Home
JournalsCollections
For Authors For Reviewers For Editorial Board Members
Article Processing Charges Open Access
Ethics Advertising Policy
Editorial Policy Resource Center
Company Information Contact Us
Publications > Journals > Gene Expression> Article Full Text
Review Article
OPEN ACCESS

Download PDF

The Emerging Role of (p)ppGpp in DNA Repair and Associated Bacterial Survival against Fluoroquinolones

  • Smitha Sivapragasam* 
Gene Expression   2024

doi: 10.14218/GE.2024.00033

Received:

Revised:

Accepted:

Published online:

 Author information

Citation: Sivapragasam S. The Emerging Role of (p)ppGpp in DNA Repair and Associated Bacterial Survival against Fluoroquinolones. Gene Expr. Published online: Sep 12, 2024. doi: 10.14218/GE.2024.00033.

Abstract

(p)ppGpp binds to RNA polymerase, causing stalling at damaged DNA sites and subsequent backtracking, which facilitates the recognition and removal of damaged DNA by repair proteins. Additionally, (p)ppGpp regulates DNA repair proteins involved in the Save Our Soul response and mutagenic strand break repair pathways, which are crucial for repairing damages induced by Ultraviolet light and other DNA-damaging agents, including antibiotics. Through these repair pathways, (p)ppGpp plays a vital role in mending strand breaks induced by ciprofloxacin, a fluoroquinolone antibiotic. (p)ppGpp mediates bacterial survival by inhibiting the transcription of mismatch repair proteins while simultaneously upregulating error-prone polymerases mediated by stress-induced sigma factors, thereby facilitating mutagenesis. The function of (p)ppGpp in fine-tuning DNA repair proteins to support bacterial survival against antibiotics via stress-induced mutagenesis is an emerging topic in the field of antibiotic resistance research. Currently, limited information is available on how (p)ppGpp interconnects the various DNA repair pathways that directly influence bacterial resistance to antibiotics. (p)ppGpp is also known to promote bacterial persistence against ofloxacin, another fluoroquinolone, by regulating proteins that induce membrane depolarization. The overlapping functions of (p)ppGpp as a master regulator in DNA repair during stress and bacterial persistence are yet to be fully elucidated. This review focuses on recent publications highlighting (p)ppGpp as a potential link connecting DNA repair pathways to bacterial survival strategies against fluoroquinolone antibiotics.

Keywords

(p)ppGpp, Nucleotide excision repair, SOS response, Mutagenic strand break repair, Stringent response, Bacterial survival, Fluoroquinolones

Introduction

Bacteria constantly encounter starvation or stress in their host or environment, necessitating efficient DNA repair to maintain genome stability. Phosphorylated guanosines, known as (p)ppGpp, are synthesized during stress and starvation in bacteria and they act as signaling molecules that regulate the function of critical proteins thereby leading to a global reprogramming of almost all essential cellular processes. (p)ppGpp was first identified by Cashel and Gallant through thin-layer chromatography of nucleotide extracts from Escherichia coli (E. coli) bacterial cultures starved of amino acids.1,2 They demonstrated that upon ribosomal stalling, caused by uncharged transfer RNA binding in the absence of amino acids, RelA, a ribosome-associated protein, synthesizes (p)ppGpp from guanosine triphosphate (GTP) or guanosine diphosphate. Since then, several research groups have worked to elucidate the function of (p)ppGpp through genetic and biochemical studies. (p)ppGpp plays a vital role in maintaining GTP/ppGpp homeostasis within cells.3 It binds to several enzymes involved in nucleotide biosynthesis, leading to the inhibition of GTP biosynthesis during starvation or stringent response.4–7 However, cells require substantial amounts of Guanosine triphosphate and Adenosine triphosphate (ATP) for replication and growth. During starvation and stringent response, ppGpp mediates an alternative pathway of GTP synthesis. This occurs through ppGpp binding to the transcription factor - xanthine dehydrogenase regulator, leading to upregulation of the purine salvage pathway mediated by the xanthine dehydrogenase enzyme, thus maintaining a basal level of the GTP pool. This basal supply of GTP substrate contributes to (p)ppGpp synthesis under stringent conditions.8–10 Therefore the availability of (p)ppGpp during stringent conditions is dependent upon the regulation of GTP levels by the enzymes of purine metabolism that salvage purines.

(p)ppGpp binds to various cellular targets, inhibiting key processes such as transcription, translation, and replication. Notably, it binds to RNA polymerase, hindering transcription,11–14 and to DnaG primase, inhibiting replication.15 Furthermore, (p)ppGpp interacts with initiation factor-2 and elongation factor-G, impeding translation.16,17 The regulatory mechanism of ppGpp also occurs at the promoter level, either by interacting with another transcription factor or by directly binding to RNA polymerase, which can then bind to the discriminator sequence present upstream of the transcription start site of genes. For example, (p)ppGpp-bound RNA polymerase binds to the promoter of dnaA, which codes for a replication initiation protein, thereby inhibiting its transcription.18–20 Additionally, the sigma subunits of RNA polymerases are regulated by ppGpp-bound RNA polymerases at their promoters.11,21 A similar regulation is found at the promoter regions of various stress response genes whose expression is influenced by ppGpp generated during stringent conditions.22,23 Though (p)ppGpp acts as a master regulator of essential cellular processes, how they regulate various DNA repair proteins during stress or stringent conditions remains largely unexplored.

Bacterial DNA repair pathways,24–26 operate meticulously to rectify lesions in their genome caused by diverse DNA-damaging agents. This review delves into the involvement of (p)ppGpp in some of the major DNA repair pathways including nucleotide excision repair, mismatch repair, and mutagenic strand break repair. However, further studies investigating the in vivo role of (p)ppGpp in these pathways in genome maintenance under cellular context are still needed. Additionally, this review article explores bacterial stress survival mechanisms involving various DNA repair pathways, such as the Save Our Soul response, stress-induced mutagenesis, ciprofloxacin (CPX)-induced mutagenesis, which aid bacterial survival in the presence of antibiotics.27,28 The overlapping function of (p)ppGpp in membrane depolarization that leads to bacterial cell survival in the presence of antibiotics is not completely understood. However, studying this function will help us understand how (p)ppGpp can contribute to various mechanisms of antibiotic resistance. The viewpoints presented and the questions raised in this review will help guide future research in understanding the role of (p)ppGpp in these DNA repair mechanisms and their relation to antibiotic associated bacterial survival.

Cooperative function of RNA polymerase and ppGpp plays an important role in nucleotide excision repair (NER)

NER eliminates bulky DNA lesions, such as cyclobutane pyrimidine dimers (CPDs) and 6,4-photoproducts, induced by Ultraviolet (UV) radiation. There are two major NER pathways: global genomic NER and transcription-coupled NER (TC-NER). Global genomic NER removes UV-induced DNA lesions throughout the genome, affecting both non-transcribed and transcribed strands. In contrast, TC-NER specifically targets the transcribed strand. TC-NER begins with the stalling of RNA polymerase at DNA lesions.29,30In vivo studies using excision repair sequencing showed a higher transcribed strand/non-transcribed strand repair ratio, indicating that transcribed strands were repaired much faster than non-transcribed strands in wild-type E. coli cells upon UV exposure.31,32 However, analysis of DNA damage and repair of CPDs at single nucleotide resolution using the CPD-seq technique revealed that CPD repair by the TC-NER pathway occurs globally across all regions of the genome,33 including sense strands, antisense strands, and intergenic regions where transcription by RNA polymerase is required.34–36 The process of induction of genome-wide transcription by UV irradiation is termed as “pervasive transcription”. Also, based on in vivo and in vitro techniques, Mutation Frequency Decline (Mfd), a forward translocase protein was considered to be critical for TC-NER.31,32In vivo live cell imaging studies identified that the Mfd protein associates with RNA polymerase to aid the transcription elongation process during normal growth even in the absence of DNA damage.37 Cryo-electron microscopy studies revealed that Mfd protein binding to DNA induces structural changes in Mfd, leading to Mfd-UvrA binding via the ATPase motif IVa and exhibiting translocase activity via motif Ic.38 Single-molecule imaging in E. coli cells elucidated that ATP hydrolysis by UvrA is required for the Mfd-UvrA2 complex interaction with DNA. UvrB loading onto the template strand at sites of stalled RNA polymerases is synchronized with the dissociation of Mfd from DNA.39 Additionally, a comparison of UV-irradiated E. coli cells and NER-deficient cells indicated that the concentration of UvrA increases during the Save Our Soul (SOS) response in wildtype cells, aiding Mfd turnover and recruitment at sites of UV lesions where RNA polymerase stalls.37,39–41 However, solid evidence for this mechanism remains to be elucidated.34,35 Mfd was considered sufficient for transcription-coupled NER in E. coli,31,32 but Δmfd mutants were not found to be as sensitive to UV radiation,42–44 suggesting that Mfd might not be the most critical player in regulating TC-NER in E. coli.35 Therefore, evidences so far indicated that Mfd protein fundamentally functions during the process of transcription apart from playing a role in the nucleotide excision repair pathway.

RNA polymerase backtracking, a mechanism where RNA polymerase slides in reverse orientation, is essential for regulation of gene transcription and maintenance of genome stability.45 In bacteria, transcription fidelity and prevention of collisions between transcription and replication processes depend on RNA polymerase backtracking of transcription complex containing mis-incorporated bases by binding to the transcription factor DksA in the presence of the signaling molecule guanosine tetraphosphate (ppGpp).46 Although the backtracking of RNA polymerase aids proofreading, excessive backtracking, such as in the case of arrested elongation complexes, can occasionally cause codirectional collisions. These collisions may lead to double-strand breaks, posing a threat to bacterial survival.47 Notably, ppGpp accumulates upon exposure to DNA-damaging agents (like UV radiation),48 binds to RNA polymerase, induces backtracking activity, and coordinates the transition of RNA polymerase between transcription elongation and NER.49,50 Cryo-electron microscopy studies revealed two ppGpp binding sites within RNA polymerase structures.49,50 ppGpp binding to Site 1 is required for RNA polymerase backtracking during NER, while binding to Site 2, together with the transcription factor DksA, inhibits transcription initiation.49,50 During nutrient starvation and stringent response, ppGpp binding to Site 2 inhibits transcription initiation at promoter regions.51,52 Upon encountering bulky lesions caused by UV light or other damaging agents like nitrofurazone (NFZ) or 4-nitroquinoline-1-oxide (4NQO), ppGpp binding to Site 1 facilitates RNA polymerase backtracking in association with UvrD (a helicase) in an additive fashion promoting NER.48 The combined action of ppGpp and UvrD in backtracking RNA polymerase facilitates the recruitment of UvrA2BC excision nuclease to the lesion site, leading to damage excision.34–36,44,48In vitro biochemical experiments implicated UvrD’s helicase action in unwinding the excised oligo and displacing UvrA2BC from DNA,53 but this concept warrants further in vivo experiments.35 DNA polymerase I can exclusively perform this helicase function in the absence of UvrD.54 Mutants of relA and spoT, which are deficient in ppGpp synthesis, are extremely sensitive to UV, 4NQO, and NFZ damage due to the failure of RNA polymerase backtracking, leading to compromised repair. Deletion of transcription elongation factors GreA and GreB, which act as anti-backtracking factors, can rescue the mutant phenotypes associated with (p)ppGpp and UvrD proteins by mitigating the compromised repair mechanism.44,48 NusA, another transcription elongation factor, assists in UvrD-facilitated RNA polymerase backtracking upon encountering a DNA lesion.44,48,55 Recently, RNA polymerase was identified as playing a major role in the ribonucleotide excision repair pathway,56 however, the function of (p)ppGpp in this repair pathway is yet to be studied. Overall, nucleotide excision repair is orchestrated by RNA polymerase with the inevitable co-action of ppGpp at a global level upon exposure to DNA-damaging agents, including UV light (Fig. 1). However, the faithful regeneration of the damaged genome after repair might depend upon the prevailing environment (nutrient-rich or nutrient-deficient) and the degree of damage caused by UV light or genotoxic agents. Overall, the function of (p)ppGpp in nucleotide excision repair in bacterial genome maintenance is yet to be fully understood. An impeccable comprehensive analysis of DNA damage and repair upon exposure to various DNA damages that induce bulky adducts in the genome during stringent response might help understand the functional role of (p)ppGpp by nucleotide excision repair pathway in bacteria.

(p)ppGpp-dependent repair pathways (black arrows) illustrating the role of (p)ppGpp and the set of proteins regulated by (p)ppGpp in each repair pathway.
Fig. 1  (p)ppGpp-dependent repair pathways (black arrows) illustrating the role of (p)ppGpp and the set of proteins regulated by (p)ppGpp in each repair pathway.

Red arrows indicate the DNA repair pathways that are known to aid bacterial survival as persisters and gamblers in the presence of fluoroquinolones. Blue color arrow indicates downregulation, while purple color indicates upregulation in the presence of (p)ppGpp. (Created with Biorender.com) ArcZ, small RNA that regulates ArcA/B regulon; DinB, DNA polymerase IV named for its DNA Damage, inducible role; DsrA, small RNA named from Downstream Regulatory RNA A; HokB, Toxin protein belonging to the toxin, antitoxin system (name derived from ‘Host Killing’); MutS/MutH, mismatch repair proteins that play a role in preventing mutations; Obg, GTPase protein named after its association with SpoO sporulation factor of Bacillus; RecA, Recombinase A; RecBCD, Recombinase BCD; RuvC, recombination protein that resolves UV induced damaged complexes that undergo recombination; SOS, Save Our Soul; UmuCD, translesion synthesis polymerases named after their role in UV mutagenesis.

Downregulation of mismatch repair proteins by (p)ppGpp

MutS, MutL, and MutH are crucial proteins in the mismatch repair system, responsible for recognizing misincorporated bases in the DNA resulting from spontaneous deamination reactions, DNA synthesis during replication, and repair synthesis following recombination events.57–61 Defects in the mismatch repair system lead to the accumulation of mutations in the genome.62–64 MutH plays a role in methyl-directed mismatch repair by recognizing hemi-methylated DNA and cleaving the newly synthesized unmethylated strand containing the mismatched base.65 In the absence of DNA adenine methylase, which methylates DNA at GATC sequences, MutH fails to recognize the newly synthesized DNA, resulting in cleavage of both parent and daughter strands.66 MutL aids the UvrD helicase in unwinding the strand with the mismatch, after which the resulting single strand is bound by single-strand binding protein.67,68 Exonucleases, including ExoI, ExoVII, ExoX, and RecJ, act on the cleaved strand, followed by repair synthesis by DNA polymerase III and ligation by DNA ligase to complete the repair process.57,58

During the stationary phase, the concentrations of MutS and MutH decrease approximately tenfold in E. coli cells.69 Although the downregulation of mutL has not been identified, there is a limitation in the availability of functional MutL protein during the stationary phase.70 Furthermore, in the presence of RpoS, a general stress response regulator, the transcript levels of mutS and mutH decrease about four-fold and two-fold, respectively (Fig. 1).71 While the regulatory mechanisms of MutS, MutH, and other mismatch repair proteins during the exponential and stationary phases are yet to be studied,72 it should be noted that RpoS synthesis and activation are positively regulated by (p)ppGpp during the stationary phase or in response to limited nutrients in the media. The anti-adapter proteins IraD, IraP, and IraM, which stabilize the sigma (S) factor by preventing its degradation by ClpXP proteases, are upregulated by ppGpp during DNA damage, phosphate starvation, and magnesium starvation, respectively.73–75 The ppGpp-mediated stabilization of sigma (S) could be a potential reason for the downregulation of mismatch repair during starvation. Notably, bacteria utilize the mismatch repair system to genetically adapt by modulating their mutation rates to survive challenging environmental conditions.64,76 The role of (p)ppGpp in the regulation of mismatch repair pathway might occur (i) through stabilization of RpoS and (ii) through downregulation of MutS and MutH. However, further studies are required to verify the role of (p)ppGpp in regulation of the mismatch repair pathway proteins that lead to mutagenesis in the bacterial genome.

Role of (p)ppGpp in recombinational repair and mutagenic strand break repair

Recombinational repair is crucial for cells to repair strand breaks that may occur during physiological replication-transcription conflicts or exposure to antibiotics that induce strand breaks.49,77–79 Both single-strand breaks and double-strand breaks are repaired through recombinational repair mechanisms. The Recombinase BCD (RecBCD) proteins play a key role by recognizing double-strand breaks in the DNA and initiating recombination events at the site of the Chi sequence, which is a hotspot for homologous recombination in E. coli (crossover hot spot instigator).80–82 Additionally, RecBCD proteins assist in loading the Recombinase A (RecA) protein onto single-stranded DNA, thereby initiating strand invasion and subsequent recombination events.81,83,84 The backtracking action of RNA polymerase upon ppGpp binding has been identified as being involved in double-strand break repair in E. coli upon exposure to the antibiotic phleomycin. Phleomycin sensitizes ppGpp null mutants and RNA polymerase Site 1 mutants similarly, suggesting that ppGpp binding to Site 1 of RNA polymerase could be involved in mending double-strand breaks.85 Double-strand break-induced error-prone repair processes in the presence of ppGpp might help bacteria adapt to environmental stresses.86 In E. coli, ppGpp and pppGpp inhibit replication by binding directly to DnaG, a primase essential for replication elongation.80,87–89 Additionally, in vitro and in vivo experiments show that ppGpp inhibits the promoter of dnaA, downregulating its transcription and consequently inhibiting replication initiation.18,19 This allows cells to take some time to repair the damaged genome and restore the normal functions upon encountering favorable conditions. Studies have shown that (p)ppGpp induction using serine hydroxamate leads to the accumulation of single stranded DNA (ssDNA) of plasmid pHV16101-1 in B. subtilis. This increased ssDNA accumulation occurs because (p)ppGpp binds to primase DnaG and inhibits its activity during the replication process.15 Furthermore, (p)ppGpp synthesized during UV-induced DNA damage stress prevents replication-transcription conflicts by mediating replication inhibition at lesion sites.80 Recombinase FOR (RecFOR) proteins are another set of recombination proteins involved in repairing gapped single-strand breaks and plasmid recombination events by loading RecA at these sites. RuvABC is a Holliday junction-specific resolvase that resolves harmful recombination intermediates formed during UV irradiation in E. coli and its absence causes cell death. However, in the absence of Ruv proteins, increased levels of (p)ppGpp rescue cells from death upon UV exposure.80 RecG is another helicase/resolvase involved in the resolution of Holliday junction intermediates and other recombination intermediates not resolved by Ruv proteins. RecG also plays a role in replication fork progression by mediating (p)ppGpp-dependent modulation of RNA polymerase.90 The binding of (p)ppGpp to RNA polymerase destabilizes stalled RNA polymerases at UV lesion sites and promotes RecFOR-mediated loading of RecA, thereby activating fork regression. Such activation promotes lesion bypass by translesion polymerases, thus avoiding strand breaks but resulting in mutagenesis and increased survival.91 When cells are exposed to phleomycin, double-strand breaks are induced in the genome; ppGpp, together with UvrD, aids backtracking of RNA polymerase, which assists in double-strand break repair. The RecA protein facilitates the double-strand break repair mechanism.85 Also, (p)ppGpp might promote mutagenic double-strand break repair during stress, which requires both homologous recombination repair proteins and SOS response proteins such as LexA, RecA, RecB, RecC, RuvA, RuvB, and RuvC.92 Additionally, in the mutagenic double-strand break repair pathway, ppGpp mediates the regulation of sigma S protein during starvation or stationary phase through the upregulation of error-prone polymerases pol IV and pol V, which aid in mutagenic DNA break repair.93 Sigma E, another stress response protein activated by ppGpp, promotes spontaneous breakage of DNA. It has been reported that Sigma E is essential for both double-strand break repair and stress-induced mutagenesis.94 Therefore, (p)ppGpp might play a role in homologous recombination pathway by regulating expression of recombination repair proteins that might help restore genome integrity. Upon exposure to certain antibiotics like phleomycin or ciprofloxacin, (p)ppGpp is also shown to promote mutagenic double-strand break repair leading to a compromised genome.

ppGpp is required for an efficient SOS response

UV radiation in E. coli induces single-strand breaks, triggering the SOS response. This response activates the cleavage of LexA protein by RecA, leading to the derepression of genes typically inhibited by LexA.95,96 The gene products of these derepressed genes are involved in repairing DNA damage and restoring genome stability. Although the SOS response aims to restore the genome, severe or prolonged DNA damage can result in mutagenesis of the genomic landscape.97–99 The SOS response in E. coli involves a series of sequential events,100 engaging approximately fifty genes, including lexA, recA, polII, polIV (DinB), polV (umuCD), and sulA. Studies have shown that the stringent response induces genes such as recA, ruvA, and umuD, whose gene products also function in the SOS response (Fig. 1).11,101 Furthermore, deletion mutants of relA or spoT display a delayed SOS response in E. coli.100 The control of ppGpp synthesis by the RelA protein during stress suggests a potential overlapping role of (p)ppGpp in the SOS and stringent responses. Recent findings from Rosenberg’s group identified that ppGpp binding to Site 1 of RNA polymerase is crucial for the SOS response that promotes CPX-induced mutagenesis.79 Additionally, research by Nudler’s group identified that ppGpp binding to Site 1 of RNA polymerase facilitates nucleotide excision repair (NER), the failure of which renders bacterial cells sensitive to UV and other genotoxic agents, namely NFZ and 4NQO.50 Therefore, (p)ppGpp binding to RNA polymerase at Site 1 is essential for (i) the nucleotide excision repair pathway, which serves as the first line of defense against DNA damage induced by UV light, and (ii) an efficient SOS response during ciprofloxacin-induced mutagenesis. If the nucleotide excision repair pathway fails to restore genomic integrity, an SOS response is triggered in UV-exposed cells. However, whether the induction of the SOS response during UV-induced DNA repair also requires (p)ppGpp remains an open question. Nonetheless, the role of (p)ppGpp in inducing the SOS response appears to be crucial for ciprofloxacin-induced mutagenesis, which contributes to antibiotic resistance in bacteria.

Stress-induced mutagenesis

Stress-induced mutagenesis involves cells sensing various growth-limiting factors in the environment and,102 in turn, activating generalized stress response proteins, such as alternative sigma factors, SOS response proteins, and other DNA repair proteins, including a specific set of error-prone polymerases that induce mutations in the genome. Although this pathway compromises genome integrity, it offers the advantage of increased cell survival. In stress-induced mutagenesis, (p)ppGpp downregulates mismatch repair proteins and high-fidelity polymerases, which is necessary for bacterial adaptation and survival against antibiotics.49,103 ppGpp and DksA promote the translation and stabilization of Sigma S protein, which subsequently upregulates the transcription of small RNAs DsrA and ArcZ and also the IraP protein.104 The small RNA DsrA enhances rpoS messenger RNA (mRNA) transcription by binding to its inhibitory stem-loop structure in the 5′-UTR and prevents rpoS mRNA degradation by RNase E,105 while the IraP protein stabilizes RpoS protein expression. This upregulation of RpoS, a global regulator of the general stress response, induces a switch from high-fidelity polymerases to error-prone polymerases responsible for stress-induced mutagenesis and survival.106 Therefore, (p)ppGpp is a master regulator of stress-induced mutagenesis pathway without which bacterial cells might succumb to death upon exposure to stress conditions including DNA damaging agents and antibiotics.

CPX-induced mutagenesis and bacterial survival against fluoroquinolone antibiotics as persisters and gamblers

CPX is a fluoroquinolone antibiotic that binds to topoisomerase II and induces strand breaks.79 At minimal antibiotic concentration of CPX, around 20% of the cell subpopulation shows an increased number of mutations upon survival against this antibiotic. The Rosenberg group identified that in this subpopulation of bacteria, termed gamblers, cells risk genome mutability compared to the rest of the population.77 During this process, CPX-induced strand breaks initiate the SOS response, which leads to increased reactive oxygen species within the cells due to impaired aerobic respiration or electron transport chain, triggering the stringent response.77 This is followed by the concerted action of (p)ppGpp and DksA, favoring RpoS activation and the expression of error-prone polymerases as observed in stress-induced mutagenesis. Fluorescent cell sorting experiments identified that the gambler subpopulation of bacteria exhibits an active general stress response. The sigma S active gambler cell subpopulation can generate 400-fold more mutants compared to the sigma S inactive population upon exposure to CPX.77,79 This survival is dependent on the adaptive mutations facilitated by DNA repair pathways that rely on (p)ppGpp. The absence of the stringent response-induced (p)ppGpp, leads to bacterial cell death upon treatment with fluoroquinolone antibiotics. Biochemical and genetic studies have shown that the binding of ppGpp at two distinct sites in the beta subunit of RNA polymerase is essential for this mutagenesis and survival mechanism. While binding of ppGpp to Site 1 is essential for the SOS DNA-damage response that aids in the backtracking of RNA polymerase during elongation, the binding of ppGpp along with DksA to Site 2 on RNA polymerase initiates transcription by sigma S (σS), a global regulator of the general stress response or stringent response. Stringent cells give rise to a higher number of AmpR and RifR mutants compared to stringent off cells. (p)ppGpp binding-mediated backtracking of RNA polymerase also leads to the pausing of RecBCD nuclease activity on the double-strand break, ensuring the loading of RecA on ssDNA, forming a RecA-activated nucleoprotein filament that induces the SOS response and subsequent double-strand break repair. In the presence of (p)ppGpp, Sigma S protein, together with recombination proteins such as RecA, RecBCD, RuvC, polIV, polV, and polII, aids in this mutagenesis process via mutagenic double-strand break repair. It should be noted that CPX-induced mutagenesis occurs at highly transcribed regions of the genome,79 associated with higher occupancy of RNA polymerase. Therefore, RNA polymerase and ppGpp are crucial to CPX-induced mutagenesis that occurs during transcription in bacteria, aiding the survival of the gambler subpopulation (Fig. 1).107

Antibiotic persistence in the presence of the minimal inhibitory concentration of ofloxacin,27 another fluoroquinolone antibiotic, has been shown to induce membrane depolarization in a subpopulation of cells that exhibit increased expression of the toxin HokB. The Obg protein, a universally conserved GTPase found in bacteria, has been identified to trigger persistence by inducing HokB protein expression, a process that requires (p)ppGpp (Fig. 1).108 Moreover, the ObgE protein has also been identified to function as a checkpoint regulator of replication. Genetic studies indicated that ObgE acts in conjunction with RecA and RecB repair proteins to prevent strand breaks and fork regression during replication arrest upon exposure to replication inhibitors or during the stringent response.109,110 However, the in vivo role of (p)ppGpp binding to ObgE in resolving the replication fork conflicts that might arise during the stringent response is yet to be studied. While several factors affect persister formation in bacteria, the (p)ppGpp signaling molecule plays a significant role in persister formation in most bacterial species, although there are some exceptions.111 The mechanism of Obg-mediated antibiotic persistence in the presence of (p)ppGpp is not yet completely understood. Additionally, it remains unexplored whether the gambler subpopulation and antibiotic persister subpopulation arise during exposure to CPX within the host, where the concentration of the antibiotic might vary in different tissues of the body.112–117 It should be noted that (p)ppGpp levels increase in human and mouse gut microbes during the fasting phase,118 which might enhance adaptive mutations and aid in the survival of antibiotic-resistant microbes, including persisters and gamblers.28 It is intriguing to investigate if the gambler subpopulation carrying adaptive mutations can subsequently multiply into an antibiotic-resistant population upon prolonged exposure to the minimal antibiotic concentration of CPX. Since (p)ppGpp is involved in both gambler cell and antibiotic persister cell formation in the presence of fluoroquinolones,119 ppGpp could potentially serve as a link that connects DNA repair pathways to bacterial survival against antibiotics (Fig. 1).

Limitations

It should be noted that (p)ppGpp independent mechanisms of antibiotic resistance development in bacteria are not discussed in this review.

Conclusions

The stress signaling molecule (p)ppGpp primarily binds to RNA polymerase, inducing backtracking upon encountering DNA lesions. This interaction promotes nucleotide excision repair (NER) and the Save our Soul response by recruiting repair proteins. (p)ppGpp also regulates proteins belonging to the homologous recombination repair pathway that help maintain genome integrity upon exposure to DNA damaging agents. Consequently, prolonged stress may favor mutagenic repair pathways that involve downregulation of mismatch repair proteins, thereby compromising genomic integrity. Stress-induced mutagenesis in the presence of antibiotics like ciprofloxacin (CPX), leads to adaptive mutations in the genome potentially passing antibiotic resistance to successive generations. The involvement of several DNA repair pathways discussed above underscores the complex interplay between (p)ppGpp-mediated DNA repair pathways and antibiotic resistance. Understanding these regulatory mechanisms is essential for developing effective strategies to combat antibiotic resistance.

Declarations

Acknowledgement

The author is thankful to Dr. John J Wyrick (Washington State University), Dr. Kathiresan Selvam (Washington State University) and other Wyrick lab members for their help, support and useful comments on this review. The author would like to acknowledge all the authors whose work was not cited.

Funding

SS is supported by grants from National Institute of Environmental Health Sciences R01ES028698, R01ES032814, and R21ES035139 awarded to Dr. John J Wyrick, Washington State University.

Conflict of interest

None.

Authors’ contributions

SS is the sole author of the manuscript.

References

  1. Potrykus K, Cashel M. p)ppGpp: still magical?. Annu Rev Microbiol 2008;62:35-51 View Article PubMed/NCBI
  2. Cashel M, Gallant J. Two compounds implicated in the function of the RC gene of Escherichia coli. Nature 1969;221(5183):838-841 View Article PubMed/NCBI
  3. Salzer A, Wolz C. Role of (p)ppGpp in antibiotic resistance, tolerance, persistence and survival in Firmicutes. Microlife 2023;4:uqad009 View Article PubMed/NCBI
  4. Kriel A, Bittner AN, Kim SH, Liu K, Tehranchi AK, Zou WY, et al. Direct regulation of GTP homeostasis by (p)ppGpp: a critical component of viability and stress resistance. Mol Cell 2012;48(2):231-241 View Article PubMed/NCBI
  5. Bittner AN, Kriel A, Wang JD. Lowering GTP level increases survival of amino acid starvation but slows growth rate for Bacillus subtilis cells lacking (p)ppGpp. J Bacteriol 2014;196(11):2067-2076 View Article PubMed/NCBI
  6. Anderson BW, Hao A, Satyshur KA, Keck JL, Wang JD. Molecular Mechanism of Regulation of the Purine Salvage Enzyme XPRT by the Alarmones pppGpp, ppGpp, and pGpp. J Mol Biol 2020;432(14):4108-4126 View Article PubMed/NCBI
  7. Anderson BW, Schumacher MA, Yang J, Turdiev A, Turdiev H, Schroeder JW, et al. The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus. Nucleic Acids Res 2022;50(2):847-866 View Article PubMed/NCBI
  8. Sivapragasam S, Deochand DK, Meariman JK, Grove A. The Stringent Response Induced by Phosphate Limitation Promotes Purine Salvage in Agrobacterium fabrum. Biochemistry 2017;56(43):5831-5843 View Article PubMed/NCBI
  9. Sivapragasam S, Grove A. Streptomyces coelicolor XdhR is a direct target of (p)ppGpp that controls expression of genes encoding xanthine dehydrogenase to promote purine salvage. Mol Microbiol 2016;100(4):701-718 View Article PubMed/NCBI
  10. Sivapragasam S, Ghosh A, Kumar S, Johnson DT, Grove A. Similar solutions to a common challenge: regulation of genes encoding Ralstonia solanacearum xanthine dehydrogenase. FEMS Microbiol Lett 2021;368(4):fnab022 View Article PubMed/NCBI
  11. Durfee T, Hansen AM, Zhi H, Blattner FR, Jin DJ. Transcription profiling of the stringent response in Escherichia coli. J Bacteriol 2008;190(3):1084-1096 View Article PubMed/NCBI
  12. Traxler MF, Summers SM, Nguyen HT, Zacharia VM, Hightower GA, Smith JT, et al. The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli. Mol Microbiol 2008;68(5):1128-1148 View Article PubMed/NCBI
  13. Barker MM, Gaal T, Josaitis CA, Gourse RL. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol 2001;305(4):673-688 View Article PubMed/NCBI
  14. Barker MM, Gaal T, Gourse RL. Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J Mol Biol 2001;305(4):689-702 View Article PubMed/NCBI
  15. Wang JD, Sanders GM, Grossman AD. Nutritional control of elongation of DNA replication by (p)ppGpp. Cell 2007;128(5):865-875 View Article PubMed/NCBI
  16. Diez S, Ryu J, Caban K, Gonzalez RL, Dworkin J. The alarmones (p)ppGpp directly regulate translation initiation during entry into quiescence. Proc Natl Acad Sci U S A 2020;117(27):15565-15572 View Article PubMed/NCBI
  17. Mitkevich VA, Ermakov A, Kulikova AA, Tankov S, Shyp V, Soosaar A, et al. Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP, GTP, or ppGpp. J Mol Biol 2010;402(5):838-846 View Article PubMed/NCBI
  18. Chiaramello AE, Zyskind JW. Coupling of DNA replication to growth rate in Escherichia coli: a possible role for guanosine tetraphosphate. J Bacteriol 1990;172(4):2013-2019 View Article PubMed/NCBI
  19. Fernández-Coll L, Maciag-Dorszynska M, Tailor K, Vadia S, Levin PA, Szalewska-Palasz A, et al. The Absence of (p)ppGpp Renders Initiation of Escherichia coli Chromosomal DNA Synthesis Independent of Growth Rates. mBio 2020;11(2):e03223-19 View Article PubMed/NCBI
  20. Sanchez-Vazquez P, Dewey CN, Kitten N, Ross W, Gourse RL. Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase. Proc Natl Acad Sci U S A 2019;116(17):8310-8319 View Article PubMed/NCBI
  21. Lemke JJ, Durfee T, Gourse RL. DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade. Mol Microbiol 2009;74(6):1368-1379 View Article PubMed/NCBI
  22. Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol 2005;187(5):1591-1603 View Article PubMed/NCBI
  23. Loewen PC, Hu B, Strutinsky J, Sparling R. Regulation in the rpoS regulon of Escherichia coli. Can J Microbiol 1998;44(8):707-717 View Article PubMed/NCBI
  24. Wozniak KJ, Simmons LA. Bacterial DNA excision repair pathways. Nat Rev Microbiol 2022;20(8):465-477 View Article PubMed/NCBI
  25. Kamat A, Badrinarayanan A. SOS-independent bacterial DNA damage responses: diverse mechanisms, unifying function. Curr Opin Microbiol 2023;73:102323 View Article PubMed/NCBI
  26. Sánchez-Osuna M, Cortés P, Lee M, Smith AT, Barbé J, Erill I. Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes. Nucleic Acids Res 2021;49(19):11050-11066 View Article PubMed/NCBI
  27. Pacios O, Blasco L, Bleriot I, Fernandez-Garcia L, Ambroa A, López M, et al. p)ppGpp and Its Role in Bacterial Persistence: New Challenges. Antimicrob Agents Chemother 2020;64(10):e01283-20 View Article PubMed/NCBI
  28. Das B, Bhadra RK. p)ppGpp Metabolism and Antimicrobial Resistance in Bacterial Pathogens. Front Microbiol 2020;11:563944 View Article PubMed/NCBI
  29. Lans H, Hoeijmakers JHJ, Vermeulen W, Marteijn JA. The DNA damage response to transcription stress. Nat Rev Mol Cell Biol 2019;20(12):766-784 View Article PubMed/NCBI
  30. Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, et al. Structural basis for the initiation of eukaryotic transcription-coupled DNA repair. Nature 2017;551(7682):653-657 View Article PubMed/NCBI
  31. Adebali O, Sancar A, Selby CP. Mfd translocase is necessary and sufficient for transcription-coupled repair in Escherichia coli. J Biol Chem 2017;292(45):18386-18391 View Article PubMed/NCBI
  32. Adebali O, Chiou YY, Hu J, Sancar A, Selby CP. Genome-wide transcription-coupled repair in Escherichia coli is mediated by the Mfd translocase. Proc Natl Acad Sci U S A 2017;114(11):E2116-E2125 View Article PubMed/NCBI
  33. Mao P, Smerdon MJ, Roberts SA, Wyrick JJ. Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution. Proc Natl Acad Sci U S A 2016;113(32):9057-9062 View Article PubMed/NCBI
  34. Bharati BK, Gowder M, Zheng F, Alzoubi K, Svetlov V, Kamarthapu V, et al. Crucial role and mechanism of transcription-coupled DNA repair in bacteria. Nature 2022;604(7904):152-159 View Article PubMed/NCBI
  35. Nudler E. Transcription-coupled global genomic repair in E. coli. Trends Biochem Sci 2023;48(10):873-882 View Article PubMed/NCBI
  36. Martinez B, Bharati BK, Epshtein V, Nudler E. Pervasive Transcription-coupled DNA repair in E. coli. Nat Commun 2022;13(1):1702 View Article PubMed/NCBI
  37. Ho HN, van Oijen AM, Ghodke H. The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage. Nat Commun 2018;9(1):1570 View Article PubMed/NCBI
  38. Brugger C, Zhang C, Suhanovsky MM, Kim DD, Sinclair AN, Lyumkis D, et al. Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. Nat Commun 2020;11(1):3740 View Article PubMed/NCBI
  39. Ho HN, van Oijen AM, Ghodke H. Single-molecule imaging reveals molecular coupling between transcription and DNA repair machinery in live cells. Nat Commun 2020;11(1):1478 View Article PubMed/NCBI
  40. Ghodke H, Ho HN, van Oijen AM. Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair. Nat Commun 2020;11(1):1477 View Article PubMed/NCBI
  41. Selby CP, Lindsey-Boltz LA, Li W, Sancar A. Molecular Mechanisms of Transcription-Coupled Repair. Annu Rev Biochem 2023;92:115-144 View Article PubMed/NCBI
  42. Cohen SE, Lewis CA, Mooney RA, Kohanski MA, Collins JJ, Landick R, et al. Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proc Natl Acad Sci U S A 2010;107(35):15517-15522 View Article PubMed/NCBI
  43. George DL, Witkin EM. Slow excision repair in an mfd mutant of Escherichia coli B/r. Mol Gen Genet 1974;133(4):283-291 View Article PubMed/NCBI
  44. Epshtein V, Kamarthapu V, McGary K, Svetlov V, Ueberheide B, Proshkin S, et al. UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature 2014;505(7483):372-377 View Article PubMed/NCBI
  45. Nudler E. RNA polymerase backtracking in gene regulation and genome instability. Cell 2012;149(7):1438-1445 View Article PubMed/NCBI
  46. Roghanian M, Zenkin N, Yuzenkova Y. Bacterial global regulators DksA/ppGpp increase fidelity of transcription. Nucleic Acids Res 2015;43(3):1529-1536 View Article PubMed/NCBI
  47. Dutta D, Shatalin K, Epshtein V, Gottesman ME, Nudler E. Linking RNA polymerase backtracking to genome instability in E. coli. Cell 2011;146(4):533-543 View Article PubMed/NCBI
  48. Kamarthapu V, Epshtein V, Benjamin B, Proshkin S, Mironov A, Cashel M, et al. ppGpp couples transcription to DNA repair in E. coli. Science 2016;352(6288):993-996 View Article PubMed/NCBI
  49. Rasouly A, Nudler E. RNA polymerase and ppGpp deliver a one-two punch to antibiotics. Mol Cell 2023;83(8):1204-1205 View Article PubMed/NCBI
  50. Weaver JW, Proshkin S, Duan W, Epshtein V, Gowder M, Bharati BK, et al. Control of transcription elongation and DNA repair by alarmone ppGpp. Nat Struct Mol Biol 2023;30(5):600-607 View Article PubMed/NCBI
  51. Gourse RL, Chen AY, Gopalkrishnan S, Sanchez-Vazquez P, Myers A, Ross W. Transcriptional Responses to ppGpp and DksA. Annu Rev Microbiol 2018;72:163-184 View Article PubMed/NCBI
  52. Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, et al. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA. Mol Cell 2018;69(5):828-839.e5 View Article PubMed/NCBI
  53. Husain I, Van Houten B, Thomas DC, Abdel-Monem M, Sancar A. Effect of DNA polymerase I and DNA helicase II on the turnover rate of UvrABC excision nuclease. Proc Natl Acad Sci U S A 1985;82(20):6774-6778 View Article PubMed/NCBI
  54. Van Houten B, Gamper H, Hearst JE, Sancar A. Analysis of sequential steps of nucleotide excision repair in Escherichia coli using synthetic substrates containing single psoralen adducts. J Biol Chem 1988;263(32):16553-16560 View Article PubMed/NCBI
  55. Epshtein V. UvrD helicase: an old dog with a new trick: how one step backward leads to many steps forward. Bioessays 2015;37(1):12-19 View Article PubMed/NCBI
  56. Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, et al. RNA polymerase drives ribonucleotide excision DNA repair in E. coli. Cell 2023;186(11):2425-2437.e21 View Article PubMed/NCBI
  57. Li GM. Mechanisms and functions of DNA mismatch repair. Cell Res 2008;18(1):85-98 View Article PubMed/NCBI
  58. Burdett V, Baitinger C, Viswanathan M, Lovett ST, Modrich P. In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair. Proc Natl Acad Sci U S A 2001;98(12):6765-6770 View Article PubMed/NCBI
  59. Modrich P. Mechanisms in E. coli and Human Mismatch Repair (Nobel Lecture). Angew Chem Int Ed Engl 2016;55(30):8490-8501 View Article PubMed/NCBI
  60. Hao P, LeBlanc SJ, Case BC, Elston TC, Hingorani MM, Erie DA, et al. Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby. Proc Natl Acad Sci U S A 2020;117(30):17775-17784 View Article PubMed/NCBI
  61. Zhou H, Zhang L, Xu Q, Zhang L, Yu Y, Hua X. The mismatch repair system (mutS and mutL) in Acinetobacter baylyi ADP1. BMC Microbiol 2020;20(1):40 View Article PubMed/NCBI
  62. Glickman BW, Radman M. Escherichia coli mutator mutants deficient in methylation-instructed DNA mismatch correction. Proc Natl Acad Sci U S A 1980;77(2):1063-1067 View Article PubMed/NCBI
  63. Rydberg B. Bromouracil mutagenesis and mismatch repair in mutator strains of Escherichia coli. Mutat Res 1978;52(1):11-24 View Article PubMed/NCBI
  64. Lee H, Popodi E, Tang H, Foster PL. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc Natl Acad Sci U S A 2012;109(41):E2774-E2783 View Article PubMed/NCBI
  65. Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W. MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage. Mol Cell 2005;20(1):155-166 View Article PubMed/NCBI
  66. Putnam CD. Evolution of the methyl directed mismatch repair system in Escherichia coli. DNA Repair (Amst) 2016;38:32-41 View Article PubMed/NCBI
  67. Dao V, Modrich P. Mismatch-, MutS-, MutL-, and helicase II-dependent unwinding from the single-strand break of an incised heteroduplex. J Biol Chem 1998;273(15):9202-9207 View Article PubMed/NCBI
  68. Guarné A, Ramon-Maiques S, Wolff EM, Ghirlando R, Hu X, Miller JH, et al. Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair. EMBO J 2004;23(21):4134-4145 View Article PubMed/NCBI
  69. Feng G, Tsui HC, Winkler ME. Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells. J Bacteriol 1996;178(8):2388-2396 View Article PubMed/NCBI
  70. Harris RS, Feng G, Ross KJ, Sidhu R, Thulin C, Longerich S, et al. Mismatch repair protein MutL becomes limiting during stationary-phase mutation. Genes Dev 1997;11(18):2426-2437 View Article PubMed/NCBI
  71. Tsui HC, Feng G, Winkler ME. Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12. J Bacteriol 1997;179(23):7476-7487 View Article PubMed/NCBI
  72. Marinus MG. DNA Mismatch Repair. EcoSal Plus 2012;5(1) View Article PubMed/NCBI
  73. Bougdour A, Gottesman S. ppGpp regulation of RpoS degradation via anti-adaptor protein IraP. Proc Natl Acad Sci U S A 2007;104(31):12896-12901 View Article PubMed/NCBI
  74. Bougdour A, Cunning C, Baptiste PJ, Elliott T, Gottesman S. Multiple pathways for regulation of sigmaS (RpoS) stability in Escherichia coli via the action of multiple anti-adaptors. Mol Microbiol 2008;68(2):298-313 View Article PubMed/NCBI
  75. Merrikh H, Ferrazzoli AE, Lovett ST. Growth phase and (p)ppGpp control of IraD, a regulator of RpoS stability, in Escherichia coli. J Bacteriol 2009;191(24):7436-7446 View Article PubMed/NCBI
  76. Schroeder JW, Yeesin P, Simmons LA, Wang JD. Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2018;53(1):29-48 View Article PubMed/NCBI
  77. Pribis JP, García-Villada L, Zhai Y, Lewin-Epstein O, Wang AZ, Liu J, et al. Gamblers: An Antibiotic-Induced Evolvable Cell Subpopulation Differentiated by Reactive-Oxygen-Induced General Stress Response. Mol Cell 2019;74(4):785-800.e7 View Article PubMed/NCBI
  78. Bos J, Zhang Q, Vyawahare S, Rogers E, Rosenberg SM, Austin RH. Emergence of antibiotic resistance from multinucleated bacterial filaments. Proc Natl Acad Sci U S A 2015;112(1):178-183 View Article PubMed/NCBI
  79. Zhai Y, Minnick PJ, Pribis JP, Garcia-Villada L, Hastings PJ, Herman C, et al. ppGpp and RNA-polymerase backtracking guide antibiotic-induced mutable gambler cells. Mol Cell 2023;83(8):1298-1310.e4 View Article PubMed/NCBI
  80. Sinha AK, Løbner-Olesen A, Riber L. Bacterial Chromosome Replication and DNA Repair During the Stringent Response. Front Microbiol 2020;11:582113 View Article PubMed/NCBI
  81. Smith GR. How RecBCD enzyme and Chi promote DNA break repair and recombination: a molecular biologist’s view. Microbiol Mol Biol Rev 2012;76(2):217-228 View Article PubMed/NCBI
  82. Bianco PR, Kowalczykowski SC. The recombination hotspot Chi is recognized by the translocating RecBCD enzyme as the single strand of DNA containing the sequence 5′-GCTGGTGG-3′. Proc Natl Acad Sci U S A 1997;94(13):6706-6711 View Article PubMed/NCBI
  83. Shibata T, DasGupta C, Cunningham RP, Radding CM. Purified Escherichia coli recA protein catalyzes homologous pairing of superhelical DNA and single-stranded fragments. Proc Natl Acad Sci U S A 1979;76(4):1638-1642 View Article PubMed/NCBI
  84. Ogawa T, Wabiko H, Tsurimoto T, Horii T, Masukata H, Ogawa H. Characteristics of purified recA protein and the regulation of its synthesis in vivo. Cold Spring Harb Symp Quant Biol 1979;43(Pt 2):909-915 View Article PubMed/NCBI
  85. Sivaramakrishnan P, Sepúlveda LA, Halliday JA, Liu J, Núñez MAB, Golding I, et al. The transcription fidelity factor GreA impedes DNA break repair. Nature 2017;550(7675):214-218 View Article PubMed/NCBI
  86. Galhardo RS, Hastings PJ, Rosenberg SM. Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 2007;42(5):399-435 View Article PubMed/NCBI
  87. Rymer RU, Solorio FA, Tehranchi AK, Chu C, Corn JE, Keck JL, et al. Binding mechanism of metal⋅NTP substrates and stringent-response alarmones to bacterial DnaG-type primases. Structure 2012;20(9):1478-1489 View Article PubMed/NCBI
  88. Maciag M, Kochanowska M, Lyzeń R, Wegrzyn G, Szalewska-Pałasz A. ppGpp inhibits the activity of Escherichia coli DnaG primase. Plasmid 2010;63(1):61-67 View Article PubMed/NCBI
  89. Maciąg-Dorszyńska M, Szalewska-Pałasz A, Węgrzyn G. Different effects of ppGpp on Escherichia coli DNA replication in vivo and in vitro. FEBS Open Bio 2013;3:161-164 View Article PubMed/NCBI
  90. McGlynn P, Lloyd RG. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell 2000;101(1):35-45 View Article PubMed/NCBI
  91. Trautinger BW, Jaktaji RP, Rusakova E, Lloyd RG. RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol Cell 2005;19(2):247-258 View Article PubMed/NCBI
  92. Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, et al. Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 2012;338(6112):1344-1348 View Article PubMed/NCBI
  93. Rosenberg SM, Shee C, Frisch RL, Hastings PJ. Stress-induced mutation via DNA breaks in Escherichia coli: a molecular mechanism with implications for evolution and medicine. Bioessays 2012;34(10):885-892 View Article PubMed/NCBI
  94. Gibson JL, Lombardo MJ, Thornton PC, Hu KH, Galhardo RS, Beadle B, et al. The sigma(E) stress response is required for stress-induced mutation and amplification in Escherichia coli. Mol Microbiol 2010;77(2):415-430 View Article PubMed/NCBI
  95. Little JW. Mechanism of specific LexA cleavage: autodigestion and the role of RecA coprotease. Biochimie 1991;73(4):411-421 View Article PubMed/NCBI
  96. Little JW, Mount DW. The SOS regulatory system of Escherichia coli. Cell 1982;29(1):11-22 View Article PubMed/NCBI
  97. Patel M, Jiang Q, Woodgate R, Cox MM, Goodman MF. A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev Biochem Mol Biol 2010;45(3):171-184 View Article PubMed/NCBI
  98. Walker GC. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol Rev 1984;48(1):60-93 View Article PubMed/NCBI
  99. Fuchs RP, Fujii S. Translesion DNA synthesis and mutagenesis in prokaryotes. Cold Spring Harb Perspect Biol 2013;5(12):a012682 View Article PubMed/NCBI
  100. Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ. The SOS system: A complex and tightly regulated response to DNA damage. Environ Mol Mutagen 2019;60(4):368-384 View Article PubMed/NCBI
  101. Kaushik V, Tiwari M, Tiwari V. Interaction of RecA mediated SOS response with bacterial persistence, biofilm formation, and host response. Int J Biol Macromol 2022;217:931-943 View Article PubMed/NCBI
  102. Zhu M, Mu H, Dai X. Integrated control of bacterial growth and stress response by (p)ppGpp in Escherichia coli: A seesaw fashion. iScience 2024;27(2):108818 View Article PubMed/NCBI
  103. Qi W, Jonker MJ, de Leeuw W, Brul S, Ter Kuile BH. Role of RelA-synthesized (p)ppGpp and ROS-induced mutagenesis in de novo acquisition of antibiotic resistance in E. coli. iScience 2024;27(4):109579 View Article PubMed/NCBI
  104. Girard ME, Gopalkrishnan S, Grace ED, Halliday JA, Gourse RL, Herman C. DksA and ppGpp Regulate the σ(S) Stress Response by Activating Promoters for the Small RNA DsrA and the Anti-Adapter Protein IraP. J Bacteriol 2018;200(2):e00463-17 View Article PubMed/NCBI
  105. McCullen CA, Benhammou JN, Majdalani N, Gottesman S. Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation. J Bacteriol 2010;192(21):5559-5571 View Article PubMed/NCBI
  106. Ponder RG, Fonville NC, Rosenberg SM. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol Cell 2005;19(6):791-804 View Article PubMed/NCBI
  107. García-Villada L, Degtyareva NP, Brooks AM, Goldberg JB, Doetsch PW. A role for the stringent response in ciprofloxacin resistance in Pseudomonas aeruginosa. Sci Rep 2024;14(1):8598 View Article PubMed/NCBI
  108. Verstraeten N, Knapen WJ, Kint CI, Liebens V, Van den Bergh B, Dewachter L, et al. Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance. Mol Cell 2015;59(1):9-21 View Article PubMed/NCBI
  109. Foti JJ, Schienda J, Sutera VA, Lovett ST. A bacterial G protein-mediated response to replication arrest. Mol Cell 2005;17(4):549-560 View Article PubMed/NCBI
  110. Kreuzer KN. DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harb Perspect Biol 2013;5(11):a012674 View Article PubMed/NCBI
  111. Bhaskar A, De Piano C, Gelman E, McKinney JD, Dhar N. Elucidating the role of (p)ppGpp in mycobacterial persistence against antibiotics. IUBMB Life 2018;70(9):836-844 View Article PubMed/NCBI
  112. Cars O. Pharmacokinetics of antibiotics in tissues and tissue fluids: a review. Scand J Infect Dis Suppl 1990;74:23-33 View Article PubMed/NCBI
  113. Finazzi S, Luci G, Olivieri C, Langer M, Mandelli G, Corona A, et al. Tissue Penetration of Antimicrobials in Intensive Care Unit Patients: A Systematic Review-Part I. Antibiotics (Basel) 2022;11(9):1164 View Article PubMed/NCBI
  114. van Os W, Zeitlinger M. Predicting Antimicrobial Activity at the Target Site: Pharmacokinetic/Pharmacodynamic Indices versus Time-Kill Approaches. Antibiotics (Basel) 2021;10(12):1485 View Article PubMed/NCBI
  115. Day NJ, Santucci P, Gutierrez MG. Host cell environments and antibiotic efficacy in tuberculosis. Trends Microbiol 2024;32(3):270-279 View Article PubMed/NCBI
  116. Kiem S, Schentag JJ. Interpretation of antibiotic concentration ratios measured in epithelial lining fluid. Antimicrob Agents Chemother 2008;52(1):24-36 View Article PubMed/NCBI
  117. Tetro N, Moushaev S, Rubinchik-Stern M, Eyal S. The Placental Barrier: the Gate and the Fate in Drug Distribution. Pharm Res 2018;35(4):71 View Article PubMed/NCBI
  118. Ontai-Brenning A, Hamchand R, Crawford JM, Goodman AL. Gut microbes modulate (p)ppGpp during a time-restricted feeding regimen. mBio 2023;14(6):e0190723 View Article PubMed/NCBI
  119. Ruiz J. Unusual and Unconsidered Mechanisms of Bacterial Resilience and Resistance to Quinolones. Life (Basel) 2024;14(3):383 View Article PubMed/NCBI

Copyright © 2024 Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial 4.0 License (CC BY-NC 4.0), permitting all non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

  • © 2024 Xia & He Publishing Inc.
  • Total visits : 2750579
  • Visits today : 1872