1
|
Łazowski K, Woodgate R, Fijalkowska IJ. Escherichia coli DNA replication: the old model organism still holds many surprises. FEMS Microbiol Rev 2024; 48:fuae018. [PMID: 38982189 PMCID: PMC11253446 DOI: 10.1093/femsre/fuae018] [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: 05/09/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024] Open
Abstract
Research on Escherichia coli DNA replication paved the groundwork for many breakthrough discoveries with important implications for our understanding of human molecular biology, due to the high level of conservation of key molecular processes involved. To this day, it attracts a lot of attention, partially by virtue of being an important model organism, but also because the understanding of factors influencing replication fidelity might be important for studies on the emergence of antibiotic resistance. Importantly, the wide access to high-resolution single-molecule and live-cell imaging, whole genome sequencing, and cryo-electron microscopy techniques, which were greatly popularized in the last decade, allows us to revisit certain assumptions about the replisomes and offers very detailed insight into how they work. For many parts of the replisome, step-by-step mechanisms have been reconstituted, and some new players identified. This review summarizes the latest developments in the area, focusing on (a) the structure of the replisome and mechanisms of action of its components, (b) organization of replisome transactions and repair, (c) replisome dynamics, and (d) factors influencing the base and sugar fidelity of DNA synthesis.
Collapse
Affiliation(s)
- Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, United States
| | - Iwona J Fijalkowska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| |
Collapse
|
2
|
Amor-Guéret M. Loss of cytidine deaminase expression as a potential attempt to counteract the process of carcinogenesis by reducing basal PARP-1 activity and increasing tau levels. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167213. [PMID: 38714266 DOI: 10.1016/j.bbadis.2024.167213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/01/2024] [Accepted: 05/01/2024] [Indexed: 05/09/2024]
Abstract
Cytidine deaminase (CDA) is a pyrimidine salvage pathway enzyme that catalyzes the hydrolytic deamination of free cytidine and deoxycytidine to uridine and deoxyuridine, respectively. Our team discovered that CDA deficiency is associated with several aspects of genetic instability, such as increased sister chromatid exchange and ultrafine anaphase bridge frequencies. Based on these results, we sought (1) to determine how CDA deficiency contributes to genetic instability, (2) to explore the possible relationships between CDA deficiency and carcinogenesis, and (3) to develop a new anticancer treatment targeting CDA-deficient tumors. This review summarizes our major findings indicating that CDA deficiency is associated with a genetic instability that does not confer an increased cancer risk. In light of our results and published data, I propose a novel hypothesis that loss of CDA, by reducing basal PARP-1 activity and increasing Tau levels, may reflect an attempt to prevent, slow or reverse the process of carcinogenesis.
Collapse
Affiliation(s)
- Mounira Amor-Guéret
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France; CNRS UMR 3348, Centre Universitaire, 91405 Orsay, France; Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405 Orsay, France.
| |
Collapse
|
3
|
Alabi OA. Comparative chemical analysis, mutagenicity, and genotoxicity of Petroleum refinery wastewater and its contaminated river using prokaryotic and eukaryotic assays. PROTOPLASMA 2023; 260:89-101. [PMID: 35467135 DOI: 10.1007/s00709-022-01763-0] [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: 02/12/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Concern on the toxicity of final wastewater generated by the petroleum refining industry has increased in recent years due to the potential health threats associated with their release into the waterways. This study determined the mutagenic and genotoxic potential of petroleum refinery wastewater and a receiving river using the Ames fluctuation test on Salmonella typhimurium strains TA100 and TA98, SOS chromotest on Escherichia coli PQ37, and piscine peripheral micronucleus (MN) assay. Analyses of the physicochemical parameters, heavy metal, and organic contents of the samples were also performed. Ames test result showed that the two tested samples were mutagenic with TA100 strain as the more responsive strain for both the refinery wastewater and the river sample in terms of the calculated mutagenic index. A similar result was obtained in the SOS chromotest; however, the E. coli PQ37 system recorded a slightly higher sensitivity for detecting genotoxins than the Salmonella assay in the two samples. MN data showed induction of a concentration-dependent significant (p < 0.05) increase in the frequency of MN by both samples when compared with the negative control. Generally, the refinery wastewater induced the highest mutagenicity and genotoxicity compared to the river sample in the three assays used. Haemoglobin, platelets, red blood cells, mean corpuscular volume, total white blood cells, heterophils, haematocrit, and eosinophils reduced significantly with increased lymphocytes, basophils, mean corpuscular haemoglobin, and mean corpuscular haemoglobin concentration in fishes exposed to both samples. Total petroleum hydrocarbon, benzene, toluene, phenol index, polycyclic aromatic hydrocarbons, cadmium, mercury, nickel, lead, and vanadium contents analysed in the samples were believed to be responsible for the observed genotoxicity and mutagenicity. The findings of this study revealed that petroleum refinery wastewater is a potential mutagenic and genotoxic risk to the environment.
Collapse
|
4
|
Cyto-genotoxic potential of petroleum refinery wastewater mixed with domestic sewage used for irrigation of food crops in the vicinity of an oil refinery. Heliyon 2021; 7:e08116. [PMID: 34693051 PMCID: PMC8515247 DOI: 10.1016/j.heliyon.2021.e08116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/02/2020] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
Petroleum refinery wastewater combined with domestic sewage were collected from the open channel in the vicinity of Mathura oil refinery, UP (India) and analysed by inductively coupled plasma optical emission spectrometry (ICP-OES) and gas chromatography-mass spectrometry (GC-MS) for elemental analysis and organic pollutants, respectively. Several potentially toxic and non-toxic elements were found to be present in the wastewater samples. GC-MS analysis revealed the presence of several organic contaminants including pesticides. Wastewater samples were extracted using amberlite XAD4/8 resins and liquid-liquid extraction procedures using different organic solvents. The extracts were tested for their cyto-genotoxic potential using bacterial (Salmonella mutagenicity test, E. coli K-12 DNA repair defective mutants, Bacteriophage λ assay) and plant (Vigna mungo phytotoxicity test, Allium cepa chromosomal aberration assay) systems. A significant increase was observed in the number of revertants of TA97a, TA98 and TA100 strains with the test samples and XAD concentrated samples were found to be more mutagenic than liquid-liquid extracts. Colony forming units (CFUs) of DNA repair defective mutants of E. coli K-12 recA, lexA and polA declined significantly as compared to their isogenic wild-type counterparts with the test samples. Significant reduction in plaque forming units (PFUs) of bacteriophage λ was also found on treatment with the solvent extracts. Presence of several toxic pollutants in the wastewater apply prohibitive action on the seed germination process. Germination rate of Vigna mungo seeds as well as radicle and plumule lengths were found to be affected when treated with different concentration of wastewater as compared to control. Present study also indicated concentration dependent reduction in mitotic index of A. cepa i.e., 16.38% at 5% and 9.74% at 100% wastewater and percentage of aberrant cells were highest at 100% effluent. Present findings indicated that mutagenicity/genotoxicity of wastewater is due to the mixture of genotoxins; poses serious hazards to the receiving waterbodies which require continuous monitoring and remedial measures for their improvement.
Collapse
|
5
|
Pancsa R, Fichó E, Molnár D, Surányi ÉV, Trombitás T, Füzesi D, Lóczi H, Szijjártó P, Hirmondó R, Szabó JE, Tóth J. dNTPpoolDB: a manually curated database of experimentally determined dNTP pools and pool changes in biological samples. Nucleic Acids Res 2021; 50:D1508-D1514. [PMID: 34643700 PMCID: PMC8728230 DOI: 10.1093/nar/gkab910] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 12/02/2022] Open
Abstract
Stimulated by the growing interest in the role of dNTP pools in physiological and malignant processes, we established dNTPpoolDB, the database that offers access to quantitative data on dNTP pools from a wide range of species, experimental and developmental conditions (https://dntppool.org/). The database includes measured absolute or relative cellular levels of the four canonical building blocks of DNA and of exotic dNTPs, as well. In addition to the measured quantity, dNTPpoolDB contains ample information on sample source, dNTP quantitation methods and experimental conditions including any treatments and genetic manipulations. Functions such as the advanced search offering multiple choices from custom-built controlled vocabularies in 15 categories in parallel, the pairwise comparison of any chosen pools, and control-treatment correlations provide users with the possibility to quickly recognize and graphically analyse changes in the dNTP pools in function of a chosen parameter. Unbalanced dNTP pools, as well as the balanced accumulation or depletion of all four dNTPs result in genomic instability. Accordingly, key roles of dNTP pool homeostasis have been demonstrated in cancer progression, development, ageing and viral infections among others. dNTPpoolDB is designated to promote research in these fields and fills a longstanding gap in genome metabolism research.
Collapse
Affiliation(s)
- Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Erzsébet Fichó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary.,Cytocast Kft., Vecsés, Hungary
| | - Dániel Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Éva Viola Surányi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Tamás Trombitás
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Dóra Füzesi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Hanna Lóczi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Péter Szijjártó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Rita Hirmondó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Judit E Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, H-1111, Hungary
| |
Collapse
|
6
|
Targeting the bacterial SOS response for new antimicrobial agents: drug targets, molecular mechanisms and inhibitors. Future Med Chem 2021; 13:143-155. [PMID: 33410707 DOI: 10.4155/fmc-2020-0310] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance is a pressing threat to global health, with multidrug-resistant pathogens becoming increasingly prevalent. The bacterial SOS pathway functions in response to DNA damage that occurs during infection, initiating several pro-survival and resistance mechanisms, such as DNA repair and hypermutation. This makes SOS pathway components potential targets that may combat drug-resistant pathogens and decrease resistance emergence. This review discusses the mechanism of the SOS pathway; the structure and function of potential targets AddAB, RecBCD, RecA and LexA; and efforts to develop selective small-molecule inhibitors of these proteins. These inhibitors may serve as valuable tools for target validation and provide the foundations for desperately needed novel antibacterial therapeutics.
Collapse
|
7
|
Kapoor I, Varshney U. Diverse roles of nucleoside diphosphate kinase in genome stability and growth fitness. Curr Genet 2020; 66:671-682. [PMID: 32249353 DOI: 10.1007/s00294-020-01073-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Nucleoside diphosphate kinase (NDK), a ubiquitous enzyme, catalyses reversible transfer of the γ phosphate from nucleoside triphosphates to nucleoside diphosphates and functions to maintain the pools of ribonucleotides and deoxyribonucleotides in the cell. As even a minor imbalance in the nucleotide pools can be mutagenic, NDK plays an antimutator role in maintaining genome integrity. However, the mechanism of the antimutator roles of NDK is not completely understood. In addition, NDKs play important roles in the host-pathogen interactions, metastasis, gene regulation, and various cellular metabolic processes. To add to these diverse roles of NDK in cells, a recent study now reveals that NDK may even confer mutator phenotypes to the cell by acting on the damaged deoxyribonucleoside diphosphates that may be formed during the oxidative stress. In this review, we discuss the roles of NDK in homeostasis of the nucleotide pools and genome integrity, and its possible implications in conferring growth/survival fitness to the organisms in the changing environmental niches.
Collapse
Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India. .,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
| |
Collapse
|
8
|
Maslowska KH, Makiela‐Dzbenska K, Fijalkowska IJ. The SOS system: A complex and tightly regulated response to DNA damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:368-384. [PMID: 30447030 PMCID: PMC6590174 DOI: 10.1002/em.22267] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 05/10/2023]
Abstract
Genomes of all living organisms are constantly threatened by endogenous and exogenous agents that challenge the chemical integrity of DNA. Most bacteria have evolved a coordinated response to DNA damage. In Escherichia coli, this inducible system is termed the SOS response. The SOS global regulatory network consists of multiple factors promoting the integrity of DNA as well as error-prone factors allowing for survival and continuous replication upon extensive DNA damage at the cost of elevated mutagenesis. Due to its mutagenic potential, the SOS response is subject to elaborate regulatory control involving not only transcriptional derepression, but also post-translational activation, and inhibition. This review summarizes current knowledge about the molecular mechanism of the SOS response induction and progression and its consequences for genome stability. Environ. Mol. Mutagen. 60:368-384, 2019. © 2018 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
Collapse
Affiliation(s)
- Katarzyna H. Maslowska
- Cancer Research Center of Marseille, CNRS, UMR7258Inserm, U1068; Institut Paoli‐Calmettes, Aix‐Marseille UniversityMarseilleFrance
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| | | | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| |
Collapse
|
9
|
Khan S, Anas M, Malik A. Mutagenicity and genotoxicity evaluation of textile industry wastewater using bacterial and plant bioassays. Toxicol Rep 2019; 6:193-201. [PMID: 30859068 PMCID: PMC6396094 DOI: 10.1016/j.toxrep.2019.02.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/23/2019] [Accepted: 02/12/2019] [Indexed: 11/25/2022] Open
Abstract
Textile industrial wastewater samples were taken from the Panki site 5 industrial area of Kanpur city, India. Atomic Absorption spectrophotometer and Gas Chromatography-Mass spectrometry techniques have shown that the wastewater contained several heavy metals and organic pollutants (Khan and Malik, 2017) [1]. Further, in order to explore the potential toxicity of these pollutants present in the effluent, a battery of short-term biological assays (Ames test, DNA repair defective mutation assay and Allium cepa chromosomal aberration test) were used. Wastewater samples were concentrated with XAD-4/8 resins and liquid-liquid extraction procedure. XAD-concentrated samples were more mutagenic than the liquid-liquid extracted samples. Ames TA98 and polA (SOS defective) strains were the most responsive strains. The wastewater also resulted in significant decline in mitotic index and induced chromosomal aberrations in A. cepa roots. The findings thus showed that the combination of physico-chemical analysis alongwith the toxicity assessment (using short term biological assays) would provide valuable and more realistic information about the joint toxicity of chemical pollutants present in the textile effluent.
Collapse
Affiliation(s)
| | | | - Abdul Malik
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| |
Collapse
|
10
|
Foster PL, Niccum BA, Popodi E, Townes JP, Lee H, MohammedIsmail W, Tang H. Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair Defective Escherichia coli. Genetics 2018; 209:1029-1042. [PMID: 29907647 PMCID: PMC6063221 DOI: 10.1534/genetics.118.301237] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/14/2018] [Indexed: 11/18/2022] Open
Abstract
Mismatch repair (MMR) is a major contributor to replication fidelity, but its impact varies with sequence context and the nature of the mismatch. Mutation accumulation experiments followed by whole-genome sequencing of MMR-defective Escherichia coli strains yielded ≈30,000 base-pair substitutions (BPSs), revealing mutational patterns across the entire chromosome. The BPS spectrum was dominated by A:T to G:C transitions, which occurred predominantly at the center base of 5'NAC3'+5'GTN3' triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations. Mononucleotide runs were also hotspots for BPSs, and the rate at which these occurred increased with run length. Comparison with ≈2000 BPSs accumulated in MMR-proficient strains revealed that both kinds of hotspots appeared in the wild-type spectrum and so are likely to be sites of frequent replication errors. In MMR-defective strains transitions were strand biased, occurring twice as often when A and C rather than T and G were on the lagging-strand template. Loss of nucleotide diphosphate kinase increases the cellular concentration of dCTP, which resulted in increased rates of mutations due to misinsertion of C opposite A and T. In an mmr ndk double mutant strain, these mutations were more frequent when the template A and T were on the leading strand, suggesting that lagging-strand synthesis was more error-prone, or less well corrected by proofreading, than was leading strand synthesis.
Collapse
Affiliation(s)
- Patricia L Foster
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Brittany A Niccum
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Ellen Popodi
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Jesse P Townes
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Heewook Lee
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405
| | - Wazim MohammedIsmail
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405
| | - Haixu Tang
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405
| |
Collapse
|
11
|
LC-MS/MS proteomic analysis of starved Bacillus subtilis cells overexpressing ribonucleotide reductase (nrdEF): implications in stress-associated mutagenesis. Curr Genet 2017. [PMID: 28624879 DOI: 10.1007/s00294-017-0722-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The non-appropriate conditions faced by nutritionally stressed bacteria propitiate error-prone repair events underlying stationary-phase- or stress-associated mutagenesis (SPM). The genetic and molecular mechanisms involved in SPM have been deeply studied but the biochemical aspects of this process have so far been less explored. Previous evidence showed that under conditions of nutritional stress, non-dividing cells of strain B. subtilis YB955 overexpressing ribonucleotide reductase (RNR) exhibited a strong propensity to generate true reversions in the hisC952 (amber), metB5 (ochre) and leuC425 (missense) mutant alleles. To further advance our knowledge on the metabolic conditions underlying this hypermutagenic phenotype, a high-throughput LC-MS/MS proteomic analysis was performed in non-dividing cells of an amino acid-starved strain, deficient for NrdR, the RNR repressor. Compared with the parental strain, the level of 57 proteins was found to increase and of 80 decreases in the NrdR-deficient strain. The proteomic analysis revealed an altered content in proteins associated with the stringent response, nucleotide metabolism, DNA repair, and cell signaling in amino acid-starved cells of the ∆nrdR strain. Overall, our results revealed that amino acid-starved cells of strain B. subtilis ∆nrdR that escape from growth-limiting conditions exhibit a complex proteomic pattern reminiscent of a disturbed metabolism. Future experiments aimed to understand the consequences of disrupting the cell signaling pathways unveiled in this study, will advance our knowledge on the genetic adaptations deployed by bacteria to escape from growth-limiting environments.
Collapse
|
12
|
Scott TA, Quintaneiro LM, Norvaisas P, Lui PP, Wilson MP, Leung KY, Herrera-Dominguez L, Sudiwala S, Pessia A, Clayton PT, Bryson K, Velagapudi V, Mills PB, Typas A, Greene NDE, Cabreiro F. Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans. Cell 2017; 169:442-456.e18. [PMID: 28431245 PMCID: PMC5406385 DOI: 10.1016/j.cell.2017.03.040] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/09/2017] [Accepted: 03/28/2017] [Indexed: 01/05/2023]
Abstract
Fluoropyrimidines are the first-line treatment for colorectal cancer, but their efficacy is highly variable between patients. We queried whether gut microbes, a known source of inter-individual variability, impacted drug efficacy. Combining two tractable genetic models, the bacterium E. coli and the nematode C. elegans, we performed three-way high-throughput screens that unraveled the complexity underlying host-microbe-drug interactions. We report that microbes can bolster or suppress the effects of fluoropyrimidines through metabolic drug interconversion involving bacterial vitamin B6, B9, and ribonucleotide metabolism. Also, disturbances in bacterial deoxynucleotide pools amplify 5-FU-induced autophagy and cell death in host cells, an effect regulated by the nucleoside diphosphate kinase ndk-1. Our data suggest a two-way bacterial mediation of fluoropyrimidine effects on host metabolism, which contributes to drug efficacy. These findings highlight the potential therapeutic power of manipulating intestinal microbiota to ensure host metabolic health and treat disease.
Collapse
Affiliation(s)
- Timothy A Scott
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 6BT, UK
| | - Leonor M Quintaneiro
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 6BT, UK; UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Povilas Norvaisas
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 6BT, UK; Department of Computer Science, University College London, London WC1E 6BT, UK
| | - Prudence P Lui
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 6BT, UK
| | - Matthew P Wilson
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Kit-Yi Leung
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Lucia Herrera-Dominguez
- European Molecular Biology Laboratory (EMBL) Heidelberg, Genome Biology, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Sonia Sudiwala
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Alberto Pessia
- Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland
| | - Peter T Clayton
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Kevin Bryson
- Department of Computer Science, University College London, London WC1E 6BT, UK
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland
| | - Philippa B Mills
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Athanasios Typas
- European Molecular Biology Laboratory (EMBL) Heidelberg, Genome Biology, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nicholas D E Greene
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Filipe Cabreiro
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 6BT, UK.
| |
Collapse
|
13
|
Chi C, Ronai D, Than MT, Walker CJ, Sewell AK, Han M. Nucleotide levels regulate germline proliferation through modulating GLP-1/Notch signaling in C. elegans. Genes Dev 2016; 30:307-20. [PMID: 26833730 PMCID: PMC4743060 DOI: 10.1101/gad.275107.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study, Chi et al. researched the link between known nutrient-sensing systems and reproductive programs. Using a model system in C. elegans, they show that a Notch signaling pathway senses the level of uridine/thymidine and controls germline proliferation, delineating a previously unknown nucleotide-sensing mechanism for controlling reproductivity. Animals alter their reproductive programs to accommodate changes in nutrient availability, yet the connections between known nutrient-sensing systems and reproductive programs are underexplored, and whether there is a mechanism that senses nucleotide levels to coordinate germline proliferation is unknown. We established a model system in which nucleotide metabolism is perturbed in both the nematode Caenorhabditis elegans (cytidine deaminases) and its food (Escherichia coli); when fed food with a low uridine/thymidine (U/T) level, germline proliferation is arrested. We provide evidence that this impact of U/T level on the germline is critically mediated by GLP-1/Notch and MPK-1/MAPK, known to regulate germline mitotic proliferation. This germline defect is suppressed by hyperactivation of glp-1 or disruption of genes downstream from glp-1 to promote meiosis but not by activation of the IIS or TORC1 pathways. Moreover, GLP-1 expression is post-transcriptionally modulated by U/T levels. Our results reveal a previously unknown nucleotide-sensing mechanism for controlling reproductivity.
Collapse
Affiliation(s)
- Congwu Chi
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Diana Ronai
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Minh T Than
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Cierra J Walker
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Aileen K Sewell
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Min Han
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| |
Collapse
|
14
|
Transcriptome Analysis of Escherichia coli during dGTP Starvation. J Bacteriol 2016; 198:1631-44. [PMID: 27002130 DOI: 10.1128/jb.00218-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/16/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Our laboratory recently discovered that Escherichia coli cells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for thymineless death (TLD). Conditions for specific dGTP starvation can be achieved by depriving an E. coli optA1 gpt strain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses of actively growing optA1 gpt cells subjected to hypoxanthine deprivation for increasing periods. The data show that upon Hx withdrawal, the optA1 gpt strain displays a diminished ability to derepress the de novo purine biosynthesis genes, likely due to internal guanine accumulation. The impairment in fully inducing the purR regulon may be a contributing factor to the lethality of dGTP starvation. At later time points, and coinciding with cell lethality, strong induction of the SOS response was observed, supporting the concept of replication stress as a final cause of death. No evidence was observed in the starved cells for the participation of other stress responses, including the rpoS-mediated global stress response, reinforcing the lack of feedback of replication stress to the global metabolism of the cell. The genome-wide expression data also provide direct evidence for increased genome complexity during dGTP starvation, as a markedly increased gradient was observed for expression of genes located near the replication origin relative to those located toward the replication terminus. IMPORTANCE Control of the supply of the building blocks (deoxynucleoside triphosphates [dNTPs]) for DNA replication is important for ensuring genome integrity and cell viability. When cells are starved specifically for one of the four dNTPs, dGTP, the process of DNA replication is disturbed in a manner that can lead to eventual death. In the present study, we investigated the transcriptional changes in the bacterium E. coli during dGTP starvation. The results show increasing DNA replication stress with an increased time of starvation, as evidenced by induction of the bacterial SOS system, as well as a notable lack of induction of other stress responses that could have saved the cells from cell death by slowing down cell growth.
Collapse
|
15
|
Tse L, Kang TM, Yuan J, Mihora D, Becket E, Maslowska KH, Schaaper RM, Miller JH. Extreme dNTP pool changes and hypermutability in dcd ndk strains. Mutat Res 2015; 784-785:16-24. [PMID: 26789486 DOI: 10.1016/j.mrfmmm.2015.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/10/2015] [Accepted: 12/17/2015] [Indexed: 11/16/2022]
Abstract
Cells lacking deoxycytidine deaminase (DCD) have been shown to have imbalances in the normal dNTP pools that lead to multiple phenotypes, including increased mutagenesis, increased sensitivity to oxidizing agents, and to a number of antibiotics. In particular, there is an increased dCTP pool, often accompanied by a decreased dTTP pool. In the work presented here, we show that double mutants of Escherichia coli lacking both DCD and NDK (nucleoside diphosphate kinase) have even more extreme imbalances of dNTPs than mutants lacking only one or the other of these enzymes. In particular, the dCTP pool rises to very high levels, exceeding even the cellular ATP level by several-fold. This increased level of dCTP, coupled with more modest changes in other dNTPs, results in exceptionally high mutation levels. The high mutation levels are attenuated by the addition of thymidine. The results corroborate the critical importance of controlling DNA precursor levels for promoting genome stability. We also show that the addition of certain exogenous nucleosides can influence replication errors in DCD-proficient strains that are deficient in mismatch repair.
Collapse
Affiliation(s)
- Lawrence Tse
- Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Tina Manzhu Kang
- Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Jessica Yuan
- Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Danielle Mihora
- Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Elinne Becket
- Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Katarzyna H Maslowska
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States
| | - Jeffrey H Miller
- Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California and the David Geffen School of Medicine, Los Angeles, CA 90095, United States.
| |
Collapse
|