scholarly journals Genetic background affects epistatic interactions between two beneficial mutations

2013 ◽  
Vol 9 (1) ◽  
pp. 20120328 ◽  
Author(s):  
Yinhua Wang ◽  
Carolina Díaz Arenas ◽  
Daniel M. Stoebel ◽  
Tim F. Cooper
Keyword(s):  
Escherichia Coli ◽  
Genetic Background ◽  
General Pattern ◽  
Experimental Studies ◽  
Natural Isolate ◽  
Phenotypic Effect ◽  
Fitness Effect ◽  
Epistatic Interactions ◽  
Beneficial Mutations ◽  
E Coli

The phenotypic effect of mutations can depend on their genetic background, a phenomenon known as epistasis. Many experimental studies have found that epistasis is pervasive, and some indicate that it may follow a general pattern dependent on the fitness effect of the interacting mutations. These studies have, however, typically examined the effect of interactions between a small number of focal mutations in a single genetic background. Here, we extend this approach by considering how the interaction between two beneficial mutations that were isolated from a population of laboratory evolved Escherichia coli changes when they are added to divergent natural isolate strains of E. coli . We find that interactions between the focal mutations and the different genetic backgrounds are common. Moreover, the pair-wise interaction between the focal mutations also depended on their genetic background, being more negative in backgrounds with higher absolute fitness. Together, our results indicate the presence of interactions between focal mutations, but also caution that these interactions depend quantitatively on the wider genetic background.

scholarly journals Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness

2016 ◽  
Vol 113 (18) ◽  
pp. 5047-5052 ◽  
Author(s):  
Yinhua Wang ◽  
Carolina Diaz Arenas ◽  
Daniel M. Stoebel ◽  
Kenneth Flynn ◽  
Ethan Knapp ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Natural Populations ◽  
Donor Strain ◽  
Fitness Effect ◽  
Beneficial Mutations ◽  
E Coli ◽  
Experimental Systems ◽  
Natural Isolates ◽  
Selection Of ◽  
New Mutations

The effect of a mutation depends on its interaction with the genetic background in which it is assessed. Studies in experimental systems have demonstrated that such interactions are common among beneficial mutations and often follow a pattern consistent with declining evolvability of more fit genotypes. However, these studies generally examine the consequences of interactions between a small number of focal mutations. It is not clear, therefore, that findings can be extrapolated to natural populations, where new mutations may be transferred between genetically divergent backgrounds. We build on work that examined interactions between four beneficial mutations selected in a laboratory-evolved population of Escherichia coli to test how they interact with the genomes of diverse natural isolates of the same species. We find that the fitness effect of transferred mutations depends weakly on the genetic and ecological similarity of recipient strains relative to the donor strain in which the mutations were selected. By contrast, mutation effects were strongly inversely correlated to the initial fitness of the recipient strain. That is, there was a pattern of diminishing returns whereby fit strains benefited proportionally less from an added mutation. Our results strengthen the view that the fitness of a strain can be a major determinant of its ability to adapt. They also support a role for barriers of transmission, rather than differential selection of transferred DNA, as an explanation of observed phylogenetically determined patterns of restricted recombination among E. coli strains.

scholarly journals Inactivation of Umuc Protein Significantly Reduces Resistance to Ciprofloxacin and SOS Mutagenesis in Escherichia coli Mutants Harboring Intact Umud Gene

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Razieh Pourahmad Jaktaji ◽  
Sayedeh Marzieh Nourbakhsh Rezaei
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
Genetic Background ◽  
Pcr Amplification ◽  
Sos Response ◽  
Rpob Gene ◽  
Dilution Method ◽  
E Coli ◽  
Sos Mutagenesis ◽  
Dna Polymerase V

Background: Ciprofloxacin induces SOS response and mutagenesis by activation of UmuD’2C (DNA polymerase V) and DinB (DNA polymerase IV) in Escherichia coli, leading to antibiotic resistance during therapy. Inactivation of DNA polymerase V can result in the inhibition of mutagenesis in E. coli. Objectives: The aim of this research was to investigate the effect of UmuC inactivation on resistance to ciprofloxacin and SOS mutagenesis in E. coli mutants. Methods: Ciprofloxacin-resistant mutants were produced in a umuC- genetic background in the presence of increasing concentrations of ciprofloxacin. The minimum inhibitory concentration of umuC-mutants was measured by broth dilution method. Alterations in the rifampin resistance-determing region of rpoB gene were assessed by PCR amplification and DNA sequencing. The expression of SOS genes was measured by quantitative real-time PCR assay. Results: Results showed that despite the induction of SOS response (overexpression of recA, dinB, and umuD genes) following exposure to ciprofloxacin in E. coliumuC mutants, resistance to ciprofloxacin and SOS mutagenesis significantly decreased. However, rifampicin-resistant clones emerged in this genetic background. One of these clones showed mutations in the rifampicin resistance-determining region of rpoB (cluster II). The low mutation frequency of E. coli might be associated with the presence and overexpression of umuD gene, which could somehow limit the activity of DinB, the location and type of mutations in the β subunit of RNA polymerase. Conclusions: In conclusion, for increasing the efficiency of ciprofloxacin against Gram-negative bacteria, use of an inhibitor of umuC, along with ciprofloxacin, would be helpful.

scholarly journals Analyzing the Genetic Characteristics of a Tryptophan-overproducing Escherichia Coli

2020 ◽  
Author(s):  
Dongqin Ding ◽  
Danyang Bai ◽  
Jinlong Li ◽  
Zhitao Mao ◽  
Yaru Zhu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genetic Background ◽  
Great Influence ◽  
Random Mutagenesis ◽  
Underlying Structure ◽  
Carbon Utilization ◽  
Genetic Characteristics ◽  
E Coli ◽  
Long Time ◽  
Dynamics Simulations

Abstract Background: L-tryptophan (L-trp) production in Escherichia coli has been developed by employing random mutagenesis and selection for a long time, but this approach produces an unclear genetic background. Results: We generated the L-trp overproducer TPD5 by combining an intracellular L-trp biosensor and fluorescence-activated cell sorting (FACS) in E. coli, and succeeded in elucidating the genetic basis for L-trp overproduction. The most significant identified positive mutations affected TnaA (deletion), AroG (S211F), TrpE (A63V), and RpoS (nonsense mutation Q33*). The underlying structure-function relationships of the feedback-resistant AroG (S211F) and TrpE (A63V) mutants were uncovered based on protein structure modeling and molecular dynamics simulations, respectively. According to transcriptomic analysis, the global regulator RpoS not only has a great influence on cell growth and morphology, but also on carbon utilization and the direction of carbon flow. Finally, by balancing the concentrations of the L-trp precursors serine and glutamine based on the above analysis, we further increased the titer of L-trp to 3.18 g/L with a yield of 0.18 g/g. Conclusions: The analysis of the genetic characteristics of an L-trp overproducing E. coli provides valuable information on L-trp synthesis and elucidates the phenotype and complex cellular properties in a high-yielding strain, which opens the possibility to transfer beneficial mutations and reconstruct an overproducer with a clean genetic background.

scholarly journals Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Andrew B Morgenthaler ◽  
Wallis R Kinney ◽  
Christopher C Ebmeier ◽  
Corinne M Walsh ◽  
Daniel J Snyder ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Metabolic Pathway ◽  
Weak Link ◽  
Experimental Studies ◽  
Wild Type ◽  
Gene Encoding ◽  
Evolutionary Trajectory ◽  
Adaptive Mutations ◽  
E Coli ◽  
Essential Function

New enzymes often evolve by gene amplification and divergence. Previous experimental studies have followed the evolutionary trajectory of an amplified gene, but have not considered mutations elsewhere in the genome when fitness is limited by an evolving gene. We have evolved a strain of Escherichia coli in which a secondary promiscuous activity has been recruited to serve an essential function. The gene encoding the ‘weak-link’ enzyme amplified in all eight populations, but mutations improving the newly needed activity occurred in only one. Most adaptive mutations occurred elsewhere in the genome. Some mutations increase expression of the enzyme upstream of the weak-link enzyme, pushing material through the dysfunctional metabolic pathway. Others enhance production of a co-substrate for a downstream enzyme, thereby pulling material through the pathway. Most of these latter mutations are detrimental in wild-type E. coli, and thus would require reversion or compensation once a sufficient new activity has evolved.

scholarly journals Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Kelly N. Phillips ◽  
Scott Widmann ◽  
Huei-Yi Lai ◽  
Jennifer Nguyen ◽  
J. Christian J. Ray ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Natural Variation ◽  
Genetic Relatedness ◽  
Regulatory Function ◽  
Natural Isolate ◽  
Content Type ◽  
E Coli ◽  
Wide Range ◽  
Operon Regulation ◽  
Regulatory Functions

ABSTRACT Transcription of bacterial genes is controlled by the coordinated action of cis- and trans-acting regulators. The activity and mode of action of these regulators can reflect different requirements for gene products in different environments. A well-studied example is the regulatory function that integrates the environmental availability of glucose and lactose to control the Escherichia coli lac operon. Most studies of lac operon regulation have focused on a few closely related strains. To determine the range of natural variation in lac regulatory function, we introduced a reporter construct into 23 diverse E. coli strains and measured expression with combinations of inducer concentrations. We found a wide range of regulatory functions. Several functions were similar to the one observed in a reference lab strain, whereas others depended weakly on the presence of cAMP. Some characteristics of the regulatory function were explained by the genetic relatedness of strains, indicating that differences varied on relatively short time scales. The regulatory characteristics explained by genetic relatedness were among those that best predicted the initial growth of strains following transition to a lactose environment, suggesting a role for selection. Finally, we transferred the lac operon, with the lacI regulatory gene, from five natural isolate strains into a reference lab strain. The regulatory function of these hybrid strains revealed the effect of local and global regulatory elements in controlling expression. Together, this work demonstrates that regulatory functions can be varied within a species and that there is variation within a species to best match a function to particular environments. IMPORTANCE The lac operon of Escherichia coli is a classic model for studying gene regulation. This study has uncovered features such as the environmental input logic controlling gene expression, as well as gene expression bistability and hysteresis. Most lac operon studies have focused on a few lab strains, and it is not known how generally those findings apply to the diversity of E. coli strains. We examined the environmental dependence of lac gene regulation in 20 natural isolates of E. coli and found a wide range of regulatory responses. By transferring lac genes from natural isolate strains into a common reference strain, we found that regulation depends on both the lac genes themselves and on the broader genetic background, indicating potential for still-greater regulatory diversity following horizontal gene transfer. Our results reveal that there is substantial natural variation in the regulation of the lac operon and indicate that this variation can be ecologically meaningful.

Enrichment and Elimination of mutY Mutators in Escherichia coli Populations

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1055-1062 ◽  
Author(s):  
Lucinda Notley-McRobb ◽  
Shona Seeto ◽  
Thomas Ferenci
Keyword(s):  
Escherichia Coli ◽  
The Other ◽  
Mutation Rates ◽  
Beneficial Mutation ◽  
Glucose Limitation ◽  
Epistatic Interactions ◽  
Beneficial Mutations ◽  
Bacterial Populations ◽  
Kinetics Of ◽  
Selection Event

Abstract The kinetics of mutator sweeps was followed in two independent populations of Escherichia coli grown for up to 350 generations in glucose-limited continuous culture. A rapid elevation of mutation rates was observed in both populations within 120-150 generations, as was apparent from major increases in the proportion of the populations with unselected mutations in fhuA. The increase in mutation rates was due to sweeps by mutY mutators. In both cultures, the enrichment of mutators resulted from hitchhiking with identified beneficial mutations increasing fitness under glucose limitation; mutY hitchhiked with mgl mutations in one culture and ptsG in the other. In both cases, mutators were enriched to constitute close to 100% of the population before a periodic selection event reduced the frequency of unselected mutations and mutators in the cultures. The high proportion of mutators persisted for 150 generations in one population but began to be eliminated within 50 generations in the other. The persistence of mutator, as well as experimental data showing that mutY bacteria were as fit as near-isogenic mutY+ bacteria in competition experiments, suggest that mutator load by deleterious mutations did not explain the rapidly diminishing proportion of mutators in the populations. The nonmutators sweeping out mutators were also unlikely to have arisen by reversion or antimutator mutations; the mutY mutations were major deletions in each case and the bacteria sweeping out mutators contained intact mutY. By following mgl allele frequencies in one population, we discovered that mutators were outcompeted by bacteria that had rare mgl mutations previously as well as additional beneficial mutation(s). The pattern of appearance of mutY, but not its elimination, conforms to current models of mutator sweeps in bacterial populations. A mutator with a narrow mutational spectrum like mutY may be lost if the requirement for beneficial mutations is for changes other than GC → TA transversions. Alternatively, epistatic interactions between mutator mutation and beneficial mutations need to be postulated to explain mutator elimination.

Isolation and partial characterization of an Escherichia coli mutant resistant to colicin A

1975 ◽  
Vol 21 (10) ◽  
pp. 1595-1601 ◽  
Author(s):  
Marc Lavoie ◽  
Leo G. Mathieu
Keyword(s):  
Escherichia Coli ◽  
Methylene Blue ◽  
Parent Strain ◽  
General Pattern ◽  
Sodium Dodecyl ◽  
Triphenyltetrazolium Chloride ◽  
E Coli ◽  
Receptor Sites ◽  
Acridine Dyes

An Escherichia coli K12 mutant resistant to colicin A-CA31 apparently through loss of its receptor sites has been isolated and partially characterized. Resistance to colicin A was accompanied with a decreased sensitivity to colicins L-398 and E2-CA42, and to acridine dyes. The mutant strain displayed the same general pattern of tolerance or sensitivity as the parent strain towards eight antibiotics, colicins C, D, E1, E3, F2, F3, G, I, K, and N; phages T1, T2, T5, T6, T7, F2, λ vir, P1kc, [Formula: see text] 80, and BF23; and to methylene blue, triphenyltetrazolium chloride, ethylene-diaminetetraacetate (EDTA), deoxycholate, and sodium dodecyl sulfate. Conjugation and transduction experiments showed that a locus controlling resistance to colicin A-CA31 mapped at 21 min on the genetic map of this E. coli K12 strain.

scholarly journals Hydroxycinnamate (hca) Catabolic Genes from Acinetobacter sp. Strain ADP1 Are Repressed by HcaR and Are Induced by Hydroxycinnamoyl-Coenzyme A Thioesters

2003 ◽  
Vol 69 (9) ◽  
pp. 5398-5409 ◽  
Author(s):  
Donna Parke ◽  
L. Nicholas Ornston
Keyword(s):  
Escherichia Coli ◽  
Sequence Analysis ◽  
Genetic Background ◽  
Open Reading Frames ◽  
Aldehyde Dehydrogenases ◽  
E Coli ◽  
Catabolic Genes ◽  
Coa Thioesters ◽  
Reading Frames

ABSTRACT Hydroxycinnamates are plant products catabolized through the diphenol protocatechuate in the naturally transformable bacterium Acinetobacter sp. strain ADP1. Genes for protocatechuate catabolism are central to the dca-pca-qui-pob-hca chromosomal island, for which gene designations corresponding to catabolic function are dca (dicarboxylic acid), pca (protocatechuate), qui (quinate), pob (p-hydroxybenzoate), and hca (hydroxycinnamate). Acinetobacter hcaC had been cloned and shown to encode a hydroxycinnamate:coenzyme A (CoA) SH ligase that acts upon caffeate, p-coumarate, and ferulate, but genes for conversion of hydroxycinnamoyl-CoA to protocatechuate had not been characterized. In this investigation, DNA from pobS to an XbaI site 5.3 kb beyond hcaC was captured in the plasmid pZR8200 by a strategy that involved in vivo integration of a cloning vector near the hca region of the chromosome. pZR8200 enabled Escherichia coli to convert p-coumarate to protocatechuate in vivo. Sequence analysis of the newly cloned DNA identified five open reading frames designated hcaA, hcaB, hcaK, hcaR, and ORF1. An Acinetobacter strain with a knockout of HcaA, a homolog of hydroxycinnamoyl-CoA hydratase/lyases, was unable to grow at the expense of hydroxycinnamates, whereas a strain mutated in HcaB, homologous to aldehyde dehydrogenases, grew poorly with ferulate and caffeate but well with p-coumarate. A chromosomal fusion of lacZ to the hcaE gene was used to monitor expression of the hcaABCDE promoter. LacZ was induced over 100-fold by growth in the presence of caffeate, p-coumarate, or ferulate. The protein deduced to be encoded by hcaR shares 28% identity with the aligned E. coli repressor, MarR. A knockout of hcaR produced a constitutive phenotype, as assessed in the hcaE::lacZ-Kmr genetic background, revealing HcaR to be a repressor as well. Expression of hcaE::lacZ in strains with knockouts in hcaA, hcaB, or hcaC revealed unambiguously that hydroxycinnamoyl-CoA thioesters relieve repression of the hcaABCDE genes by HcaR.

scholarly journals Lazarus effects: the frequency and genetic causes of Escherichia coli population recovery under lethal heat stress

2016 ◽  
Author(s):  
Shaun M. Hug ◽  
Brandon S. Gaut
Keyword(s):  
Escherichia Coli ◽  
Antagonistic Pleiotropy ◽  
Lethal Temperature ◽  
Epistatic Interactions ◽  
Genetic Changes ◽  
E Coli ◽  
Evolutionary Innovation ◽  
Fitness Benefits ◽  
Fitness Tradeoffs ◽  
Lazarus Effect

ABSTRACTSometimes populations crash and yet recover before being lost completely. Such recoveries have been observed incidentally in evolution experiments using Escherichia coli, and this phenomenon has been termed the “Lazarus effect.” To investigate how often recovery occurs and the genetic changes that drive it, we evolved ~300 populations of E. coli at lethally high temperatures (43.0°) for five days and sequenced the genomes of recovered populations. Our results revealed that the Lazarus effect is uncommon, but frequent enough, at ~9% of populations, to be a potent source of evolutionary innovation. Population sequencing uncovered a set of mutations adaptive to lethal 43.0°C that were mostly distinct from those that were beneficial at a high but nonlethal temperature (42.2°). Mutations within two operons—the heat shock hslUV operon and the RNA polymerase rpoBC operon—drove adaptation to lethal temperature. Mutations in hslUV exhibited little antagonistic pleiotropy at 37.0°C and may have arisen neutrally prior to subjection to lethal temperature. In contrast, rpoBC mutations provided greater fitness benefits than hslUV mutants, but were less prevalent and caused stronger fitness tradeoffs at lower temperatures. Recovered populations fixed mutations in only one operon or the other, but not both, indicating that epistatic interactions between beneficial mutations were important even at the earliest stages of adaptation.

scholarly journals High Prevalence of Colistin-Resistant Escherichia coli with Chromosomally Carried mcr-1 in Healthy Residents in Vietnam

mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Takahiro Yamaguchi ◽  
Ryuji Kawahara ◽  
Kouta Hamamoto ◽  
Itaru Hirai ◽  
Diep Thi Khong ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Developing Countries ◽  
Genetic Background ◽  
Fecal Microbiota ◽  
Public Health Issue ◽  
Resistant Bacteria ◽  
Healthy Human ◽  
Content Type ◽  
E Coli ◽  
High Prevalence

ABSTRACT The wide distribution of colistin-resistant bacteria in developing countries has become a common phenomenon. To understand the mechanisms underlying their distribution, we studied the mcr genetic background of colistin-resistant Escherichia coli isolates from the fecal microbiota of healthy human residents from a community in Vietnam with a high prevalence of colistin-resistant E. coli with mcr. Fifty-seven colistin-resistant isolates were obtained from 98 residents; one isolate was collected from each individual and analyzed for mcr. We found that 36.8% of the isolates carried chromosomal mcr-1. Further, 63.2% and 1.8% of the isolates carried mcr-1 on the plasmid and the plasmid/chromosome, respectively. Whole-genome sequencing of genetically unrelated isolates showed that the majority (6 of 7) of the isolates had the chromosomal mcr-1 in a complete ancestral mcr-1 transposon Tn6330, ISApl1-mcr-1-PAP2-ISApl1, which was inserted at various positions on the chromosomes. In addition, the majority (87.5%) of Tn6330 of mcr-1-carrying plasmids (n = 8) lacked both upstream and downstream ISApl1 transposons. The results obtained in this study indicate that plasmid-to-chromosomal transfer of mcr-1 may have occurred recently in the fecal microbiota of the residents. Additionally, Tn6330 on the chromosome may lose ISApl1 from the transposon during multiplication to gain a more stable mcr-1 state on the chromosome. Stabilization of resistance by the chromosomal incorporation of mcr-1 would be an additional challenge in combating the dissemination of resistant bacteria. IMPORTANCE Elucidation of the mechanism of the wide dissemination of colistin-resistant bacteria in communities of developing countries is an urgent public health issue. In this study, we investigated the genetic background of the colistin resistance gene mcr in E. coli isolates from the fecal microbiota of healthy human residents living in a community in Vietnam with a high prevalence of colistin-resistant E. coli. Our study revealed for the first time, a surprisingly high percentage (36.8%) of colistin-resistant E. coli carrying chromosomal mcr-1, the emergence of which may have occurred recently, in the fecal microbiota of the community residents. The mcr-1 transposon on the chromosome may develop into a more stable genotype by the loss of insertion sequences (ISs). Our results are valuable in understanding the mechanism underlying the increasing prevalence of colistin-resistant bacteria within a community.

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