The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria

Within the last decade, it has become clear that DNA replication and transcription are routinely in conflict with each other in growing cells. Much of the seminal work on this topic has been carried out in bacteria, specifically, Escherichia coli and Bacillus subtilis; therefore, studies of conflicts in these species deserve special attention. Collectively, the recent findings on conflicts have fundamentally changed the way we think about DNA replication in vivo. Furthermore, new insights on this topic have revealed that the conflicts between replication and transcription significantly influence many key parameters of cellular function, including genome organization, mutagenesis, and evolution of stress response and virulence genes. In this review, we discuss the consequences of replication-transcription conflicts on the life of bacteria and describe some key strategies cells use to resolve them. We put special emphasis on two critical aspects of these encounters: ( a) the consequences of conflicts on replisome stability and dynamics, and ( b) the resulting increase in spontaneous mutagenesis.

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Anatomy of a twin DNA replication factory

Biochemical Society Transactions ◽

10.1042/bst20200640 ◽

2020 ◽

Vol 48 (6) ◽

pp. 2769-2778

Author(s):

Huilin Li ◽

Nina Y. Yao ◽

Michael E. O'Donnell

Keyword(s):

Escherichia Coli ◽

Saccharomyces Cerevisiae ◽

Bacillus Subtilis ◽

Dna Replication ◽

In Vivo Studies ◽

Replication Forks ◽

Structural Studies ◽

Replication Factory ◽

Higher Eukaryotes

The replication of DNA in chromosomes is initiated at sequences called origins at which two replisome machines are assembled at replication forks that move in opposite directions. Interestingly, in vivo studies observe that the two replication forks remain fastened together, often referred to as a replication factory. Replication factories containing two replisomes are well documented in cellular studies of bacteria (Escherichia coli and Bacillus subtilis) and the eukaryote, Saccharomyces cerevisiae. This basic twin replisome factory architecture may also be preserved in higher eukaryotes. Despite many years of documenting the existence of replication factories, the molecular details of how the two replisome machines are tethered together has been completely unknown in any organism. Recent structural studies shed new light on the architecture of a eukaryote replisome factory, which brings with it a new twist on how a replication factory may function.

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Genome-wide comparison of phage M13-infected vs. uninfectedEscherichia coli

Canadian Journal of Microbiology ◽

10.1139/w04-113 ◽

2005 ◽

Vol 51 (1) ◽

pp. 29-35 ◽

Cited By ~ 14

Author(s):

Fredrik Karlsson ◽

Ann-Christin Malmborg-Hager ◽

Ann-Sofie Albrekt ◽

Carl A.K Borrebaeck

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Acid Stress ◽

Phage Infection ◽

Transcriptional Analysis ◽

Filamentous Phage ◽

Phosphotransferase System ◽

E Coli ◽

Genome Wide

To identify Escherichia coli genes potentially regulated by filamentous phage infection, we used oligonucleotide microarrays. Genome-wide comparison of phage M13-infected and uninfected E. coli, 2 and 20 min after infection, was performed. The analysis revealed altered transcription levels of 12 E. coli genes in response to phage infection, and the observed regulation of phage genes correlated with the known in vivo pattern of M13 mRNA species. Ten of the 12 host genes affected could be grouped into 3 different categories based on cellular function, suggesting a coordinated response. The significantly upregulated genes encode proteins involved in reactions of the energy-generating phosphotransferase system and transcription processing, which could be related to phage transcription. No genes belonging to any known E. coli stress response pathways were scored as upregulated. Furthermore, phage infection led to significant downregulation of transcripts of the bacterial genes gadA, gadB, hdeA, gadE, slp, and crl. These downregulated genes are normally part of the host stress response mechanisms that protect the bacterium during conditions of acid stress and stationary phase transition. The phage-infected cells demonstrated impaired function of the oxidative and the glutamate-dependent acid resistance systems. Thus, global transcriptional analysis and functional analysis revealed previously unknown host responses to filamentous phage infection.Key words: filamentous phage infection, global transcriptional analysis, AR, Escherichia coli.

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Yogurt Containing Bioactive Molecules Produced by Lactobacillus acidophilus La-5 Exerts a Protective Effect against Enterohemorrhagic Escherichia coli in Mice

Journal of Food Protection ◽

10.4315/0362-028x.jfp-11-508 ◽

2012 ◽

Vol 75 (10) ◽

pp. 1796-1805 ◽

Cited By ~ 18

Author(s):

MOHAMED ZEINHOM ◽

ANGELA M. TELLEZ ◽

VERONIQUE DELCENSERIE ◽

A. M. EL-KHOLY ◽

S. H. EL-SHINAWY ◽

...

Keyword(s):

Escherichia Coli ◽

Protective Effect ◽

Lactobacillus Acidophilus ◽

Virulence Genes ◽

Clinical Manifestations ◽

Enterohemorrhagic Escherichia Coli ◽

Bioactive Molecules ◽

Necrosis Factor Alpha ◽

In Vivo Effects

An active fraction extracted from Lactobacillus acidophilus La5 cell-free spent medium (LAla-5AF) was incorporated in a dairy matrix and tested to assess its antivirulent effect against enterohemorrhagic Escherichia coli (EHEC). Mice in experimental groups were fed for 4 days with yogurt supplemented with LAla-5AF. On the fifth day, mice were challenged with a single dose (107 CFU per mouse) of E. coli O157:H7. The clinical manifestations of the infection were significantly less severe in mice fed the yogurt supplemented with LAla-5AF. EHEC attachment and colonization was attenuated by LAla-5AF. Tumor necrosis factor alpha production was down-regulated, which might indicate a protective effect in the kidney during EHEC infection. To investigate the mechanisms associated with the in vivo effects observed, LAla-5AF was tested by reverse transcription real-time PCR to confirm its effects on the expression of several virulence genes of EHEC O157. The results showed that these fractions were able to down-regulate several virulence genes of EHEC, including stxB2, qseA, luxS, tir, ler, eaeA, and hlyB.

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Genetic characterization and virulence of enterotoxigenic Escherichia coli mutants which have lost virulence genes in vivo.

Infection and Immunity ◽

10.1128/iai.58.12.4156-4158.1990 ◽

1990 ◽

Vol 58 (12) ◽

pp. 4156-4158 ◽

Cited By ~ 14

Author(s):

T A Casey ◽

H W Moon

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Genetic Characterization ◽

Enterotoxigenic Escherichia Coli

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Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ

The Journal of Cell Biology ◽

10.1083/jcb.201005007 ◽

2010 ◽

Vol 190 (4) ◽

pp. 613-621 ◽

Cited By ~ 67

Author(s):

Julio O. Ortiz ◽

Florian Brandt ◽

Valério R.F. Matias ◽

Lau Sennels ◽

Juri Rappsilber ◽

...

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Spatial Organization ◽

Three Dimensional ◽

E Coli ◽

Escherichia Coli Cells ◽

Three Dimensional Configuration

Ribosomes arranged in pairs (100S) have been related with nutritional stress response and are believed to represent a “hibernation state.” Several proteins have been identified that are associated with 100S ribosomes but their spatial organization has hitherto not been characterized. We have used cryoelectron tomography to reveal the three-dimensional configuration of 100S ribosomes isolated from starved Escherichia coli cells and we have described their mode of interaction. In situ studies with intact E. coli cells allowed us to demonstrate that 100S ribosomes do exist in vivo and represent an easily reversible state of quiescence; they readily vanish when the growth medium is replenished.

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Recombination of bacteriophage λ in recD mutants of Escherichia coli

Genome ◽

10.1139/g89-013 ◽

1989 ◽

Vol 31 (1) ◽

pp. 53-67 ◽

Cited By ~ 45

Author(s):

David S. Thaler ◽

Elizabeth Sampson ◽

Imran Siddiqi ◽

Susan M. Rosenberg ◽

Lynn C. Thomason ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Replication ◽

Homologous Recombination ◽

Restriction Enzyme ◽

Null Alleles ◽

Mutant Strains ◽

Recbcd Enzyme ◽

Mutant Cells ◽

D Subunit

RecBCD enzyme is centrally important in homologous recombination in Escherichia coli and is the source of ExoV activity. Null alleles of either the recB or the recC genes, which encode the B and C subunits, respectively, manifest no recombination and none of the nuclease functions characteristic of the holoenzyme. Loss of the D subunit, by a recD mutation, likewise results in loss of ExoV activity. However, mutants lacking the D subunit are competent for homologous recombination. We report that the distribution of exchanges along the chromosome of Red−Gam−phage λ is strikingly altered by recD null mutations in the host. When λ DNA replication is blocked, recombination in recD mutant strains is high near λ's right end. In contrast, recombination in isogenic recD+ strains is approximately uniform along λ unless the λ chromosome contains a χ sequence. Recombination in recD mutant strains is focused toward the site of action of a type II restriction enzyme acting in vivo on λ. The distribution of exchanges in isogenic recD+ strains is scarcely altered by the restriction enzyme (unless the phage contains an otherwise silent χ). The distribution of exchanges in recD mutants is strongly affected by λ DNA replication. The distribution of exchanges on λ growing in rec+ cells is not influenced by DNA replication. The exchange distribution along λ in recD mutant cells is independent of χ in a variety of conditions. Recombination in rec+ cells is χ influenced. Recombination in recD mutants depends on recC function, occurs in strains deleted for rac prophage, and is independent of recJ, which is known to be required for λ recombination via the RecF pathway. We entertain two models for recombination in recD mutants: (i) recombination in recD mutants may proceed via double-chain break–repair, as it does in λ's Red pathway and E. coli's RecE pathway; (ii) the RecBC enzyme, missing its D subunit, is equivalent to the wild-type, RecBCD, enzyme after that enzyme has been activated by a χ sequence.Key words: χ sequence, RecBCD pathway, Red pathway, RecBC‡ pathway.

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The stringent response blocks DNA replication outside the ori region in Bacillus subtilis and at the origin in Escherichia coli

Journal of Molecular Biology ◽

10.1016/0022-2836(91)90657-r ◽

1991 ◽

Vol 219 (4) ◽

pp. 605-613 ◽

Cited By ~ 73

Author(s):

Alain Levine ◽

Françoise Vannier ◽

Mohammed Dehbi ◽

Gilles Henckes ◽

Simone J. Séror

Keyword(s):

Escherichia Coli ◽

Bacillus Subtilis ◽

Dna Replication ◽

Stringent Response

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Acetolactate Synthase from Bacillus subtilis Serves as a 2-Ketoisovalerate Decarboxylase for Isobutanol Biosynthesis in Escherichia coli

Applied and Environmental Microbiology ◽

10.1128/aem.01160-09 ◽

2009 ◽

Vol 75 (19) ◽

pp. 6306-6311 ◽

Cited By ~ 65

Author(s):

Shota Atsumi ◽

Zhen Li ◽

James C. Liao

Keyword(s):

Escherichia Coli ◽

Amino Acids ◽

Bacillus Subtilis ◽

Lactococcus Lactis ◽

Acetolactate Synthase ◽

Side Chains ◽

Decarboxylase Activity ◽

Small Side

ABSTRACTA pathway toward isobutanol production previously constructed inEscherichia coliinvolves 2-ketoacid decarboxylase (Kdc) fromLactococcus lactisthat decarboxylates 2-ketoisovalerate (KIV) to isobutyraldehyde. Here, we showed that a strain lacking Kdc is still capable of producing isobutanol. We found that acetolactate synthase fromBacillus subtilis(AlsS), which originally catalyzes the condensation of two molecules of pyruvate to form 2-acetolactate, is able to catalyze the decarboxylation of KIV like Kdc both in vivo and in vitro. Mutational studies revealed that the replacement of Q487 with amino acids with small side chains (Ala, Ser, and Gly) diminished only the decarboxylase activity but maintained the synthase activity.

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Mixed culture models for predicting intestinal microbial interactions between Escherichia coli and Lactobacillus in the presence of probiotic Bacillus subtilis

Beneficial Microbes ◽

10.3920/bm2015.0033 ◽

2015 ◽

Vol 6 (6) ◽

pp. 871-877 ◽

Cited By ~ 7

Author(s):

J.J. Yang ◽

C.C. Niu ◽

X.H. Guo

Keyword(s):

Escherichia Coli ◽

Bacillus Subtilis ◽

Mixed Culture ◽

Lactobacillus Reuteri ◽

Microbial Interactions ◽

Lactobacillus Species ◽

E Coli ◽

Culture Models ◽

Static Conditions

Bacillus has been proposed as a probiotic due to its in vivo effectiveness in the gastrointestinal tract through antimicrobial activities. The present study investigates the effects of Lactobacillus alone or in the presence of Bacillus subtilis MA139 on the inhibition of pathogenic Escherichia coli K88. Mixed cultures were used to predict the possible interactions among these bacteria within the intestinal tract of animals. B. subtilis MA139 was first assayed for its inhibition against E. coli K88 both under shaking and static culture conditions. A co-culture assay was employed under static conditions to test the inhibitory effects of Lactobacillus reuteri on E. coli K88, with or without addition of B. subtilis MA139. The results showed that B. subtilis MA139 had marked inhibition against E. coli K88 under shaking conditions and weak inhibition under static conditions. Lactobacillus alone as well as in combination with B. subtilis MA139 spores exerted strong inhibition against E. coli K88 under static conditions. However, the inhibition by Lactobacillus in combination with B. subilis spores was much higher than that by Lactobacillus alone (P<0.01). B. subtilis MA139 significantly decreased the pH and oxidation-reduction potential values of the co-culture broth compared to that of Lactobacillus alone (P<0.05). The viability of Lactobacillus increased when co-cultured with B. subtilis MA139 because of significantly higher Lactobacillus counts and lower pH values in the broth (P<0.05). The role of Bacillus in the mixed culture models suggests that Bacillus may produce beneficial effects by increasing the viability of lactobacilli and subsequently inhibiting the growth of pathogenic E. coli. Therefore, the combination of Bacillus and Lactobacillus species as a probiotic is recommended.

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