mutations are focused near the replication origin. Rare, heavily mutagenized, revertants have acquired a plasmid tra mutation that eliminates conjugation ability. These findings support the new model, in which revertants are initiated by rare pre-existing cells (105) with many copies of the F’lac plasmid. These cells divide under selection, producing daughters that mate. Recombination between donor and recipient plasmids initiates rolling-circle plasmid over-replication, causing a mutagenic elevation of DinB level. A lac+ reversion event starts chromosome replication and mutagenesis by accumulated DinB. After reversion, plasmid transfer moves the revertant lac+ allele into an unmutagenized cell, and away from associated mutations. Thus, natural selection explains why mutagenesis appears stress-induced and directed.

Infection of Escherichia coli with bacteriophages

1969 ◽  
Vol 27 ◽  
pp. 370-371
Author(s):  
Manfred E. Bayer
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Cell Surface ◽  
Virus Type ◽  
Infection Process ◽  
Adsorption Site ◽  
The Other ◽  
Specific Receptors ◽  
Bacterial Receptors

The first step in the infection of a bacterium by a virus consists of a collision between cell and bacteriophage. The presence of virus-specific receptors on the cell surface will trigger a number of events leading eventually to release of the phage nucleic acid. The execution of the various "steps" in the infection process varies from one virus-type to the other, depending on the anatomy of the virus. Small viruses like ØX 174 and MS2 adsorb directly with their capsid to the bacterial receptors, while other phages possess attachment organelles of varying complexity. In bacteriophages T3 (Fig. 1) and T7 the small conical processes of their heads point toward the adsorption site; a welldefined baseplate is attached to the head of P22; heads without baseplates are not infective.

The Nature of the Intramembrane Particle

1980 ◽  
Vol 38 ◽  
pp. 688-691
Author(s):  
A.J. Verkleij
Keyword(s):  
Escherichia Coli ◽  
Tight Junction ◽  
Gap Junction ◽  
The Other ◽  
Fracture Face ◽  
Band 3 Protein ◽  
Satisfactory Explanation ◽  
Freeze Fracturing ◽  
Intramembrane Particle ◽  
Luminal Membrane

Freeze-fracturing splits membranes into two helves, thus allowing an examination of the membrane interior. The 5-10 rm particles visible on both monolayers are widely assumed to be proteinaceous in nature. Most membranes do not reveal impressions complementary to particles on the opposite fracture face, if the membranes are fractured under conditions without etching. Even if it is considered that shadowing, contamination or fracturing itself might obscure complementary pits', there is no satisfactory explanation why under similar physical circimstances matching halves of other membranes can be visualized. A prominent example of uncomplementarity is found in the erythrocyte manbrane. It is wall established that band 3 protein and possibly glycophorin represents these nonccmplanentary particles. On the other hand a number of membrane types show pits opposite the particles. Scme well known examples are the ";gap junction',"; tight junction, the luminal membrane of the bladder epithelial cells and the outer membrane of Escherichia coli.

scholarly journals Lac Operon Boolean Models: Dynamical Robustness and Alternative Improvements

Mathematics ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 600 ◽  
Author(s):  
Marco Montalva-Medel ◽  
Thomas Ledger ◽  
Gonzalo A. Ruz ◽  
Eric Goles
Keyword(s):  
Escherichia Coli ◽  
Limit Cycles ◽  
The Other ◽  
Lac Operon ◽  
Boolean Models ◽  
Bistable Behavior

In Veliz-Cuba and Stigler 2011, Boolean models were proposed for the lac operon in Escherichia coli capable of reproducing the operon being OFF, ON and bistable for three (low, medium and high) and two (low and high) parameters, representing the concentration ranges of lactose and glucose, respectively. Of these 6 possible combinations of parameters, 5 produce results that match with the biological experiments of Ozbudak et al., 2004. In the remaining one, the models predict the operon being OFF while biological experiments show a bistable behavior. In this paper, we first explore the robustness of two such models in the sense of how much its attractors change against any deterministic update schedule. We prove mathematically that, in cases where there is no bistability, all the dynamics in both models lack limit cycles while, when bistability appears, one model presents 30% of its dynamics with limit cycles while the other only 23%. Secondly, we propose two alternative improvements consisting of biologically supported modifications; one in which both models match with Ozbudak et al., 2004 in all 6 combinations of parameters and, the other one, where we increase the number of parameters to 9, matching in all these cases with the biological experiments of Ozbudak et al., 2004.

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