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Hallgren J, Jonas K. Nutritional control of bacterial DNA replication. Curr Opin Microbiol 2024; 77:102403. [PMID: 38035509 DOI: 10.1016/j.mib.2023.102403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023]
Abstract
All cells must ensure precise regulation of DNA replication initiation in coordination with growth rate and in response to nutrient availability. According to a long-standing model, DNA replication initiation is tightly coupled to cell mass increase in bacteria. Despite controversies regarding this model, recent studies have provided additional support of this idea. The exact molecular mechanisms linking cell growth with DNA replication under different nutrient conditions remain elusive. However, recent studies in Caulobacter crescentus and Escherichia coli have provided insights into the regulation of DNA replication initiation in response to starvation. These mechanisms include the starvation-dependent regulation of DnaA abundance as well as mechanisms involving the small signaling molecule (p)ppGpp. In this review, we discuss these mechanisms in the context of previous findings. We highlight species-dependent similarities and differences and consider the precise growth conditions, in which the different mechanisms are active.
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Affiliation(s)
- Joel Hallgren
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | - Kristina Jonas
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden.
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2
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Knöppel A, Broström O, Gras K, Elf J, Fange D. Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle. Proc Natl Acad Sci U S A 2023; 120:e2213795120. [PMID: 37220276 PMCID: PMC10235992 DOI: 10.1073/pnas.2213795120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 04/07/2023] [Indexed: 05/25/2023] Open
Abstract
Escherichia coli coordinates replication and division cycles by initiating replication at a narrow range of cell sizes. By tracking replisomes in individual cells through thousands of division cycles in wild-type and mutant strains, we were able to compare the relative importance of previously described control systems. We found that accurate triggering of initiation does not require synthesis of new DnaA. The initiation size increased only marginally as DnaA was diluted by growth after dnaA expression had been turned off. This suggests that the conversion of DnaA between its active ATP- and inactive ADP-bound states is more important for initiation size control than the total free concentration of DnaA. In addition, we found that the known ATP/ADP converters DARS and datA compensate for each other, although the removal of them makes the initiation size more sensitive to the concentration of DnaA. Only disruption of the regulatory inactivation of DnaA mechanism had a radical impact on replication initiation. This result was corroborated by the finding that termination of one round of replication correlates with the next initiation at intermediate growth rates, as would be the case if RIDA-mediated conversion from DnaA-ATP to DnaA-ADP abruptly stops at termination and DnaA-ATP starts accumulating.
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Affiliation(s)
- Anna Knöppel
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala75124, Sweden
| | - Oscar Broström
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala75124, Sweden
| | - Konrad Gras
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala75124, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala75124, Sweden
| | - David Fange
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala75124, Sweden
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3
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Wang X, Wang J, Liu SY, Guo JS, Fang F, Chen YP, Yan P. Mechanisms of survival mediated by the stringent response in Pseudomonas aeruginosa under environmental stress in drinking water systems: Nitrogen deficiency and bacterial competition. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130941. [PMID: 36758433 DOI: 10.1016/j.jhazmat.2023.130941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Pseudomonas aeruginosa causes public health problems in drinking water systems. This study investigated the potential role of the stringent response in regulating the adaptive physiological metabolic behaviors of P. aeruginosa to low nitrogen stress and bacterial competition in drinking water systems. The results indicated that guanosine tetraphosphate (ppGpp) concentrations in P. aeruginosa increased to 135.5 pmol/g SS under short-term nitrogen deficiency. Meanwhile, the expression levels of the ppGpp synthesis genes (ppx, relA) and degradation gene (spoT) were upregulated by 37.0% and downregulated by 26.8%, respectively, indicating that the stringent response was triggered. The triggered stringent response inhibited the growth of P. aeruginosa and enhanced the metabolic activity of P. aeruginosa to adapt to nutrient deprivation. The interspecific competition significantly affected the regulation of the stringent response in P. aeruginosa. During short-term nitrogen deficiency, the extracellular polymeric substances concentration of P. aeruginosa decreased significantly, leading to desorption and diffusion of attached bacteria and increased ecological risks. The regulatory effect of stringent response on P. aeruginosa gradually weakened under long-term nitrogen deficiency. However, the expression of pathogenic genes (nalD/PA3310) and flagellar assembly genes (fliC) in P. aeruginosa was upregulated by the stringent response, which increased the risk of disease.
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Affiliation(s)
- Xu Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Jing Wang
- Chongqing Jianzhu College, Chongqing 400072, China
| | - Shao-Yang Liu
- Department of Chemistry and Physics, Troy University, Troy, AL 36082, USA
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China.
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Abstract
As rapidly growing bacteria begin to exhaust essential nutrients, they enter a state of reduced growth, ultimately leading to stasis or quiescence. Investigation of the response to nutrient limitation has focused largely on the consequences of amino acid starvation, known as the "stringent response." Here, an uncharged tRNA in the A-site of the ribosome stimulates the ribosome-associated protein RelA to synthesize the hyperphosphorylated guanosine nucleotides (p)ppGpp that mediate a global slowdown of growth and biosynthesis. Investigations of the stringent response typically employ experimental methodologies that rapidly stimulate (p)ppGpp synthesis by abruptly increasing the fraction of uncharged tRNAs, either by explicit amino starvation or by inhibition of tRNA charging. Consequently, these methodologies inhibit protein translation, thereby interfering with the cellular pathways that respond to nutrient limitation. Thus, complete and/or rapid starvation is a problematic experimental paradigm for investigating bacterial responses to physiologically relevant nutrient-limited states.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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5
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Homologs of the Escherichia coli F Element Protein TraR, Including Phage Lambda Orf73, Directly Reprogram Host Transcription. mBio 2022; 13:e0095222. [PMID: 35583320 PMCID: PMC9239242 DOI: 10.1128/mbio.00952-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacterial cells and their associated plasmids and bacteriophages encode numerous small proteins of unknown function. One example, the 73-amino-acid protein TraR, is encoded by the transfer operon of the conjugative F plasmid of Escherichia coli. TraR is a distant homolog of DksA, a protein found in almost all proteobacterial species that is required for ppGpp to regulate transcription during the stringent response. TraR and DksA increase or decrease transcription initiation depending on the kinetic features of the promoter by binding directly to RNA polymerase without binding to DNA. Unlike DksA, whose full activity requires ppGpp as a cofactor, TraR is fully active by itself and unaffected by ppGpp. TraR belongs to a family of divergent proteins encoded by proteobacterial bacteriophages and other mobile elements. Here, we experimentally addressed whether other members of the TraR family function like the F element-encoded TraR. Purified TraR and all 5 homologs that were examined bound to RNA polymerase, functioned at lower concentrations than DksA, and complemented a dksA-null strain for growth on minimal medium. One of the homologs, λ Orf73, encoded by bacteriophage lambda, was examined in greater detail. λ Orf73 slowed host growth and increased phage burst size. Mutational analysis suggested that λ Orf73 and TraR have a similar mechanism for inhibiting rRNA and r-protein promoters. We suggest that TraR and its homologs regulate host transcription to divert cellular resources to phage propagation or conjugation without induction of ppGpp and a stringent response.
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Behrmann MS, Perera HM, Hoang JM, Venkat TA, Visser BJ, Bates D, Trakselis MA. Targeted chromosomal Escherichia coli:dnaB exterior surface residues regulate DNA helicase behavior to maintain genomic stability and organismal fitness. PLoS Genet 2021; 17:e1009886. [PMID: 34767550 PMCID: PMC8612530 DOI: 10.1371/journal.pgen.1009886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/24/2021] [Accepted: 10/18/2021] [Indexed: 12/05/2022] Open
Abstract
Helicase regulation involves modulation of unwinding speed to maintain coordination of DNA replication fork activities and is vital for replisome progression. Currently, mechanisms for helicase regulation that involve interactions with both DNA strands through a steric exclusion and wrapping (SEW) model and conformational shifts between dilated and constricted states have been examined in vitro. To better understand the mechanism and cellular impact of helicase regulation, we used CRISPR-Cas9 genome editing to study four previously identified SEW-deficient mutants of the bacterial replicative helicase DnaB. We discovered that these four SEW mutations stabilize constricted states, with more fully constricted mutants having a generally greater impact on genomic stress, suggesting a dynamic model for helicase regulation that involves both excluded strand interactions and conformational states. These dnaB mutations result in increased chromosome complexities, less stable genomes, and ultimately less viable and fit strains. Specifically, dnaB:mut strains present with increased mutational frequencies without significantly inducing SOS, consistent with leaving single-strand gaps in the genome during replication that are subsequently filled with lower fidelity. This work explores the genomic impacts of helicase dysregulation in vivo, supporting a combined dynamic regulatory mechanism involving a spectrum of DnaB conformational changes and relates current mechanistic understanding to functional helicase behavior at the replication fork. DNA replication is a vital biological process, and the proteins involved are structurally and functionally conserved across all domains of life. As our fundamental knowledge of genes and genetics grows, so does our awareness of links between acquired genetic mutations and disease. Understanding how genetic material is replicated accurately and efficiently and with high fidelity is the foundation to identifying and solving genome-based diseases. E. coli are model organisms, containing core replisome proteins, but lack the complexity of the human replication system, making them ideal for investigating conserved replisome behaviors. The helicase enzyme acts at the forefront of the replication fork to unwind the DNA helix and has also been shown to help coordinate other replisome functions. In this study, we examined specific mutations in the helicase that have been shown to regulate its conformation and speed of unwinding. We investigate how these mutations impact the growth, fitness, and cellular morphology of bacteria with the goal of understanding how helicase regulation mechanisms affect an organism’s ability to survive and maintain a stable genome.
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Affiliation(s)
- Megan S. Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, United States of America
| | - Himasha M. Perera
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, United States of America
| | - Joy M. Hoang
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, United States of America
| | - Trisha A. Venkat
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, United States of America
| | - Bryan J. Visser
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Bates
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael A. Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, United States of America
- * E-mail:
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7
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Campion C, Charbon G, Thomsen TT, Nielsen PE, Løbner-Olesen A. Antisense inhibition of the Escherichia coli NrdAB aerobic ribonucleotide reductase is bactericidal due to induction of DNA strand breaks. J Antimicrob Chemother 2021; 76:2802-2814. [PMID: 34450639 PMCID: PMC8521395 DOI: 10.1093/jac/dkab305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/16/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Antisense peptide nucleic acids (PNAs) constitute an alternative to traditional antibiotics, by their ability to silence essential genes. OBJECTIVES To evaluate the antibacterial effects of antisense PNA-peptide conjugates that target the gene encoding the alpha subunit (NrdA) of the Escherichia coli ribonucleotide reductase (RNR). METHODS Bacterial susceptibility of a series of NrdA-targeting PNAs was studied by MIC determination and time-kill analysis. Western-blot analysis, gene complementation and synergy with hydroxyurea were employed to determine the efficiency of NrdA-PNA antisense treatment. The effect on chromosome replication was addressed by determining the DNA synthesis rate, by flow cytometry analysis, by quantitative PCR and by fluorescence microscopy. The use of DNA repair mutants provided insight into the bactericidal action of NrdA-PNA. RESULTS Treatment with NrdA-PNA specifically inhibited growth of E. coli, as well as NrdA protein translation at 4 μM. Also, the DNA synthesis rate was reduced, preventing completion of chromosome replication and resulting in formation of double-stranded DNA breaks and cell death. CONCLUSIONS These data present subunits of the NrdAB RNR as a target for future antisense microbial agents and provide insight into the bacterial physiological response to RNR-targeting antimicrobials.
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Affiliation(s)
- Christopher Campion
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark.,Department of Biology, Faculty of Science, Section for Functional Genomics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Godefroid Charbon
- Department of Biology, Faculty of Science, Section for Functional Genomics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Thomas T Thomsen
- Department of Biology, Faculty of Science, Section for Functional Genomics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Henrik Harpestreng Vej 4A, 2100 Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark
| | - Anders Løbner-Olesen
- Department of Biology, Faculty of Science, Section for Functional Genomics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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8
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Charbon G, Frimodt-Møller J, Løbner-Olesen A. Arresting chromosome replication upon energy starvation in Escherichia coli. Curr Genet 2021; 67:877-882. [PMID: 34345967 PMCID: PMC8593061 DOI: 10.1007/s00294-021-01202-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 11/01/2022]
Abstract
Most organisms possess several cell cycle checkpoints to preserve genome stability in periods of stress. Upon starvation, the absence of chromosomal duplication in the bacterium Escherichia coli is ensured by holding off commencement of replication. During normal growth, accumulation of the initiator protein DnaA along with cell cycle changes in its activity, ensure that DNA replication starts only once per cell cycle. Upon nutrient starvation, the prevailing model is that an arrest in DnaA protein synthesis is responsible for the absence of initiation. Recent indications now suggest that DnaA degradation may also play a role. Here we comment on the implications of this potential new layer of regulation.
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Affiliation(s)
- Godefroid Charbon
- Department of Biology, University of Copenhagen, Ole Maløes Vej 5, 2200, Copenhagen N, Denmark.
| | - Jakob Frimodt-Møller
- Department of Biology, University of Copenhagen, Ole Maløes Vej 5, 2200, Copenhagen N, Denmark
| | - Anders Løbner-Olesen
- Department of Biology, University of Copenhagen, Ole Maløes Vej 5, 2200, Copenhagen N, Denmark.
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9
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Menikpurage IP, Woo K, Mera PE. Transcriptional Activity of the Bacterial Replication Initiator DnaA. Front Microbiol 2021; 12:662317. [PMID: 34140937 PMCID: PMC8203912 DOI: 10.3389/fmicb.2021.662317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
In bacteria, DnaA is the most conserved DNA replication initiator protein. DnaA is a DNA binding protein that is part of the AAA+ ATPase family. In addition to initiating chromosome replication, DnaA can also function as a transcription factor either as an activator or repressor. The first gene identified to be regulated by DnaA at the transcriptional levels was dnaA. DnaA has been shown to regulate genes involved in a variety of cellular events including those that trigger sporulation, DNA repair, and cell cycle regulation. DnaA's dual functions (replication initiator and transcription factor) is a potential mechanism for DnaA to temporally coordinate diverse cellular events with the onset of chromosome replication. This strategy of using chromosome replication initiator proteins as regulators of gene expression has also been observed in archaea and eukaryotes. In this mini review, we focus on our current understanding of DnaA's transcriptional activity in various bacterial species.
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Affiliation(s)
- Inoka P Menikpurage
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kristin Woo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Paola E Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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10
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Charbon G, Mendoza-Chamizo B, Campion C, Li X, Jensen PR, Frimodt-Møller J, Løbner-Olesen A. Energy Starvation Induces a Cell Cycle Arrest in Escherichia coli by Triggering Degradation of the DnaA Initiator Protein. Front Mol Biosci 2021; 8:629953. [PMID: 34055872 PMCID: PMC8155583 DOI: 10.3389/fmolb.2021.629953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/26/2021] [Indexed: 12/16/2022] Open
Abstract
During steady-state Escherichia coli growth, the amount and activity of the initiator protein, DnaA, controls chromosome replication tightly so that initiation only takes place once per origin in each cell cycle, regardless of growth conditions. However, little is known about the mechanisms involved during transitions from one environmental condition to another or during starvation stress. ATP depletion is one of the consequences of long-term carbon starvation. Here we show that DnaA is degraded in ATP-depleted cells. A chromosome replication initiation block is apparent in such cells as no new rounds of DNA replication are initiated while replication events that have already started proceed to completion.
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Affiliation(s)
- Godefroid Charbon
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaobo Li
- National Food Institute, Microbial Biotechnology and Biorefining, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Ruhdal Jensen
- National Food Institute, Microbial Biotechnology and Biorefining, Technical University of Denmark, Kongens Lyngby, Denmark
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11
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When the metabolism meets the cell cycle in bacteria. Curr Opin Microbiol 2021; 60:104-113. [PMID: 33677348 DOI: 10.1016/j.mib.2021.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022]
Abstract
Nutrients availability is the sinews of the war for single microbial cells, driving growth and cell cycle progression. Therefore, coordinating cellular processes with nutrients availability is crucial, not only to survive upon famine or fluctuating conditions but also to rapidly thrive and colonize plentiful environments. While metabolism is traditionally seen as a set of chemical reactions taking place in cells to extract energy and produce building blocks from available nutrients, numerous connections between metabolic pathways and cell cycle phases have been documented. The few regulatory systems described at the molecular levels show that regulation is mediated either by a second messenger molecule or by a metabolite and/or a metabolic enzyme. In the latter case, a secondary moonlighting regulatory function evolved independently of the primary catalytic function of the enzyme. In this review, we summarize our current understanding of the complex cross-talks between metabolism and cell cycle in bacteria.
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12
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Riber L, Løbner‐Olesen A. Inhibition of Escherichia coli chromosome replication by rifampicin treatment or during the stringent response is overcome by de novo DnaA protein synthesis. Mol Microbiol 2020; 114:906-919. [PMID: 32458540 PMCID: PMC7818497 DOI: 10.1111/mmi.14531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 12/15/2022]
Abstract
Initiation of Escherichia coli chromosome replication is controlled by the DnaA initiator protein. Both rifampicin-mediated inhibition of transcription and ppGpp-induced changes in global transcription stops replication at the level of initiation. Here, we show that continued DnaA protein synthesis allows for replication initiation both during the rifampicin treatment and during the stringent response when the ppGpp level is high. A reduction in or cessation of de novo DnaA synthesis, therefore, causes the initiation arrest in both cases. In accordance with this, inhibition of translation with chloramphenicol also stops initiations. The initiation arrest caused by rifampicin was faster than that caused by chloramphenicol, despite of the latter inhibiting DnaA accumulation immediately. During chloramphenicol treatment transcription is still ongoing and we suggest that transcriptional events in or near the origin, that is, transcriptional activation, can allow for a few extra initiations when DnaA becomes limiting. We suggest, for both rifampicin treated cells and for cells accumulating ppGpp, that a turn-off of initiation from oriC requires a stop in de novo DnaA synthesis and that an additional lack of transcriptional activation enhances this process, that is, leads to a faster initiation stop.
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Affiliation(s)
- Leise Riber
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
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13
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Irving SE, Choudhury NR, Corrigan RM. The stringent response and physiological roles of (pp)pGpp in bacteria. Nat Rev Microbiol 2020; 19:256-271. [PMID: 33149273 DOI: 10.1038/s41579-020-00470-y] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 01/10/2023]
Abstract
The stringent response is a stress signalling system mediated by the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) in response to nutrient deprivation. Recent research highlights the complexity and broad range of functions that these alarmones control. This Review provides an update on our current understanding of the enzymes involved in ppGpp, pppGpp and guanosine 5'-monophosphate 3'-diphosphate (pGpp) (collectively (pp)pGpp) turnover, including those shown to produce pGpp and its analogue (pp)pApp. We describe the well-known interactions with RNA polymerase as well as a broader range of cellular target pathways controlled by (pp)pGpp, including DNA replication, transcription, nucleotide synthesis, ribosome biogenesis and function, as well as lipid metabolism. Finally, we review the role of ppGpp and pppGpp in bacterial pathogenesis, providing examples of how these nucleotides are involved in regulating many aspects of virulence and chronic infection.
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Affiliation(s)
- Sophie E Irving
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Naznin R Choudhury
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Rebecca M Corrigan
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
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14
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Sinha AK, Løbner-Olesen A, Riber L. Bacterial Chromosome Replication and DNA Repair During the Stringent Response. Front Microbiol 2020; 11:582113. [PMID: 32983079 PMCID: PMC7483579 DOI: 10.3389/fmicb.2020.582113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/13/2020] [Indexed: 01/23/2023] Open
Abstract
The stringent response regulates bacterial growth rate and is important for cell survival under changing environmental conditions. The effect of the stringent response is pleiotropic, affecting almost all biological processes in the cell including transcriptional downregulation of genes involved in stable RNA synthesis, DNA replication, and metabolic pathways, as well as the upregulation of stress-related genes. In this Review, we discuss how the stringent response affects chromosome replication and DNA repair activities in bacteria. Importantly, we address how accumulation of (p)ppGpp during the stringent response shuts down chromosome replication using highly different strategies in the evolutionary distant Gram-negative Escherichia coli and Gram-positive Bacillus subtilis. Interestingly, (p)ppGpp-mediated replication inhibition occurs downstream of the origin in B. subtilis, whereas replication inhibition in E. coli takes place at the initiation level, suggesting that stringent cell cycle arrest acts at different phases of the replication cycle between E. coli and B. subtilis. Furthermore, we address the role of (p)ppGpp in facilitating DNA repair activities and cell survival during exposure to UV and other DNA damaging agents. In particular, (p)ppGpp seems to stimulate the efficiency of nucleotide excision repair (NER)-dependent repair of DNA lesions. Finally, we discuss whether (p)ppGpp-mediated cell survival during DNA damage is related to the ability of (p)ppGpp accumulation to inhibit chromosome replication.
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