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Çöl B, Kürkçü MS, Di Bek E. Genome-Wide Screens Identify Genes Responsible for Intrinsic Boric Acid Resistance in Escherichia coli. Biol Trace Elem Res 2024:10.1007/s12011-024-04129-0. [PMID: 38466471 DOI: 10.1007/s12011-024-04129-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/24/2024] [Indexed: 03/13/2024]
Abstract
Boric acid (BA) has antimicrobial properties and is used to combat bacterial infections, including Enterobacteria. However, the molecular mechanisms and cellular responses to BA are still unknown. This genomics study aims to provide new information on the genes and molecular mechanisms related to the antimicrobial effect of BA in Escherichia coli. The Keio collection of E. coli was used to screen 3985 single-gene knockout strains in order to identify mutant strains that were sensitive or hypersensitive to BA at certain concentrations. The mutant strains were exposed to different concentrations of BA ranging from 0 to 120 mM in LB media. Through genome-wide screens, 92 mutants were identified that were relatively sensitive to BA at least at one concentration tested. The related biological processes in the particular cellular system were listed. This study demonstrates that intrinsic BA resistance is the result of various mechanisms acting together. Additionally, we identified eighteen out of ninety-two mutant strains (Delta_aceF, aroK, cheZ, dinJ, galS, garP, glxK, nohA, talB, torR, trmU, trpR, yddE, yfeS, ygaV, ylaC, yoaC, yohN) that exhibited sensitivity using other methods. To increase sensitivity to BA, we constructed double and triple knockout mutants of the selected sensitive mutants. In certain instances, engineered double and triple mutants exhibited significantly amplified effects. Overall, our analysis of these findings offers further understanding of the mechanisms behind BA toxicity and intrinsic resistance in E. coli.
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Affiliation(s)
- Bekir Çöl
- Faculty of Science, Department of Biology, Mugla Sitki Kocman University, Mugla, Turkey.
- Research Laboratories Center, Biotechnology Research Center, Mugla Sitki Kocman University, Mugla, Turkey.
| | - Merve Sezer Kürkçü
- Research Laboratories Center, Biotechnology Research Center, Mugla Sitki Kocman University, Mugla, Turkey
- Research and Application Center For Research Laboratories, Mugla Sitki Kocman University, Mugla, Turkey
| | - Esra Di Bek
- Research Laboratories Center, Biotechnology Research Center, Mugla Sitki Kocman University, Mugla, Turkey
- Köyceğiz Vocational School of Health Services, Department of Pharmacy Services, Mugla Sitki Kocman University, Mugla, Turkey
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Kruszewska-Naczk B, Grinholc M, Waleron K, Bandow JE, Rapacka-Zdończyk A. Can antimicrobial blue light contribute to resistance development? Genome-wide analysis revealed aBL-protective genes in Escherichia coli. Microbiol Spectr 2024; 12:e0249023. [PMID: 38063383 PMCID: PMC10782963 DOI: 10.1128/spectrum.02490-23] [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: 06/19/2023] [Accepted: 10/24/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Increasing antibiotic resistance and the lack of new antibiotic-like compounds to combat bacterial resistance are significant problems of modern medicine. The development of new alternative therapeutic strategies is extremely important. Antimicrobial blue light (aBL) is an innovative approach to combat multidrug-resistant microorganisms. aBL has a multitarget mode of action; however, the full mechanism of aBL antibacterial action requires further investigation. In addition, the potential risk of resistance development to this treatment should be considered.
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Affiliation(s)
- Beata Kruszewska-Naczk
- Laboratory of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Mariusz Grinholc
- Laboratory of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße, Bochum, Germany
| | - Aleksandra Rapacka-Zdończyk
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
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Genome-wide and protein kinase-focused RNAi screens reveal conserved and novel damage response pathways in Trypanosoma brucei. PLoS Pathog 2017; 13:e1006477. [PMID: 28742144 PMCID: PMC5542689 DOI: 10.1371/journal.ppat.1006477] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/03/2017] [Accepted: 06/17/2017] [Indexed: 12/21/2022] Open
Abstract
All cells are subject to structural damage that must be addressed for continued growth. A wide range of damage affects the genome, meaning multiple pathways have evolved to repair or bypass the resulting DNA lesions. Though many repair pathways are conserved, their presence or function can reflect the life style of individual organisms. To identify genome maintenance pathways in a divergent eukaryote and important parasite, Trypanosoma brucei, we performed RNAi screens to identify genes important for survival following exposure to the alkylating agent methyl methanesulphonate. Amongst a cohort of broadly conserved and, therefore, early evolved repair pathways, we reveal multiple activities not so far examined functionally in T. brucei, including DNA polymerases, DNA helicases and chromatin factors. In addition, the screens reveal Trypanosoma- or kinetoplastid-specific repair-associated activities. We also provide focused analyses of repair-associated protein kinases and show that loss of at least nine, and potentially as many as 30 protein kinases, including a nuclear aurora kinase, sensitises T. brucei to alkylation damage. Our results demonstrate the potential for synthetic lethal genome-wide screening of gene function in T. brucei and provide an evolutionary perspective on the repair pathways that underpin effective responses to damage, with particular relevance for related kinetoplastid pathogens. By revealing that a large number of diverse T. brucei protein kinases act in the response to damage, we expand the range of eukaryotic signalling factors implicated in genome maintenance activities. Damage to the genome is a universal threat to life. Though the repair pathways used to tackle damage can be widely conserved, lineage-specific specialisations are found, reflecting the differing life styles of extant organisms. Using RNAi coupled with next generation sequencing we have screened for genes that are important for growth of Trypanosoma brucei, a diverged eukaryotic microbe and important parasite, in the presence of alkylation damage caused by methyl methanesulphonate. We reveal both repair pathway conservation relative to characterised eukaryotes and specialisation, including uncharacterised roles for translesion DNA polymerases, DNA helicases and chromatin factors. Furthermore, we demonstrate that loss of around 15% of T. brucei protein kinases sensitises the parasites to alkylation, indicating phosphorylation signalling plays widespread and under-investigated roles in the damage response pathways of eukaryotes.
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Noguchi Y, Katayama T. The Escherichia coli Cryptic Prophage Protein YfdR Binds to DnaA and Initiation of Chromosomal Replication Is Inhibited by Overexpression of the Gene Cluster yfdQ-yfdR-yfdS-yfdT. Front Microbiol 2016; 7:239. [PMID: 26973617 PMCID: PMC4776307 DOI: 10.3389/fmicb.2016.00239] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/15/2016] [Indexed: 01/09/2023] Open
Abstract
The initiation of bacterial chromosomal replication is regulated by multiple pathways. To explore novel regulators, we isolated multicopy suppressors for the cold-sensitive hda-185 ΔsfiA(sulA) mutant. Hda is crucial for the negative regulation of the initiator DnaA and the hda-185 mutation causes severe replication overinitiation at the replication origin oriC. The SOS-associated division inhibitor SfiA inhibits FtsZ ring formation, an essential step for cell division regulation during the SOS response, and ΔsfiA enhances the cold sensitivity of hda-185 cells in colony formation. One of the suppressors comprised the yfdQ-yfdR-yfdS-yfdT gene cluster carried on a cryptic prophage. Increased copy numbers of yfdQRT or yfdQRS inhibited not only hda-185-dependent overinitiation, but also replication overinitiation in a hyperactive dnaA mutant, and in a mutant lacking an oriC-binding initiation-inhibitor SeqA. In addition, increasing the copy number of the gene set inhibited the growth of cells bearing specific, initiation-impairing dnaA mutations. In wild-type cells, multicopy supply of yfdQRT or yfdQRS also inhibited replication initiation and increased hydroxyurea (HU)-resistance, as seen in cells lacking DiaA, a stimulator of DnaA assembly on oriC. Deletion of the yfdQ-yfdR-yfdS-yfdT genes did not affect either HU resistance or initiation regulation. Furthermore, we found that DnaA bound specifically to YfdR in soluble protein extracts oversupplied with YfdQRST. Purified YfdR also bound to DnaA, and DnaA Phe46, an amino acid residue crucial for DnaA interactions with DiaA and DnaB replicative helicase was important for this interaction. Consistently, YfdR moderately inhibited DiaA-DnaA and DnaB-DnaA interactions. In addition, protein extracts oversupplied with YfdQRST inhibited replication initiation in vitro. Given the roles of yfdQ and yfdS in cell tolerance to specific environmental stresses, the yfdQ-yfdR-yfdS-yfdT genes might downregulate the initiator DnaA-oriC complex under specific growth conditions.
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Affiliation(s)
- Yasunori Noguchi
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University Fukuoka, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University Fukuoka, Japan
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5
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Chan CTY, Deng W, Li F, DeMott MS, Babu IR, Begley TJ, Dedon PC. Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes. Chem Res Toxicol 2015; 28:978-88. [PMID: 25772370 PMCID: PMC4438938 DOI: 10.1021/acs.chemrestox.5b00004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Cells respond to stress by controlling
gene expression at several
levels, with little known about the role of translation. Here, we
demonstrate a coordinated translational stress response system involving
stress-specific reprogramming of tRNA wobble modifications that leads
to selective translation of codon-biased mRNAs representing different
classes of critical response proteins. In budding yeast exposed to
four oxidants and five alkylating agents, tRNA modification patterns
accurately distinguished among chemically similar stressors, with
14 modified ribonucleosides forming the basis for a data-driven model
that predicts toxicant chemistry with >80% sensitivity and specificity.
tRNA modification subpatterns also distinguish SN1 from
SN2 alkylating agents, with SN2-induced increases
in m3C in tRNA mechanistically linked to selective translation
of threonine-rich membrane proteins from genes enriched with ACC and
ACT degenerate codons for threonine. These results establish tRNA
modifications as predictive biomarkers of exposure and illustrate
a novel regulatory mechanism for translational control of cell stress
response.
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Affiliation(s)
| | | | | | | | | | - Thomas J Begley
- ∥College of Nanoscale Science, State University of New York, Albany, New York 12203, United States
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Svilar D, Dyavaiah M, Brown AR, Tang JB, Li J, McDonald PR, Shun TY, Braganza A, Wang XH, Maniar S, St Croix CM, Lazo JS, Pollack IF, Begley TJ, Sobol RW. Alkylation sensitivity screens reveal a conserved cross-species functionome. Mol Cancer Res 2012; 10:1580-96. [PMID: 23038810 DOI: 10.1158/1541-7786.mcr-12-0168] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To identify genes that contribute to chemotherapy resistance in glioblastoma, we conducted a synthetic lethal screen in a chemotherapy-resistant glioblastoma-derived cell line with the clinical alkylator temozolomide (TMZ) and an siRNA library tailored toward "druggable" targets. Select DNA repair genes in the screen were validated independently, confirming the DNA glycosylases uracil-DNA glycosylase (UNG) and A/G-specific adenine DNA glycosylase (MYH) as well as methylpurine-DNA glycosylase (MPG) to be involved in the response to high dose TMZ. The involvement of UNG and MYH is likely the result of a TMZ-induced burst of reactive oxygen species. We then compared the human TMZ sensitizing genes identified in our screen with those previously identified from alkylator screens conducted in Escherichia coli and Saccharomyces cerevisiae. The conserved biologic processes across all three species compose an alkylation functionome that includes many novel proteins not previously thought to impact alkylator resistance. This high-throughput screen, validation and cross-species analysis was then followed by a mechanistic analysis of two essential nodes: base excision repair (BER) DNA glycosylases (UNG, human and mag1, S. cerevisiae) and protein modification systems, including UBE3B and ICMT in human cells or pby1, lip22, stp22 and aim22 in S. cerevisiae. The conserved processes of BER and protein modification were dual targeted and yielded additive sensitization to alkylators in S. cerevisiae. In contrast, dual targeting of BER and protein modification genes in human cells did not increase sensitivity, suggesting an epistatic relationship. Importantly, these studies provide potential new targets to overcome alkylating agent resistance.
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Affiliation(s)
- David Svilar
- Departments of Pharmacology& Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213-1863, USA
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7
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Chan CTY, Pang YLJ, Deng W, Babu IR, Dyavaiah M, Begley TJ, Dedon PC. Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun 2012; 3:937. [PMID: 22760636 PMCID: PMC3535174 DOI: 10.1038/ncomms1938] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 05/31/2012] [Indexed: 11/09/2022] Open
Abstract
Selective translation of survival proteins is an important facet of the cellular stress response. We recently demonstrated that this translational control involves a stress-specific reprogramming of modified ribonucleosides in tRNA. Here we report the discovery of a step-wise translational control mechanism responsible for survival following oxidative stress. In yeast exposed to hydrogen peroxide, there is a Trm4 methyltransferase-dependent increase in the proportion of tRNALEU(CAA) containing m5C at the wobble position, which causes selective translation of mRNA from genes enriched in the TTG codon. Of these genes, oxidative stress increases protein expression from the TTG-enriched ribosomal protein gene RPL22A, but not its unenriched paralog. Loss of either TRM4 or RPL22A confers hypersensitivity to oxidative stress. Proteomic analysis reveals that oxidative stress causes a significant translational bias toward proteins coded by TTG-enriched genes. These results point to stress-induced reprogramming of tRNA modifications and consequential reprogramming of ribosomes in translational control of cell survival.
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Affiliation(s)
- Clement T Y Chan
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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8
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Rooney JP, Patil A, Joseph F, Endres L, Begley U, Zappala MR, Cunningham RP, Begley TJ. Cross-species Functionome analysis identifies proteins associated with DNA repair, translation and aerobic respiration as conserved modulators of UV-toxicity. Genomics 2010; 97:133-47. [PMID: 21195161 DOI: 10.1016/j.ygeno.2010.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 12/15/2010] [Accepted: 12/18/2010] [Indexed: 10/18/2022]
Abstract
Cellular responses to DNA damage can prevent mutations and death. In this study, we have used high throughput screens and developed a comparative genomic approach, termed Functionome mapping, to discover conserved responses to UVC-damage. Functionome mapping uses gene ontology (GO) information to link proteins with similar biological functions from different organisms, and we have used it to compare 303, 311 and 288 UVC-toxicity modulating proteins from Escherichia coli, Schizosaccharomyces pombe and Saccharomyces cerevisiae, respectively. We have demonstrated that all three organisms use DNA repair, translation and aerobic respiration associated processes to modulate the toxicity of UVC, with these last two categories highlighting the importance of ribosomal proteins and electron transport machinery. Our study has demonstrated that comparative genomic approaches can be used to identify conserved responses to damage, and suggest roles for translational machinery and components of energy metabolism in optimizing the DNA damage response.
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Affiliation(s)
- John P Rooney
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer, NY 12144-3456, USA.
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Chan CTY, Dyavaiah M, DeMott MS, Taghizadeh K, Dedon PC, Begley TJ. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet 2010; 6:e1001247. [PMID: 21187895 PMCID: PMC3002981 DOI: 10.1371/journal.pgen.1001247] [Citation(s) in RCA: 322] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 11/15/2010] [Indexed: 11/18/2022] Open
Abstract
Decades of study have revealed more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA, yet the larger functional dynamics of this conserved system are unclear. To this end, we developed a highly precise mass spectrometric method to quantify tRNA modifications in Saccharomyces cerevisiae. Our approach revealed several novel biosynthetic pathways for RNA modifications and led to the discovery of signature changes in the spectrum of tRNA modifications in the damage response to mechanistically different toxicants. This is illustrated with the RNA modifications Cm, m(5)C, and m(2) (2)G, which increase following hydrogen peroxide exposure but decrease or are unaffected by exposure to methylmethane sulfonate, arsenite, and hypochlorite. Cytotoxic hypersensitivity to hydrogen peroxide is conferred by loss of enzymes catalyzing the formation of Cm, m(5)C, and m(2) (2)G, which demonstrates that tRNA modifications are critical features of the cellular stress response. The results of our study support a general model of dynamic control of tRNA modifications in cellular response pathways and add to the growing repertoire of mechanisms controlling translational responses in cells.
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Affiliation(s)
- Clement T. Y. Chan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Madhu Dyavaiah
- Department of Biomedical Sciences, Gen*NY*sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer, New York, United States of America
| | - Michael S. DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Koli Taghizadeh
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (PCD); (TJB)
| | - Thomas J. Begley
- Department of Biomedical Sciences, Gen*NY*sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer, New York, United States of America
- * E-mail: (PCD); (TJB)
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Yang Y, Gordenin DA, Resnick MA. A single-strand specific lesion drives MMS-induced hyper-mutability at a double-strand break in yeast. DNA Repair (Amst) 2010; 9:914-21. [PMID: 20663718 DOI: 10.1016/j.dnarep.2010.06.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/13/2010] [Accepted: 06/14/2010] [Indexed: 11/17/2022]
Abstract
Localized hyper-mutability (LHM) can be important in evolution, immunity, and genetic diseases. We previously reported that single-strand DNA (ssDNA) can be an important source of damage-induced LHM in yeast. Here, we establish that the generation of LHM by methyl methanesulfonate (MMS) during repair of a chromosomal double-strand break (DSB) can result in over 0.2 mutations/kb, which is approximately 20,000-fold higher than the MMS-induced mutation density without a DSB. The MMS-induced mutations associated with DSB repair were primarily due to substitutions via translesion DNA synthesis at damaged cytosines, even though there are nearly 10 times more MMS-induced lesions at other bases. Based on this mutation bias, the promutagenic lesion dominating LHM is likely 3-methylcytosine, which is single-strand specific. Thus, the dramatic increase in mutagenesis at a DSB is concluded to result primarily from the generation of non-repairable lesions in ssDNA associated with DSB repair along with efficient induction of highly mutagenic ssDNA-specific lesions. These findings with MMS-induced LHM have broad biological implications for unrepaired damage generated in ssDNA and possibly ssRNA.
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Affiliation(s)
- Yong Yang
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
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11
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Skjølberg HC, Fensgård O, Nilsen H, Grallert B, Boye E. Global transcriptional response after exposure of fission yeast cells to ultraviolet light. BMC Cell Biol 2009; 10:87. [PMID: 20015352 PMCID: PMC2806298 DOI: 10.1186/1471-2121-10-87] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 12/16/2009] [Indexed: 12/04/2022] Open
Abstract
Background In many cell types, including the fission yeast Schizosaccharomyces pombe, a set of checkpoints are induced by perturbations of the cell cycle or by DNA damage. Many of the checkpoint responses include a substantial change of the transcriptional pattern. As part of characterising a novel G1/S checkpoint in fission yeast we have investigated whether a transcriptional response is induced after irradiation with ultraviolet light. Results Microarray analyses were used to measure the global transcription levels of all open reading frames of fission yeast after 254 nm ultraviolet irradiation, which is known to induce a G1/S checkpoint. We discovered a surprisingly weak transcriptional response, which is quite unlike the marked changes detected after some other types of treatment and in several other checkpoints. Interestingly, the alterations in gene expression after ultraviolet irradiation were not similar to those observed after ionising radiation or oxidative stress. Pathway analysis suggests that there is little systematic transcriptional response to the irradiation by ultraviolet light, but a marked, coordinated transcriptional response was noted on progression of the cells from G1 to S phase. Conclusion There is little response in fission yeast to ultraviolet light at the transcriptional level. Amongst the genes induced or repressed after ultraviolet irradiation we found none that are likely to be involved in the G1/S checkpoint mechanism, suggesting that the checkpoint is not dependent upon transcriptional regulation.
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Affiliation(s)
- Henriette C Skjølberg
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Montebello, 0310 Oslo, Norway.
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A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae. BMC Genomics 2009; 10:524. [PMID: 19917080 PMCID: PMC2784802 DOI: 10.1186/1471-2164-10-524] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 11/15/2009] [Indexed: 12/22/2022] Open
Abstract
Background The understanding of the biological function, regulation, and cellular interactions of the yeast genome and proteome, along with the high conservation in gene function found between yeast genes and their human homologues, has allowed for Saccharomyces cerevisiae to be used as a model organism to deduce biological processes in human cells. Here, we have completed a systematic screen of the entire set of 4,733 haploid S. cerevisiae gene deletion strains (the entire set of nonessential genes for this organism) to identify gene products that modulate cellular toxicity to nickel sulfate (NiSO4). Results We have identified 149 genes whose gene deletion causes sensitivity to NiSO4 and 119 genes whose gene deletion confers resistance. Pathways analysis with proteins whose absence renders cells sensitive and resistant to nickel identified a wide range of cellular processes engaged in the toxicity of S. cerevisiae to NiSO4. Functional categories overrepresented with proteins whose absence renders cells sensitive to NiSO4 include homeostasis of protons, cation transport, transport ATPases, endocytosis, siderophore-iron transport, homeostasis of metal ions, and the diphthamide biosynthesis pathway. Functional categories overrepresented with proteins whose absence renders cells resistant to nickel include functioning and transport of the vacuole and lysosome, protein targeting, sorting, and translocation, intra-Golgi transport, regulation of C-compound and carbohydrate metabolism, transcriptional repression, and chromosome segregation/division. Interactome analysis mapped seven nickel toxicity modulating and ten nickel-resistance networks. Additionally, we studied the degree of sensitivity or resistance of the 111 nickel-sensitive and 72 -resistant strains whose gene deletion product has a similar protein in human cells. Conclusion We have undertaken a whole genome approach in order to further understand the mechanism(s) regulating the cell's toxicity to nickel compounds. We have used computational methods to integrate the data and generate global models of the yeast's cellular response to NiSO4. The results of our study shed light on molecular pathways associated with the cellular response of eukaryotic cells to nickel compounds and provide potential implications for further understanding the toxic effects of nickel compounds to human cells.
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13
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Zhou X, Arita A, Ellen TP, Liu X, Bai J, Rooney JP, Kurtz AD, Klein CB, Dai W, Begley TJ, Costa M. A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics 2009; 94:294-307. [PMID: 19631266 DOI: 10.1016/j.ygeno.2009.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/17/2009] [Accepted: 07/15/2009] [Indexed: 11/30/2022]
Abstract
We have used Saccharomyces cerevisiae to identify toxicologically important proteins and pathways involved in arsenic-induced toxicity and carcinogenicity in humans. We performed a systemic screen of the complete set of 4733 haploid S. cerevisiae single-gene-deletion mutants to identify those that have decreased or increased growth, relative to wild type, after exposure to sodium arsenite (NaAsO(2)). IC(50) values for all mutants were determined to further validate our results. Ultimately we identified 248 mutants sensitive to arsenite and 5 mutants resistant to arsenite exposure. We analyzed the proteins corresponding to arsenite-sensitive mutants and determined that they belonged to functional categories that include protein binding, phosphate metabolism, vacuolar/lysosomal transport, protein targeting, sorting, and translocation, cell growth/morphogenesis, cell polarity and filament formation. Furthermore, these data were mapped onto a protein interactome to identify arsenite-toxicity-modulating networks. These networks are associated with the cytoskeleton, ubiquitination, histone acetylation and the MAPK signaling pathway. Our studies have potential implications for understanding toxicity and carcinogenesis in arsenic-induced human conditions, such as cancer and aging.
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Affiliation(s)
- Xue Zhou
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
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14
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What we can learn about Escherichia coli through application of Gene Ontology. Trends Microbiol 2009; 17:269-78. [PMID: 19576778 DOI: 10.1016/j.tim.2009.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 03/04/2009] [Accepted: 04/08/2009] [Indexed: 11/21/2022]
Abstract
How we classify the genes, products and complexes that are present or absent in genomes, transcriptomes, proteomes and other datasets helps us place biological objects into subsystems with common functions, see how molecular functions are used to implement biological processes and compare the biology of different species and strains. Gene Ontology (GO) is one of the most successful systems for classifying biological function. Although GO is widely used for eukaryotic genomics, it has not yet been widely used for bacterial systems. The potential applications of GO are currently limited by the need to improve the annotation of bacterial genomes with GO and to improve how prokaryotic biology is represented in the ontology. Here, we discuss why GO should be adopted by microbiologists, and describe recent efforts to build and maintain high-quality GO annotation for Escherichia coli as a model system.
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