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Benson DR, Deng B, Kashipathy MM, Lovell S, Battaile KP, Cooper A, Gao P, Fenton AW, Zhu H. The N-terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin. Proteins 2024; 92:554-566. [PMID: 38041394 PMCID: PMC10932899 DOI: 10.1002/prot.26647] [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: 07/21/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
NADH cytochrome b5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochrome b5 (b5 ) and cytochrome b5 reductase (b5 R) domains separated by a CHORD-Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter-domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full-length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high-resolution atomic structures of the b5 domain and a construct containing the CS and b5 R domains (CS/b5 R). Ncb5or also contains an N-terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L34 MDWIRL40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to a b5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N-terminal region naturally fused to the b5 domain, we were able to obtain a high-resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25-129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp120 (corresponding to invariant Trp37 in Ncb5or) to be part of an 11-residue α-helix (S116 QMDWLKLTRT126 ) packing against two of the four helices in the b5 domain that surround heme (α2 and α5). The Trp120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr85 and Tyr88 (α2), Cys124 (α5), and Leu47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp37 in nucleating the formation of the N-terminal helix, whose location in the N/b5 module suggests a role in regulating the function of this multi-domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b5 module as reflected by its existence in a class of cytochrome b5 proteins from three kingdoms among eukaryotes.
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Affiliation(s)
- David R. Benson
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, U.S.A
| | - Bin Deng
- Department of Physical Therapy and Rehabilitation Science, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
| | - Maithri M. Kashipathy
- Department of Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Scott Lovell
- Department of Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Kevin P. Battaile
- Department of NYX, New York Structural Biology Center, Upton, NY, 11973, USA
| | - Anne Cooper
- Department of Protein Production Group, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Philip Gao
- Department of Protein Production Group, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Aron W. Fenton
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
| | - Hao Zhu
- Department of Clinical Laboratory Sciences, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
- Department of Physical Therapy and Rehabilitation Science, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
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Yamamoto K, Tochikawa S, Miura Y, Matsunobu S, Hirose Y, Eki T. Sensing chemical-induced DNA damage using CRISPR/Cas9-mediated gene-deletion yeast-reporter strains. Appl Microbiol Biotechnol 2024; 108:188. [PMID: 38300351 PMCID: PMC10834598 DOI: 10.1007/s00253-024-13020-w] [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: 07/28/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Microorganism-based genotoxicity assessments are vital for evaluating potential chemical-induced DNA damage. In this study, we developed both chromosomally integrated and single-copy plasmid-based reporter assays in budding yeast using a RNR3 promoter-driven luciferase gene. These assays were designed to compare the response to genotoxic chemicals with a pre-established multicopy plasmid-based assay. Despite exhibiting the lowest luciferase activity, the chromosomally integrated reporter assay showed the highest fold induction (i.e., the ratio of luciferase activity in the presence and absence of the chemical) compared with the established plasmid-based assay. Using CRISPR/Cas9 technology, we generated mutants with single- or double-gene deletions, affecting major DNA repair pathways or cell permeability. This enabled us to evaluate reporter gene responses to genotoxicants in a single-copy plasmid-based assay. Elevated background activities were observed in several mutants, such as mag1Δ cells, even without exposure to chemicals. However, substantial luciferase induction was detected in single-deletion mutants following exposure to specific chemicals, including mag1Δ, mms2Δ, and rad59Δ cells treated with methyl methanesulfonate; rad59Δ cells exposed to camptothecin; and mms2Δ and rad10Δ cells treated with mitomycin C (MMC) and cisplatin (CDDP). Notably, mms2Δ/rad10Δ cells treated with MMC or CDDP exhibited significantly enhanced luciferase induction compared with the parent single-deletion mutants, suggesting that postreplication and for nucleotide excision repair processes predominantly contribute to repairing DNA crosslinks. Overall, our findings demonstrate the utility of yeast-based reporter assays employing strains with multiple-deletion mutations in DNA repair genes. These assays serve as valuable tools for investigating DNA repair mechanisms and assessing chemical-induced DNA damage. KEY POINTS: • Responses to genotoxic chemicals were investigated in three types of reporter yeast. • Yeast strains with single- and double-deletions of DNA repair genes were tested. • Two DNA repair pathways predominantly contributed to DNA crosslink repair in yeast.
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Affiliation(s)
- Kosuke Yamamoto
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Shintaro Tochikawa
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Yuuki Miura
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Shogo Matsunobu
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Yuu Hirose
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
- Laboratory of Genomics and Photobiology, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Toshihiko Eki
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [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: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst 2023; 14:447-463.e8. [PMID: 37220749 PMCID: PMC10330685 DOI: 10.1016/j.cels.2023.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/30/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
The DNA damage response (DDR) ensures error-free DNA replication and transcription and is disrupted in numerous diseases. An ongoing challenge is to determine the proteins orchestrating DDR and their organization into complexes, including constitutive interactions and those responding to genomic insult. Here, we use multi-conditional network analysis to systematically map DDR assemblies at multiple scales. Affinity purifications of 21 DDR proteins, with/without genotoxin exposure, are combined with multi-omics data to reveal a hierarchical organization of 605 proteins into 109 assemblies. The map captures canonical repair mechanisms and proposes new DDR-associated proteins extending to stress, transport, and chromatin functions. We find that protein assemblies closely align with genetic dependencies in processing specific genotoxins and that proteins in multiple assemblies typically act in multiple genotoxin responses. Follow-up by DDR functional readouts newly implicates 12 assembly members in double-strand-break repair. The DNA damage response assemblies map is available for interactive visualization and query (ccmi.org/ddram/).
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Affiliation(s)
- Anton Kratz
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Minkyu Kim
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA; University of Texas Health Science Center San Antonio, Department of Biochemistry and Structural Biology, San Antonio, TX 78229, USA
| | - Marcus R Kelly
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Fan Zheng
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Christopher A Koczor
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Jianfeng Li
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Keiichiro Ono
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Yue Qin
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Christopher Churas
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jing Chen
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Rudolf T Pillich
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jisoo Park
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Maya Modak
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Rachel Collier
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Kate Licon
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Dexter Pratt
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Robert W Sobol
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA; Brown University, Department of Pathology and Laboratory Medicine and Legorreta Cancer Center, Providence, RI 02903, USA.
| | - Nevan J Krogan
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
| | - Trey Ideker
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
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Feng Y, Zhang Y, Li J, Omran RP, Whiteway M, Feng J. Transcriptional Profiling of the Candida albicans Response to the DNA Damage Agent Methyl Methanesulfonate. Int J Mol Sci 2022; 23:ijms23147555. [PMID: 35886903 PMCID: PMC9317300 DOI: 10.3390/ijms23147555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
The infection of a mammalian host by the pathogenic fungus Candida albicans involves fungal resistance to reactive oxygen species (ROS)—induced DNA damage stress generated by the defending macrophages or neutrophils. Thus, the DNA damage response in C. albicans may contribute to its pathogenicity. Uncovering the transcriptional changes triggered by the DNA damage—inducing agent MMS in many model organisms has enhanced the understanding of their DNA damage response processes. However, the transcriptional regulation triggered by MMS remains unclear in C. albicans. Here, we explored the global transcription profile in response to MMS in C. albicans and identified 306 defined genes whose transcription was significantly affected by MMS. Only a few MMS-responsive genes, such as MGT1, DDR48, MAG1, and RAD7, showed potential roles in DNA repair. GO term analysis revealed that a large number of induced genes were involved in antioxidation responses, and some downregulated genes were involved in nucleosome packing and IMP biosynthesis. Nevertheless, phenotypic assays revealed that MMS-induced antioxidation gene CAP1 and glutathione metabolism genes GST2 and GST3 showed no direct roles in MMS resistance. Furthermore, the altered transcription of several MMS—responsive genes exhibited RAD53—related regulation. Intriguingly, the transcription profile in response to MMS in C. albicans shared a limited similarity with the pattern in S. cerevisiae, including COX17, PRI2, and MGT1. Overall, C. albicans cells exhibit global transcriptional changes to the DNA damage agent MMS; these findings improve our understanding of this pathogen’s DNA damage response pathways.
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Affiliation(s)
- Yuting Feng
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226007, China; (Y.F.); (Y.Z.); (J.L.)
| | - Yan Zhang
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226007, China; (Y.F.); (Y.Z.); (J.L.)
| | - Jie Li
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226007, China; (Y.F.); (Y.Z.); (J.L.)
| | - Raha Parvizi Omran
- Biology Department, Concordia University, Montreal, QC H4B 1R6, Canada; (R.P.O.); (M.W.)
| | - Malcolm Whiteway
- Biology Department, Concordia University, Montreal, QC H4B 1R6, Canada; (R.P.O.); (M.W.)
| | - Jinrong Feng
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226007, China; (Y.F.); (Y.Z.); (J.L.)
- Correspondence: ; Tel.: +86-513-85051746
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6
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Simmons RH, Rogers CM, Bochman ML. A deep dive into the RecQ interactome: something old and something new. Curr Genet 2021; 67:761-767. [PMID: 33961099 DOI: 10.1007/s00294-021-01190-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/26/2022]
Abstract
RecQ family helicases are found in all domains of life and play roles in multiple processes that underpin genomic integrity. As such, they are often referred to as guardians or caretakers of the genome. Despite their importance, however, there is still much we do not know about their basic functions in vivo, nor do we fully understand how they interact in organisms that encode more than one RecQ family member. We recently took a multi-omics approach to better understand the Saccharomyces cerevisiae Hrq1 helicase and its interaction with Sgs1, with these enzymes being the functional homologs of the disease-linked RECQL4 and BLM helicases, respectively. Using synthetic genetic array analyses, immuno-precipitation coupled to mass spectrometry, and RNA-seq, we found that Hrq1 and Sgs1 likely participate in many pathways outside of the canonical DNA recombination and repair functions for which they are already known. For instance, connections to transcription, ribosome biogenesis, and chromatin/chromosome organization were uncovered. These recent results are briefly detailed with respect to current knowledge in the field, and possible follow-up experiments are suggested. In this way, we hope to gain a wholistic understanding of these RecQ helicases and how their mutation leads to genomic instability.
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Affiliation(s)
- Robert H Simmons
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA.
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Khandelwal Gilman KA, Han S, Won YW, Putnam CW. Complex interactions of lovastatin with 10 chemotherapeutic drugs: a rigorous evaluation of synergism and antagonism. BMC Cancer 2021; 21:356. [PMID: 33823841 PMCID: PMC8022429 DOI: 10.1186/s12885-021-07963-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
Background Evidence bearing on the role of statins in the prevention and treatment of cancer is confounded by the diversity of statins, chemotherapeutic agents and cancer types included in the numerous published studies; consequently, the adjunctive value of statins with chemotherapy remains uncertain. Methods We assayed lovastatin in combination with each of ten commonly prescribed chemotherapy drugs in highly reproducible in vitro assays, using a neutral cellular substrate, Saccharomyces cerevisiae. Cell density (OD600) data were analyzed for synergism and antagonism using the Loewe additivity model implemented with the Combenefit software. Results Four of the ten chemotherapy drugs – tamoxifen, doxorubicin, methotrexate and rapamycin – exhibited net synergism with lovastatin. The remaining six agents (5-fluorouracil, gemcitabine, epothilone, cisplatin, cyclophosphamide and etoposide) compiled neutral or antagonistic scores. Distinctive patterns of synergism and antagonism, often coexisting within the same concentration space, were documented with the various combinations, including those with net synergism scores. Two drug pairs, lovastatin combined with tamoxifen or cisplatin, were also assayed in human cell lines as proof of principle. Conclusions The synergistic interactions of tamoxifen, doxorubicin, methotrexate and rapamycin with lovastatin – because they suggest the possibility of clinical utility - merit further exploration and validation in cell lines and animal models. No less importantly, strong antagonistic interactions between certain agents and lovastatin argue for a cautious, data-driven approach before adding a statin to any chemotherapeutic regimen. We also urge awareness of adventitious statin usage by patients entering cancer treatment protocols. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07963-w.
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Affiliation(s)
| | - Seungmin Han
- Division of Cardiothoracic Surgery, Department of Surgery, College of Medicine-Tucson, University of Arizona, Tucson, AZ, USA
| | - Young-Wook Won
- Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Division of Cardiothoracic Surgery, Department of Surgery, College of Medicine-Tucson, University of Arizona, Tucson, AZ, USA
| | - Charles W Putnam
- Arizona Cancer Center, University of Arizona, Tucson, AZ, USA. .,Division of Cardiothoracic Surgery, Department of Surgery, College of Medicine-Tucson, University of Arizona, Tucson, AZ, USA.
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Oliveira RKDM, Hurtado FA, Gomes PH, Puglia LL, Ferreira FF, Ranjan K, Albuquerque P, Poças-Fonseca MJ, Silva-Pereira I, Fernandes L. Base Excision Repair AP-Endonucleases-Like Genes Modulate DNA Damage Response and Virulence of the Human Pathogen Cryptococcus neoformans. J Fungi (Basel) 2021; 7:jof7020133. [PMID: 33673204 PMCID: PMC7917787 DOI: 10.3390/jof7020133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
Pathogenic microbes are exposed to a number of potential DNA-damaging stimuli during interaction with the host immune system. Microbial survival in this situation depends on a fine balance between the maintenance of DNA integrity and the adaptability provided by mutations. In this study, we investigated the association of the DNA repair response with the virulence of Cryptococcus neoformans, a basidiomycete that causes life-threatening meningoencephalitis in immunocompromised individuals. We focused on the characterization of C. neoformansAPN1 and APN2 putative genes, aiming to evaluate a possible role of the predicted Apurinic/apyrimidinic (AP) endonucleases 1 and 2 of the base excision repair (BER) pathway on C. neoformans response to stress conditions and virulence. Our results demonstrated the involvement of the putative AP-endonucleases Apn1 and Apn2 in the cellular response to DNA damage induced by alkylation and by UV radiation, in melanin production, in tolerance to drugs and in virulence of C. neoformans in vivo. We also pointed out the potential use of DNA repair inhibitor methoxy-amine in combination with conventional antifungal drugs, for the development of new therapeutic approaches against this human fungal pathogen. This work provides new information about the DNA damage response of the highly important pathogenic fungus C. neoformans.
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Affiliation(s)
- Rayssa Karla de Medeiros Oliveira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Fabián Andrés Hurtado
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Pedro Henrique Gomes
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Luiza Lassi Puglia
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Fernanda Fonsêca Ferreira
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
| | - Kunal Ranjan
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
| | | | - Márcio José Poças-Fonseca
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
| | - Ildinete Silva-Pereira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
| | - Larissa Fernandes
- Faculty of Ceilândia, University of Brasília, Brasília 72.220-275, Brazil;
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
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Comprehensive Synthetic Genetic Array Analysis of Alleles That Interact with Mutation of the Saccharomyces cerevisiae RecQ Helicases Hrq1 and Sgs1. G3-GENES GENOMES GENETICS 2020; 10:4359-4368. [PMID: 33115720 PMCID: PMC7718751 DOI: 10.1534/g3.120.401709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Most eukaryotic genomes encode multiple RecQ family helicases, including five such enzymes in humans. For many years, the yeast Saccharomyces cerevisiae was considered unusual in that it only contained a single RecQ helicase, named Sgs1. However, it has recently been discovered that a second RecQ helicase, called Hrq1, resides in yeast. Both Hrq1 and Sgs1 are involved in genome integrity, functioning in processes such as DNA inter-strand crosslink repair, double-strand break repair, and telomere maintenance. However, it is unknown if these enzymes interact at a genetic, physical, or functional level as demonstrated for their human homologs. Thus, we performed synthetic genetic array (SGA) analyses of hrq1Δ and sgs1Δ mutants. As inactive alleles of helicases can demonstrate dominant phenotypes, we also performed SGA analyses on the hrq1-K318A and sgs1-K706A ATPase/helicase-null mutants, as well as all combinations of deletion and inactive double mutants. We crossed these eight query strains (hrq1Δ, sgs1Δ, hrq1-K318A, sgs1-K706A, hrq1Δ sgs1Δ, hrq1Δ sgs1-K706A, hrq1-K318A sgs1Δ, and hrq1-K318A sgs1-K706A) to the S. cerevisiae single gene deletion and temperature-sensitive allele collections to generate double and triple mutants and scored them for synthetic positive and negative genetic effects based on colony growth. These screens identified hundreds of synthetic interactions, supporting the known roles of Hrq1 and Sgs1 in DNA repair, as well as suggesting novel connections to rRNA processing, mitochondrial DNA maintenance, transcription, and lagging strand synthesis during DNA replication.
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10
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Genome Profiling for Aflatoxin B 1 Resistance in Saccharomyces cerevisiae Reveals a Role for the CSM2/SHU Complex in Tolerance of Aflatoxin B 1-Associated DNA Damage. G3-GENES GENOMES GENETICS 2020; 10:3929-3947. [PMID: 32994210 PMCID: PMC7642924 DOI: 10.1534/g3.120.401723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exposure to the mycotoxin aflatoxin B1 (AFB1) strongly correlates with hepatocellular carcinoma (HCC). P450 enzymes convert AFB1 into a highly reactive epoxide that forms unstable 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 (AFB1-N 7-Gua) DNA adducts, which convert to stable mutagenic AFB1 formamidopyrimidine (FAPY) DNA adducts. In CYP1A2-expressing budding yeast, AFB1 is a weak mutagen but a potent recombinagen. However, few genes have been identified that confer AFB1 resistance. Here, we profiled the yeast genome for AFB1 resistance. We introduced the human CYP1A2 into ∼90% of the diploid deletion library, and pooled samples from CYP1A2-expressing libraries and the original library were exposed to 50 μM AFB1 for 20 hs. By using next generation sequencing (NGS) to count molecular barcodes, we initially identified 86 genes from the CYP1A2-expressing libraries, of which 79 were confirmed to confer AFB1 resistance. While functionally diverse genes, including those that function in proteolysis, actin reorganization, and tRNA modification, were identified, those that function in postreplication DNA repair and encode proteins that bind to DNA damage were over-represented, compared to the yeast genome, at large. DNA metabolism genes also included those functioning in checkpoint recovery and replication fork maintenance, emphasizing the potency of the mycotoxin to trigger replication stress. Among genes involved in postreplication repair, we observed that CSM2, a member of the CSM2 (SHU) complex, functioned in AFB1-associated sister chromatid recombination while suppressing AFB1-associated mutations. These studies thus broaden the number of AFB1 resistance genes and have elucidated a mechanism of error-free bypass of AFB1-associated DNA adducts.
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11
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Rogers CM, Simmons Iii RH, Fluhler Thornburg GE, Buehler NJ, Bochman ML. Fanconi anemia-independent DNA inter-strand crosslink repair in eukaryotes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 158:33-46. [PMID: 32877700 DOI: 10.1016/j.pbiomolbio.2020.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]
Abstract
DNA inter-strand crosslinks (ICLs) are dangerous lesions that can be caused by a variety of endogenous and exogenous bifunctional compounds. Because covalently linking both strands of the double helix locally disrupts DNA replication and transcription, failure to remove even a single ICL can be fatal to the cell. Thus, multiple ICL repair pathways have evolved, with the best studied being the canonical Fanconi anemia (FA) pathway. However, recent research demonstrates that different types of ICLs (e.g., backbone distorting vs. non-distorting) can be discriminated by the cell, which then mounts a specific repair response using the FA pathway or one of a variety of FA-independent ICL repair pathways. This review focuses on the latter, covering current work on the transcription-coupled, base excision, acetaldehyde-induced, and SNM1A/RecQ4 ICL repair pathways and highlighting unanswered questions in the field. Answering these questions will provide mechanistic insight into the various pathways of ICL repair and enable ICL-inducing agents to be more effectively used as chemotherapeutics.
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Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Robert H Simmons Iii
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Gabriella E Fluhler Thornburg
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Nicholas J Buehler
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA.
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12
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Heat-shock proteases promote survival of Pseudomonas aeruginosa during growth arrest. Proc Natl Acad Sci U S A 2020; 117:4358-4367. [PMID: 32029587 DOI: 10.1073/pnas.1912082117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
When nutrients in their environment are exhausted, bacterial cells become arrested for growth. During these periods, a primary challenge is maintaining cellular integrity with a reduced capacity for renewal or repair. Here, we show that the heat-shock protease FtsH is generally required for growth arrest survival of Pseudomonas aeruginosa, and that this requirement is independent of a role in regulating lipopolysaccharide synthesis, as has been suggested for Escherichia coli We find that ftsH interacts with diverse genes during growth and overlaps functionally with the other heat-shock protease-encoding genes hslVU, lon, and clpXP to promote survival during growth arrest. Systematic deletion of the heat-shock protease-encoding genes reveals that the proteases function hierarchically during growth arrest, with FtsH and ClpXP having primary, nonredundant roles, and HslVU and Lon deploying a secondary response to aging stress. This hierarchy is partially conserved during growth at high temperature and alkaline pH, suggesting that heat, pH, and growth arrest effectively impose a similar type of proteostatic stress at the cellular level. In support of this inference, heat and growth arrest act synergistically to kill cells, and protein aggregation appears to occur more rapidly in protease mutants during growth arrest and correlates with the onset of cell death. Our findings suggest that protein aggregation is a major driver of aging and cell death during growth arrest, and that coordinated activity of the heat-shock response is required to ensure ongoing protein quality control in the absence of growth.
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13
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In yeast cells arrested at the early S-phase by hydroxyurea, rRNA gene promoters and chromatin are poised for transcription while rRNA synthesis is compromised. Mutat Res 2019; 815:20-29. [PMID: 31063901 DOI: 10.1016/j.mrfmmm.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/25/2019] [Accepted: 04/23/2019] [Indexed: 11/19/2022]
Abstract
Hydroxyurea (HU) is an inhibitor of ribonucleotide reductase that is used as a chemotherapeutic agent to treat a number of chronic diseases. Addition of HU to cell cultures causes reduction of the dNTP cellular pool below levels that are required for DNA replication. This trigger dividing cells to arrest in early S-phase of the cell cycle. Cell division hinges on ribosome biogenesis, which is tightly regulated by rRNA synthesis. Remarkably, HU represses the expression of some genes the products of which are required for rRNA maturation. To gain more information on the cellular response to HU, we employed the yeast Saccharomyces cerevisiae as model organism and analyzed the changing aspects of closed to open forms of rRNA gene chromatin during cell cycle arrest, the arrangement of RNA polymerase-I (RNAPI) on the open genes, the presence of RNAPI transcription-factors, transcription and rRNA maturation. The rRNA gene chromatin structure was analyzed by psoralen crosslinking and the distribution of RNAPI was investigated by chromatin endogenous cleavage. In HU arrested cells nearly all rRNA genes were in the open form of chromatin, but only a portion of them was engaged with RNAPI. Analyses by chromatin immuno-precipitation confirmed that the overall formation of transcription pre-initiation complexes remained unchanged, suggesting that the onset of rRNA gene activation was not significantly affected by HU. Moreover, the in vitro transcription run-on assay indicated that RNAPI retained most of its transcription elongation activity. However, in HU treated cells, we found that: (1) RNAPI accumulated next to the 5'-end of rRNA genes; (2) considerably less rRNA filaments were observed in electron micrographs of rDNA transcription units; and (3) rRNA maturation was compromised. It is established that HU inhibition of ribonucleotide reductase holds back DNA replication. This study indicates a hitherto unexplored cellular response to HU, namely altered rRNA synthesis, which could participate to hamper cell division.
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14
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Acton E, Lee AHY, Zhao PJ, Flibotte S, Neira M, Sinha S, Chiang J, Flaherty P, Nislow C, Giaever G. Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress. Open Biol 2018; 7:rsob.160330. [PMID: 28592509 PMCID: PMC5493772 DOI: 10.1098/rsob.160330] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/24/2017] [Indexed: 12/25/2022] Open
Abstract
The Yeast Knockout (YKO) collection has provided a wealth of functional annotations from genome-wide screens. An unintended consequence is that 76% of gene annotations derive from one genotype. The nutritional auxotrophies in the YKO, in particular, have phenotypic consequences. To address this issue, ‘prototrophic’ versions of the YKO collection have been constructed, either by introducing a plasmid carrying wild-type copies of the auxotrophic markers (Plasmid-Borne, PBprot) or by backcrossing (Backcrossed, BCprot) to a wild-type strain. To systematically assess the impact of the auxotrophies, genome-wide fitness profiles of prototrophic and auxotrophic collections were compared across diverse drug and environmental conditions in 250 experiments. Our quantitative profiles uncovered broad impacts of genotype on phenotype for three deletion collections, and revealed genotypic and strain-construction-specific phenotypes. The PBprot collection exhibited fitness defects associated with plasmid maintenance, while BCprot fitness profiles were compromised due to strain loss from nutrient selection steps during strain construction. The repaired prototrophic versions of the YKO collection did not restore wild-type behaviour nor did they clarify gaps in gene annotation resulting from the auxotrophic background. To remove marker bias and expand the experimental scope of deletion libraries, construction of a bona fide prototrophic collection from a wild-type strain will be required.
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Affiliation(s)
- Erica Acton
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Genome Science and Technology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy Huei-Yi Lee
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pei Jun Zhao
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Stephane Flibotte
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mauricio Neira
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sunita Sinha
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Chiang
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick Flaherty
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA, USA
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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15
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Abstract
The SLX4/FANCP tumor suppressor has emerged as a key player in the maintenance of genome stability, making pivotal contributions to the repair of interstrand cross-links, homologous recombination, and in response to replication stress genome-wide as well as at specific loci such as common fragile sites and telomeres. SLX4 does so in part by acting as a scaffold that controls and coordinates the XPF-ERCC1, MUS81-EME1, and SLX1 structure-specific endonucleases in different DNA repair and recombination mechanisms. It also interacts with other important DNA repair and cell cycle control factors including MSH2, PLK1, TRF2, and TOPBP1 as well as with ubiquitin and SUMO. This review aims at providing an up-to-date and comprehensive view on the key functions that SLX4 fulfills to maintain genome stability as well as to highlight and discuss areas of uncertainty and emerging concepts.
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Affiliation(s)
- Jean-Hugues Guervilly
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
| | - Pierre Henri Gaillard
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
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16
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Hung CW, Martínez-Márquez JY, Javed FT, Duncan MC. A simple and inexpensive quantitative technique for determining chemical sensitivity in Saccharomyces cerevisiae. Sci Rep 2018; 8:11919. [PMID: 30093662 PMCID: PMC6085351 DOI: 10.1038/s41598-018-30305-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/27/2018] [Indexed: 12/18/2022] Open
Abstract
Chemical sensitivity, growth inhibition in response to a chemical, is a powerful phenotype that can reveal insight into diverse cellular processes. Chemical sensitivity assays are used in nearly every model system, however the yeast Saccharomyces cerevisiae provides a particularly powerful platform for discovery and mechanistic insight from chemical sensitivity assays. Here we describe a simple and inexpensive approach to determine chemical sensitivity quantitatively in yeast in the form of half maximal inhibitory concentration (IC50) using common laboratory equipment. We demonstrate the utility of this method using chemicals commonly used to monitor changes in membrane traffic. When compared to traditional agar-based plating methods, this method is more sensitive and can detect defects not apparent using other protocols. Additionally, this method reduces the experimental protocol from five days to 18 hours for the toxic amino acid canavanine. Furthermore, this method provides reliable results using lower amounts of chemicals. Finally, this method is easily adapted to additional chemicals as demonstrated with an engineered system that activates the spindle assembly checkpoint in response to rapamycin with differing efficiencies. This approach provides researchers with a cost-effective method to perform chemical genetic profiling without specialized equipment.
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Affiliation(s)
- Chao-Wei Hung
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
- Department of Medicine, University of California, San Diego, California, USA.
| | | | - Fatima T Javed
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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17
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Alzahrani M, Kuwahara H, Wang W, Gao X. Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. Bioinformatics 2018; 33:2523-2531. [PMID: 28379298 PMCID: PMC5870648 DOI: 10.1093/bioinformatics/btx199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/03/2017] [Indexed: 11/24/2022] Open
Abstract
Motivation Growth phenotype profiling of genome-wide gene-deletion strains over stress conditions can offer a clear picture that the essentiality of genes depends on environmental conditions. Systematically identifying groups of genes from such high-throughput data that share similar patterns of conditional essentiality and dispensability under various environmental conditions can elucidate how genetic interactions of the growth phenotype are regulated in response to the environment. Results We first demonstrate that detecting such ‘co-fit’ gene groups can be cast as a less well-studied problem in biclustering, i.e. constant-column biclustering. Despite significant advances in biclustering techniques, very few were designed for mining in growth phenotype data. Here, we propose Gracob, a novel, efficient graph-based method that casts and solves the constant-column biclustering problem as a maximal clique finding problem in a multipartite graph. We compared Gracob with a large collection of widely used biclustering methods that cover different types of algorithms designed to detect different types of biclusters. Gracob showed superior performance on finding co-fit genes over all the existing methods on both a variety of synthetic data sets with a wide range of settings, and three real growth phenotype datasets for E. coli, proteobacteria and yeast. Availability and Implementation Our program is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Majed Alzahrani
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMCE) Division, Thuwal, 23955-6900, Saudi Arabia
| | - Hiroyuki Kuwahara
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMCE) Division, Thuwal, 23955-6900, Saudi Arabia
| | - Wei Wang
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMCE) Division, Thuwal, 23955-6900, Saudi Arabia
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18
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Abstract
A long-standing challenge in drug development is the identification of the mechanisms of action of small molecules with therapeutic potential. A number of methods have been developed to address this challenge, each with inherent strengths and limitations. We here provide a brief review of these methods with a focus on chemical-genetic methods that are based on systematically profiling the effects of genetic perturbations on drug sensitivity. In particular, application of these methods to mammalian systems has been facilitated by the recent advent of CRISPR-based approaches, which enable one to readily repress, induce, or delete a given gene and determine the resulting effects on drug sensitivity.
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Affiliation(s)
- Marco Jost
- Department
of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute,
Center for RNA Systems Biology, University of California, San Francisco, San
Francisco, California 94158, United States
- Department
of Microbiology and Immunology, University of California, San Francisco, San
Francisco, California 94158, United States
| | - Jonathan S. Weissman
- Department
of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute,
Center for RNA Systems Biology, University of California, San Francisco, San
Francisco, California 94158, United States
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19
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Deepa A, Naveena K, Anindya R. DNA repair activity of Fe(II)/2OG-dependent dioxygenases affected by low iron level in Saccharomyces cerevisiae. FEMS Yeast Res 2018; 18:4847889. [DOI: 10.1093/femsyr/foy014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/07/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Akula Deepa
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy-502285, India
| | - Kodipelli Naveena
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy-502285, India
| | - Roy Anindya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy-502285, India
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20
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De La Rosa VY, Asfaha J, Fasullo M, Loguinov A, Li P, Moore LE, Rothman N, Nakamura J, Swenberg JA, Scelo G, Zhang L, Smith MT, Vulpe CD. Editor's Highlight: High-Throughput Functional Genomics Identifies Modulators of TCE Metabolite Genotoxicity and Candidate Susceptibility Genes. Toxicol Sci 2017; 160:111-120. [PMID: 28973557 PMCID: PMC5837773 DOI: 10.1093/toxsci/kfx159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites. Genome-wide profiling studies in yeast identified the error-prone translesion synthesis (TLS) pathway as an import mechanism in response to TCE metabolites. The role of TLS DNA repair was further confirmed by functional profiling in DT40 avian cell lines, but also revealed that TLS and homologous recombination DNA repair likely play competing roles in cellular susceptibility to TCE metabolites in higher eukaryotes. These DNA repair pathways are highly conserved between yeast, DT40, and humans. We propose that in humans, mutagenic TLS is favored over homologous recombination repair in response to TCE metabolites. The results of these studies contribute to the body of evidence supporting a mutagenic mode of action for TCE-induced renal carcinogenesis mediated by reactive metabolites in humans. Our approach illustrates the potential for high-throughput in vitro functional profiling in yeast to elucidate toxicity pathways (molecular initiating events, key events) and candidate susceptibility genes for focused study.
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Affiliation(s)
- Vanessa Y. De La Rosa
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
| | - Jonathan Asfaha
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
| | - Michael Fasullo
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, New York 12205
| | - Alex Loguinov
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
| | - Peng Li
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Lee E. Moore
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jun Nakamura
- Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | | | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California 94720
| | - Martyn T. Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California 94720
| | - Chris D. Vulpe
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
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21
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Gaponova AV, Deneka AY, Beck TN, Liu H, Andrianov G, Nikonova AS, Nicolas E, Einarson MB, Golemis EA, Serebriiskii IG. Identification of evolutionarily conserved DNA damage response genes that alter sensitivity to cisplatin. Oncotarget 2017; 8:19156-19171. [PMID: 27863405 PMCID: PMC5386675 DOI: 10.18632/oncotarget.13353] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/27/2016] [Indexed: 01/08/2023] Open
Abstract
Ovarian, head and neck, and other cancers are commonly treated with cisplatin and other DNA damaging cytotoxic agents. Altered DNA damage response (DDR) contributes to resistance of these tumors to chemotherapies, some targeted therapies, and radiation. DDR involves multiple protein complexes and signaling pathways, some of which are evolutionarily ancient and involve protein orthologs conserved from yeast to humans. To identify new regulators of cisplatin-resistance in human tumors, we integrated high throughput and curated datasets describing yeast genes that regulate sensitivity to cisplatin and/or ionizing radiation. Next, we clustered highly validated genes based on chemogenomic profiling, and then mapped orthologs of these genes in expanded genomic networks for multiple metazoans, including humans. This approach identified an enriched candidate set of genes involved in the regulation of resistance to radiation and/or cisplatin in humans. Direct functional assessment of selected candidate genes using RNA interference confirmed their activity in influencing cisplatin resistance, degree of γH2AX focus formation and ATR phosphorylation, in ovarian and head and neck cancer cell lines, suggesting impaired DDR signaling as the driving mechanism. This work enlarges the set of genes that may contribute to chemotherapy resistance and provides a new contextual resource for interpreting next generation sequencing (NGS) genomic profiling of tumors.
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Affiliation(s)
- Anna V Gaponova
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Alexander Y Deneka
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Tim N Beck
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Biochemistry & Molecular Biology, Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Hanqing Liu
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Pharmaceutics, Jiangsu University, School of Pharmacy, Jingkou District Zhenjiang, Jiangsu 212013, China
| | - Gregory Andrianov
- Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Anna S Nikonova
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Emmanuelle Nicolas
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Margret B Einarson
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Ilya G Serebriiskii
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
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22
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Ferrari E, Bruhn C, Peretti M, Cassani C, Carotenuto WV, Elgendy M, Shubassi G, Lucca C, Bermejo R, Varasi M, Minucci S, Longhese MP, Foiani M. PP2A Controls Genome Integrity by Integrating Nutrient-Sensing and Metabolic Pathways with the DNA Damage Response. Mol Cell 2017. [PMID: 28648781 PMCID: PMC5526790 DOI: 10.1016/j.molcel.2017.05.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mec1ATR mediates the DNA damage response (DDR), integrating chromosomal signals and mechanical stimuli. We show that the PP2A phosphatases, ceramide-activated enzymes, couple cell metabolism with the DDR. Using genomic screens, metabolic analysis, and genetic and pharmacological studies, we found that PP2A attenuates the DDR and that three metabolic circuits influence the DDR by modulating PP2A activity. Irc21, a putative cytochrome b5 reductase that promotes the condensation reaction generating dihydroceramides (DHCs), and Ppm1, a PP2A methyltransferase, counteract the DDR by activating PP2A; conversely, the nutrient-sensing TORC1-Tap42 axis sustains DDR activation by inhibiting PP2A. Loss-of-function mutations in IRC21, PPM1, and PP2A and hyperactive tap42 alleles rescue mec1 mutants. Ceramides synergize with rapamycin, a TORC1 inhibitor, in counteracting the DDR. Hence, PP2A integrates nutrient-sensing and metabolic pathways to attenuate the Mec1ATR response. Our observations imply that metabolic changes affect genome integrity and may help with exploiting therapeutic options and repositioning known drugs.
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Affiliation(s)
- Elisa Ferrari
- Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Christopher Bruhn
- Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Marta Peretti
- Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Corinne Cassani
- Università degli Studi di Milano-Bicocca, 20126 Milan, Italy
| | | | - Mohamed Elgendy
- Istituto Europeo di Oncologia, Via Adamello 16, 20139 Milan, Italy
| | - Ghadeer Shubassi
- Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Chiara Lucca
- Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Rodrigo Bermejo
- Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain
| | - Mario Varasi
- Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Saverio Minucci
- Istituto Europeo di Oncologia, Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, 20133 Milan, Italy
| | | | - Marco Foiani
- Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, 20133 Milan, Italy.
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23
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Gueiderikh A, Rosselli F, Neto JBC. A never-ending story: the steadily growing family of the FA and FA-like genes. Genet Mol Biol 2017; 40:398-407. [PMID: 28558075 PMCID: PMC5488462 DOI: 10.1590/1678-4685-gmb-2016-0213] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/19/2016] [Indexed: 12/22/2022] Open
Abstract
Among the chromosome fragility-associated human syndromes that present cancer predisposition, Fanconi anemia (FA) is unique due to its large genetic heterogeneity. To date, mutations in 21 genes have been associated with an FA or an FA-like clinical and cellular phenotype, whose hallmarks are bone marrow failure, predisposition to acute myeloid leukemia and a cellular and chromosomal hypersensitivity to DNA crosslinking agents exposure. The goal of this review is to trace the history of the identification of FA genes, a history that started in the eighties and is not yet over, as indicated by the cloning of a twenty-first FA gene in 2016.
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Affiliation(s)
- Anna Gueiderikh
- UMR8200 - CNRS, Équipe labellisée La Ligue contre le Cancer, Villejuif, France.,Gustave Roussy Cancer Center, Villejuif, France.,Université Paris Saclay, Paris Sud - Orsay, France
| | - Filippo Rosselli
- UMR8200 - CNRS, Équipe labellisée La Ligue contre le Cancer, Villejuif, France.,Gustave Roussy Cancer Center, Villejuif, France.,Université Paris Saclay, Paris Sud - Orsay, France
| | - Januario B C Neto
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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24
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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25
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Abstract
ABSTRACT
Invasive fungal infections are becoming an increasingly important cause of human mortality and morbidity, particularly for immunocompromised populations. The fungal pathogens
Candida albicans
,
Cryptococcus neoformans
, and
Aspergillus fumigatus
collectively contribute to over 1 million human deaths annually. Hence, the importance of safe and effective antifungal therapeutics for the practice of modern medicine has never been greater. Given that fungi are eukaryotes like their human host, the number of unique molecular targets that can be exploited for drug development remains limited. Only three classes of molecules are currently approved for the treatment of invasive mycoses. The efficacy of these agents is compromised by host toxicity, fungistatic activity, or the emergence of drug resistance in pathogen populations. Here we describe our current arsenal of antifungals and highlight current strategies that are being employed to improve the therapeutic safety and efficacy of these drugs. We discuss state-of-the-art approaches to discover novel chemical matter with antifungal activity and highlight some of the most promising new targets for antifungal drug development. We feature the benefits of combination therapy as a strategy to expand our current repertoire of antifungals and discuss the antifungal combinations that have shown the greatest potential for clinical development. Despite the paucity of new classes of antifungals that have come to market in recent years, it is clear that by leveraging innovative approaches to drug discovery and cultivating collaborations between academia and industry, there is great potential to bolster the antifungal armamentarium.
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26
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Suresh S, Schlecht U, Xu W, Miranda M, Davis RW, Nislow C, Giaever G, St Onge RP. Identification of Chemical-Genetic Interactions via Parallel Analysis of Barcoded Yeast Strains. Cold Spring Harb Protoc 2016; 2016:2016/9/pdb.prot088054. [PMID: 27587778 DOI: 10.1101/pdb.prot088054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The Yeast Knockout Collection is a complete set of gene deletion strains for the budding yeast, Saccharomyces cerevisiae In each strain, one of approximately 6000 open-reading frames is replaced with a dominant selectable marker flanked by two DNA barcodes. These barcodes, which are unique to each gene, allow the growth of thousands of strains to be individually measured from a single pooled culture. The collection, and other resources that followed, has ushered in a new era in chemical biology, enabling unbiased and systematic identification of chemical-genetic interactions (CGIs) with remarkable ease. CGIs link bioactive compounds to biological processes, and hence can reveal the mechanism of action of growth-inhibitory compounds in vivo, including those of antifungal, antibiotic, and anticancer drugs. The chemogenomic profiling method described here measures the sensitivity induced in yeast heterozygous and homozygous deletion strains in the presence of a chemical inhibitor of growth (termed haploinsufficiency profiling and homozygous profiling, respectively, or HIPHOP). The protocol is both scalable and amenable to automation. After competitive growth of yeast knockout collection cultures, with and without chemical inhibitors, CGIs can be identified and quantified using either array- or sequencing-based approaches as described here.
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Affiliation(s)
- Sundari Suresh
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Weihong Xu
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Molly Miranda
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Ronald W Davis
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guri Giaever
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Robert P St Onge
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
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27
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Suresh S, Schlecht U, Xu W, Bray W, Miranda M, Davis RW, Nislow C, Giaever G, Lokey RS, St Onge RP. Systematic Mapping of Chemical-Genetic Interactions in Saccharomyces cerevisiae. Cold Spring Harb Protoc 2016; 2016:2016/9/pdb.top077701. [PMID: 27587783 DOI: 10.1101/pdb.top077701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chemical-genetic interactions (CGIs) describe a phenomenon where the effects of a chemical compound (i.e., a small molecule) on cell growth are dependent on a particular gene. CGIs can reveal important functional information about genes and can also be powerful indicators of a compound's mechanism of action. Mapping CGIs can lead to the discovery of new chemical probes, which, in contrast to genetic perturbations, operate at the level of the gene product (or pathway) and can be fast-acting, tunable, and reversible. The simple culture conditions required for yeast and its rapid growth, as well as the availability of a complete set of barcoded gene deletion strains, facilitate systematic mapping of CGIs in this organism. This process involves two basic steps: first, screening chemical libraries to identify bioactive compounds affecting growth and, second, measuring the effects of these compounds on genome-wide collections of mutant strains. Here, we introduce protocols for both steps that have great potential for the discovery and development of new small-molecule tools and medicines.
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Affiliation(s)
- Sundari Suresh
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Weihong Xu
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Walter Bray
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
| | - Molly Miranda
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Ronald W Davis
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guri Giaever
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
| | - Robert P St Onge
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
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28
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Bose RN, Moghaddas S, Belkacemi L, Tripathi S, Adams NR, Majmudar P, McCall K, Dezvareh H, Nislow C. Absence of Activation of DNA Repair Genes and Excellent Efficacy of Phosphaplatins against Human Ovarian Cancers: Implications To Treat Resistant Cancers. J Med Chem 2015; 58:8387-401. [PMID: 26455832 DOI: 10.1021/acs.jmedchem.5b00732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Phosphaplatins, platinum(II) and platinum(IV) complexes coordinated to a pyrophosphate moiety, exhibit excellent antitumor activities against a variety of cancers. To determine whether phosphaplatins trigger resistance to treatment by engaging DNA damage repair genes, a yeast genome-wide fitness assay was used. Treatment of yeast cells with pyrodach-2 (D2) or pyrodach-4 (D4) revealed no particular sensitivity to nucleotide excision repair, homologous recombination repair, or postreplication repair when compared with platin control compounds. Also, TNF receptor superfamily member 6 (FAS) protein was overexpressed in phosphaplatin-treated ovarian tumor cells, and platinum colocalized with FAS protein in lipid rafts. An overactivation of sphingomyelinase (ASMase) was noted in the treated cells, indicating participation of an extrinsic apoptotic mechanism due to increased ceramide release. Our results indicate that DNA is not the target of phosphaplatins and accordingly, that phosphaplatins might not cause resistance to treatment. Activation of ASMase and FAS along with the colocalization of platinum with FAS in lipid rafts support an extrinsic apoptotic signaling mechanism that is mediated by phosphaplatins.
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Affiliation(s)
- Rathindra N Bose
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Shadi Moghaddas
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Louiza Belkacemi
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Swarnendu Tripathi
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Nyssa R Adams
- Department of Specialty Medicine, Ohio University Heritage College of Osteopathic Medicine, Ohio University , Athens, Ohio 45701, United States
| | - Pooja Majmudar
- Department of Specialty Medicine, Ohio University Heritage College of Osteopathic Medicine, Ohio University , Athens, Ohio 45701, United States
| | - Kelly McCall
- Department of Specialty Medicine, Ohio University Heritage College of Osteopathic Medicine, Ohio University , Athens, Ohio 45701, United States
| | - Homa Dezvareh
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada
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29
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Liu F, Suryadi J, Bierbach U. Cellular Recognition and Repair of Monofunctional-Intercalative Platinum--DNA Adducts. Chem Res Toxicol 2015; 28:2170-8. [PMID: 26457537 DOI: 10.1021/acs.chemrestox.5b00327] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The cellular recognition and processing of monofunctional-intercalative DNA adducts formed by [PtCl(en)(L)](NO3)2 (P1-A1; en = ethane-1,2-diamine; L = N-[2-(acridin-9-ylamino)ethyl]-N-methylpropionamidine, acridinium cation), a cytotoxic hybrid agent with potent anticancer activity, was studied. Excision of these adducts and subsequent DNA repair synthesis were monitored in plasmids modified with platinum using incubations with mammalian cell-free extract. On the basis of the levels of [α-(32)P]-dCTP incorporation, P1-A1-DNA adducts were rapidly repaired with a rate approximately 8 times faster (t1/2 ≈ 18 min at 30 °C) than the adducts (cross-links) formed by the drug cisplatin. Cellular responses to P1-A1 and cisplatin were also studied in NCI-H460 lung cancer cells using immunocytochemistry in conjunction with confocal fluorescence microscopy. At the same dose, P1-A1, but not cisplatin, elicited a distinct requirement for DNA double-strand break repair and stalled replication fork repair, which caused nuclear fluorescent staining related to high levels of MUS81, a specialized repair endonuclease, and phosphorylated histone protein γ-H2AX. The results confirm previous observations in yeast-based chemical genomics assays. γ-H2AX fluorescence is observed as a large number of discrete foci signaling DNA double-strand breaks, pan-nuclear preapoptotic staining, and unique circularly shaped staining around the nucleoli and nuclear rim. DNA cleavage assays indicate that P1-A1 does not act as a typical topoisomerase poison, suggesting the high level of DNA double-strand breaks in cells is more likely a result of topoisomerase-independent replication fork collapse. Overall, the cellular response to platinum-acridines shares striking similarities with that reported for DNA adduct-forming derivatives of the drug doxorubicin. The results of this study are discussed in light of the cellular mechanism of action of platinum-acridines and their ability to overcome resistance to cisplatin.
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Affiliation(s)
- Fang Liu
- Department of Chemistry, Wake Forest University , Winston-Salem, North Carolina 27109, United States
| | - Jimmy Suryadi
- Department of Chemistry, Wake Forest University , Winston-Salem, North Carolina 27109, United States
| | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University , Winston-Salem, North Carolina 27109, United States
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30
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Gebre AA, Okada H, Kim C, Kubo K, Ohnuki S, Ohya Y. Profiling of the effects of antifungal agents on yeast cells based on morphometric analysis. FEMS Yeast Res 2015; 15:fov040. [DOI: 10.1093/femsyr/fov040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2015] [Indexed: 12/14/2022] Open
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31
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Kaniak-Golik A, Skoneczna A. Mitochondria-nucleus network for genome stability. Free Radic Biol Med 2015; 82:73-104. [PMID: 25640729 DOI: 10.1016/j.freeradbiomed.2015.01.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/25/2014] [Accepted: 01/13/2015] [Indexed: 12/21/2022]
Abstract
The proper functioning of the cell depends on preserving the cellular genome. In yeast cells, a limited number of genes are located on mitochondrial DNA. Although the mechanisms underlying nuclear genome maintenance are well understood, much less is known about the mechanisms that ensure mitochondrial genome stability. Mitochondria influence the stability of the nuclear genome and vice versa. Little is known about the two-way communication and mutual influence of the nuclear and mitochondrial genomes. Although the mitochondrial genome replicates independent of the nuclear genome and is organized by a distinct set of mitochondrial nucleoid proteins, nearly all genome stability mechanisms responsible for maintaining the nuclear genome, such as mismatch repair, base excision repair, and double-strand break repair via homologous recombination or the nonhomologous end-joining pathway, also act to protect mitochondrial DNA. In addition to mitochondria-specific DNA polymerase γ, the polymerases α, η, ζ, and Rev1 have been found in this organelle. A nuclear genome instability phenotype results from a failure of various mitochondrial functions, such as an electron transport chain activity breakdown leading to a decrease in ATP production, a reduction in the mitochondrial membrane potential (ΔΨ), and a block in nucleotide and amino acid biosynthesis. The loss of ΔΨ inhibits the production of iron-sulfur prosthetic groups, which impairs the assembly of Fe-S proteins, including those that mediate DNA transactions; disturbs iron homeostasis; leads to oxidative stress; and perturbs wobble tRNA modification and ribosome assembly, thereby affecting translation and leading to proteotoxic stress. In this review, we present the current knowledge of the mechanisms that govern mitochondrial genome maintenance and demonstrate ways in which the impairment of mitochondrial function can affect nuclear genome stability.
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Affiliation(s)
- Aneta Kaniak-Golik
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland.
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32
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Maurmann L, Belkacemi L, Adams NR, Majmudar PM, Moghaddas S, Bose RN. A novel cisplatin mediated apoptosis pathway is associated with acid sphingomyelinase and FAS proapoptotic protein activation in ovarian cancer. Apoptosis 2015; 20:960-74. [DOI: 10.1007/s10495-015-1124-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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33
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Abstract
Very few chemically novel agents have been approved for antibacterial chemotherapies during the last 50 yr. Yet new antibacterial drugs are needed to reduce the impact on global health of an increasing number of drug-resistant infections, including highly drug-resistant forms of tuberculosis. This review discusses how genetic approaches can be used to study the mechanism of action of whole-cell screening hits and facilitate target-driven strategies for antimicrobial drug development.
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Affiliation(s)
- Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
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34
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Abstract
Homologous DNA pairing and strand exchange are at the core of homologous recombination. These reactions are promoted by a DNA-strand-exchange protein assembled into a nucleoprotein filament comprising the DNA-pairing protein, ATP, and single-stranded DNA. The catalytic activity of this molecular machine depends on control of its dynamic instability by accessory factors. Here we discuss proteins known as recombination mediators that facilitate formation and functional activation of the DNA-strand-exchange protein filament. Although the basics of homologous pairing and DNA-strand exchange are highly conserved in evolution, differences in mediator function are required to cope with differences in how single-stranded DNA is packaged by the single-stranded DNA-binding protein in different species, and the biochemical details of how the different DNA-strand-exchange proteins nucleate and extend into a nucleoprotein filament. The set of (potential) mediator proteins has apparently expanded greatly in evolution, raising interesting questions about the need for additional control and coordination of homologous recombination in more complex organisms.
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Affiliation(s)
- Alex Zelensky
- Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands Department of Radiation Oncology, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Claire Wyman
- Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands Department of Radiation Oncology, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands
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35
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Schlecht U, Suresh S, Xu W, Aparicio AM, Chu A, Proctor MJ, Davis RW, Scharfe C, St Onge RP. A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system. BMC Genomics 2014; 15:263. [PMID: 24708151 PMCID: PMC4023593 DOI: 10.1186/1471-2164-15-263] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 03/10/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Copper is essential for the survival of aerobic organisms. If copper is not properly regulated in the body however, it can be extremely cytotoxic and genetic mutations that compromise copper homeostasis result in severe clinical phenotypes. Understanding how cells maintain optimal copper levels is therefore highly relevant to human health. RESULTS We found that addition of copper (Cu) to culture medium leads to increased respiratory growth of yeast, a phenotype which we then systematically and quantitatively measured in 5050 homozygous diploid deletion strains. Cu's positive effect on respiratory growth was quantitatively reduced in deletion strains representing 73 different genes, the function of which identify increased iron uptake as a cause of the increase in growth rate. Conversely, these effects were enhanced in strains representing 93 genes. Many of these strains exhibited respiratory defects that were specifically rescued by supplementing the growth medium with Cu. Among the genes identified are known and direct regulators of copper homeostasis, genes required to maintain low vacuolar pH, and genes where evidence supporting a functional link with Cu has been heretofore lacking. Roughly half of the genes are conserved in man, and several of these are associated with Mendelian disorders, including the Cu-imbalance syndromes Menkes and Wilson's disease. We additionally demonstrate that pharmacological agents, including the approved drug disulfiram, can rescue Cu-deficiencies of both environmental and genetic origin. CONCLUSIONS A functional screen in yeast has expanded the list of genes required for Cu-dependent fitness, revealing a complex cellular system with implications for human health. Respiratory fitness defects arising from perturbations in this system can be corrected with pharmacological agents that increase intracellular copper concentrations.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Robert P St Onge
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 855 S California Avenue, Palo Alto, CA 94304, USA.
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36
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Bochman ML, Paeschke K, Chan A, Zakian VA. Hrq1, a homolog of the human RecQ4 helicase, acts catalytically and structurally to promote genome integrity. Cell Rep 2014; 6:346-56. [PMID: 24440721 DOI: 10.1016/j.celrep.2013.12.037] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/27/2013] [Accepted: 12/24/2013] [Indexed: 11/29/2022] Open
Abstract
Human RecQ4 (hRecQ4) affects cancer and aging but is difficult to study because it is a fusion between a helicase and an essential replication factor. Budding yeast Hrq1 is homologous to the disease-linked helicase domain of RecQ4 and, like hRecQ4, is a robust 3'-5' helicase. Additionally, Hrq1 has the unusual property of forming heptameric rings. Cells lacking Hrq1 exhibited two DNA damage phenotypes: hypersensitivity to DNA interstrand crosslinks (ICLs) and telomere addition to DNA breaks. Both activities are rare; their coexistence in a single protein is unprecedented. Resistance to ICLs requires helicase activity, but suppression of telomere addition does not. Hrq1 also affects telomere length by a noncatalytic mechanism, as well as telomerase-independent telomere maintenance. Because Hrq1 binds telomeres in vivo, it probably affects them directly. Thus, the tumor-suppressing activity of RecQ4 could be due to a role in ICL repair and/or suppression of de novo telomere addition.
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Affiliation(s)
- Matthew L Bochman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Katrin Paeschke
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Angela Chan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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37
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Torres NP, Lee AY, Giaever G, Nislow C, Brown GW. A high-throughput yeast assay identifies synergistic drug combinations. Assay Drug Dev Technol 2014; 11:299-307. [PMID: 23772551 DOI: 10.1089/adt.2012.503] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Drug combinations are commonly used in the treatment of a range of diseases such as cancer, AIDS, and bacterial infections. Such combinations are less likely to be thwarted by resistance, and they have the desirable potential to be synergistic. Synergistic combinations can have decreased toxicity if lower doses of the constituent agents can be used. Conversely, antagonistic combinations can lead to lower efficacy of a treatment. Unfortunately, practical limitations, including the large number of possible combinations to be tested and the importance of optimizing concentrations and order of addition, discourage systematic studies of compound combinations. To address these limitations, we present a platform to screen drug combinations at multiple concentrations with varying orders of addition in Saccharomyces cerevisiae, at high throughput. In a proof of principle, we screened all possible pairwise combinations of 11 DNA damaging agents and found that of the 66 combinations tested, six were synergistic and three were antagonistic. The strength of two-thirds of these combinations was dependent on the order in which the drugs were added to the cells. We further tested the synergistic and antagonistic combinations in two cancer cell lines and found the combination of mitomycin C and irinotecan to be synergistic in both cell lines. This pilot study demonstrates the utility of using yeast for screening large matrices of drug combinations, and it provides a means to prioritize drug combination tests in human cells. Finally, we underscore the importance of testing the order of addition for assessing drug combinations.
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38
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Wolpaw AJ, Stockwell BR. Multidimensional profiling in the investigation of small-molecule-induced cell death. Methods Enzymol 2014; 545:265-302. [PMID: 25065894 DOI: 10.1016/b978-0-12-801430-1.00011-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Numerous morphological variations of cell death have been described. These processes depend on a complex and overlapping cellular signaling network, making molecular definition of the pathways challenging. This review describes one solution to this problem for small-molecule-induced death, the creation of high-dimensionality profiles for compounds that can be used to define and compare pathways. Such profiles have been assembled from gene expression measurements, protein quantification, chemical-genetic interactions, chemical combination interactions, cancer cell line sensitivity profiling, quantitative imaging, and modulatory profiling. We discuss the advantages and limitations of these techniques in the study of cell death.
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Affiliation(s)
- Adam J Wolpaw
- Residency Program in Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, USA; Department of Chemistry, Columbia University, New York, USA; Howard Hughes Medical Institute, Columbia University, New York, USA.
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39
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Cheung-Ong K, Giaever G, Nislow C. DNA-damaging agents in cancer chemotherapy: serendipity and chemical biology. ACTA ACUST UNITED AC 2013; 20:648-59. [PMID: 23706631 DOI: 10.1016/j.chembiol.2013.04.007] [Citation(s) in RCA: 409] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/02/2013] [Accepted: 04/08/2013] [Indexed: 12/13/2022]
Abstract
DNA-damaging agents have a long history of use in cancer chemotherapy. The full extent of their cellular mechanisms, which is essential to balance efficacy and toxicity, is often unclear. In addition, the use of many anticancer drugs is limited by dose-limiting toxicities as well as the development of drug resistance. Novel anticancer compounds are continually being developed in the hopes of addressing these limitations; however, it is essential to be able to evaluate these compounds for their mechanisms of action. This review covers the current DNA-damaging agents used in the clinic, discusses their limitations, and describes the use of chemical genomics to uncover new information about the DNA damage response network and to evaluate novel DNA-damaging compounds.
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Affiliation(s)
- Kahlin Cheung-Ong
- Department of Molecular Genetics and the Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
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A new protein complex promoting the assembly of Rad51 filaments. Nat Commun 2013; 4:1676. [PMID: 23575680 DOI: 10.1038/ncomms2678] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 02/28/2013] [Indexed: 12/17/2022] Open
Abstract
During homologous recombination, eukaryotic RecA homologue Rad51 assembles into a nucleoprotein filament on single-stranded DNA to catalyse homologous pairing and DNA-strand exchange with a homologous template. Rad51 nucleoprotein filaments are highly dynamic and regulated via the coordinated actions of various accessory proteins including Rad51 mediators. Here, we identify a new Rad51 mediator complex. The PCSS complex, comprising budding yeast Psy3, Csm2, Shu1 and Shu2 proteins, binds to recombination sites and is required for Rad51 assembly and function during meiosis. Within the hetero-tetramer, Psy3-Csm2 constitutes a core sub-complex with DNA-binding activity. In vitro, purified Psy3-Csm2 stabilizes the Rad51-single-stranded DNA complex independently of nucleotide cofactor. The mechanism of Rad51 stabilization is inferred by our high-resolution crystal structure, which reveals Psy3-Csm2 to be a structural mimic of the Rad51-dimer, a fundamental unit of the Rad51-filament. Together, these results reveal a novel molecular mechanism for this class of Rad51-mediators, which includes the human Rad51 paralogues.
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Heiskanen MA, Aittokallio T. Predicting drug-target interactions through integrative analysis of chemogenetic assays in yeast. MOLECULAR BIOSYSTEMS 2013; 9:768-79. [PMID: 23420501 DOI: 10.1039/c3mb25591c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chemical-genomic and genetic interaction profiling approaches are widely used to study mechanisms of drug action and resistance. However, there exist a number of scoring algorithms customized to different experimental assays, the relative performance of which remains poorly understood, especially with respect to different types of chemogenetic assays. Using yeast Saccharomyces cerevisiae as a test bed, we carried out a systematic evaluation among the main drug target analysis approaches in terms of predicting global drug-target interaction networks. We found drastic differences in their performance across different chemical-genomic assay types, such as those based on heterozygous and homozygous diploid or haploid deletion mutant libraries. Moreover, a relatively small overlap in the predicted targets was observed between those approaches that use either chemical-genomic screening alone or combined with genetic interaction profiling. A rank-based integration of the complementary scoring approaches led to improved overall performance, demonstrating that genetic interaction profiling provides added information on drug target prediction. Optimal performance was achieved when focusing specifically on the negative tail of the genetic interactions, suggesting that combining synthetic lethal interactions with chemical-genetic interactions provides highest information on drug-target interactions. A network view of rapamycin-interacting genes, pathways and complexes was used as an example to demonstrate the benefits of such integrated and optimized analysis of chemogenetic assays in yeast.
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Affiliation(s)
- Marja A Heiskanen
- Biomathematics Research Group, Department of Mathematics, University of Turku, FI-20014, Finland
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Cunha D, Cunha R, Côrte-Real M, Chaves SR. Cisplatin-induced cell death in Saccharomyces cerevisiae is programmed and rescued by proteasome inhibition. DNA Repair (Amst) 2013; 12:444-9. [DOI: 10.1016/j.dnarep.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/17/2013] [Accepted: 02/17/2013] [Indexed: 11/26/2022]
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Physical and genetic-interaction density reveals functional organization and informs significance cutoffs in genome-wide screens. Proc Natl Acad Sci U S A 2013; 110:7389-94. [PMID: 23589890 DOI: 10.1073/pnas.1219582110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome-wide experiments often measure quantitative differences between treated and untreated cells to identify affected strains. For these studies, statistical models are typically used to determine significance cutoffs. We developed a method termed "CLIK" (Cutoff Linked to Interaction Knowledge) that overlays biological knowledge from the interactome on screen results to derive a cutoff. The method takes advantage of the fact that groups of functionally related interacting genes often respond similarly to experimental conditions and, thus, cluster in a ranked list of screen results. We applied CLIK analysis to five screens of the yeast gene disruption library and found that it defined a significance cutoff that differed from traditional statistics. Importantly, verification experiments revealed that the CLIK cutoff correlated with the position in the rank order where the rate of true positives drops off significantly. In addition, the gene sets defined by CLIK analysis often provide further biological perspectives. For example, applying CLIK analysis retrospectively to a screen for cisplatin sensitivity allowed us to identify the importance of the Hrq1 helicase in DNA crosslink repair. Furthermore, we demonstrate the utility of CLIK to determine optimal treatment conditions by analyzing genome-wide screens at multiple rapamycin concentrations. We show that CLIK is an extremely useful tool for evaluating screen quality, determining screen cutoffs, and comparing results between screens. Furthermore, because CLIK uses previously annotated interaction data to determine biologically informed cutoffs, it provides additional insights into screen results, which supplement traditional statistical approaches.
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Singh-Babak SD, Shekhar T, Smith AM, Giaever G, Nislow C, Cowen LE. A novel calcineurin-independent activity of cyclosporin A in Saccharomyces cerevisiae. MOLECULAR BIOSYSTEMS 2013; 8:2575-84. [PMID: 22751784 DOI: 10.1039/c2mb25107h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fungi rely on regulatory networks to coordinate sensing of environmental stress with initiation of responses crucial for survival. Antifungal drugs are a specific type of environmental stress with broad clinical relevance. Small molecules with antifungal activity are ubiquitous in the environment, and are produced by a myriad of microbes in competitive natural communities. The echinocandins are fungal fermentation products and the most recently developed class of antifungals, with those in clinical use being semisynthetic derivatives that target the fungal cell wall by inhibiting 1,3-β-D-glucan synthase. Recent studies implicate the protein phosphatase calcineurin as a key regulator of cellular stress responses required for fungal survival of echinocandin-induced cell wall stress. Pharmacological inhibition of calcineurin can be achieved using the natural product and immunosuppressive drug cyclosporin A, which inhibits calcineurin by binding to the immunophilin Cpr1. This drug-protein complex inhibits the interaction between the regulatory and catalytic subunits of calcineurin, an interaction necessary for calcineurin function. Here, we report on potent activity of cyclosporin A when combined with the echinocandin micafungin against the model yeast Saccharomyces cerevisiae that is independent of its known mechanism of action of calcineurin inhibition. This calcineurin-independent synergy does not involve any of the 12 immunophilins known in yeast, individually or in combination, and is not mediated by any of the multidrug transporters encoded or controlled by YOR1, SNQ2, PDR5, PDR10, PDR11, YCF1, PDR15, ADP1, VMR1, NFT1, BPT1, YBT1, YNR070w, YOL075c, AUS1, PDR12, PDR1 and/or PDR3. Genome-wide haploinsufficiency profiling (HIP) and homozygous deletion profiling (HOP) strongly implicate the cell wall biosynthesis and integrity pathways as being central to the calcineurin-independent activity of cyclosporin A. Thus, systems level chemical genomic approaches implicate key cellular pathways in a novel mechanism of antifungal drug synergy.
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Affiliation(s)
- Sheena D Singh-Babak
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 4368, Toronto, Ontario M5S 1A8, Canada
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Moghaddas S, Majmudar P, Marin R, Dezvareh H, Qi C, Soans E, Bose RN. Phosphaplatins, next generation platinum antitumor agents: A paradigm shift in designing and defining molecular targets. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.05.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Cheung-Ong K, Song KT, Ma Z, Shabtai D, Lee AY, Gallo D, Heisler LE, Brown GW, Bierbach U, Giaever G, Nislow C. Comparative chemogenomics to examine the mechanism of action of dna-targeted platinum-acridine anticancer agents. ACS Chem Biol 2012; 7:1892-901. [PMID: 22928710 DOI: 10.1021/cb300320d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Platinum-based drugs have been used to successfully treat diverse cancers for several decades. Cisplatin, the original compound of this class, cross-links DNA, resulting in cell cycle arrest and cell death via apoptosis. Cisplatin is effective against several tumor types, yet it exhibits toxic side effects and tumors often develop resistance. To mitigate these liabilities while maintaining potency, we generated a library of non-classical platinum-acridine hybrid agents and assessed their mechanisms of action using a validated genome-wide screening approach in Saccharomyces cerevisiae and in the distantly related yeast Schizosaccharomyces pombe. Chemogenomic profiles from both S. cerevisiae and S. pombe demonstrate that several of the platinum-acridines damage DNA differently than cisplatin based on their requirement for distinct modules of DNA repair.
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Affiliation(s)
| | | | - Zhidong Ma
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina
27109, United States
| | | | | | | | | | | | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina
27109, United States
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Functional analysis with a barcoder yeast gene overexpression system. G3-GENES GENOMES GENETICS 2012; 2:1279-89. [PMID: 23050238 PMCID: PMC3464120 DOI: 10.1534/g3.112.003400] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/22/2012] [Indexed: 01/26/2023]
Abstract
Systematic analysis of gene overexpression phenotypes provides an insight into gene function, enzyme targets, and biological pathways. Here, we describe a novel functional genomics platform that enables a highly parallel and systematic assessment of overexpression phenotypes in pooled cultures. First, we constructed a genome-level collection of ~5100 yeast barcoder strains, each of which carries a unique barcode, enabling pooled fitness assays with a barcode microarray or sequencing readout. Second, we constructed a yeast open reading frame (ORF) galactose-induced overexpression array by generating a genome-wide set of yeast transformants, each of which carries an individual plasmid-born and sequence-verified ORF derived from the Saccharomyces cerevisiae full-length EXpression-ready (FLEX) collection. We combined these collections genetically using synthetic genetic array methodology, generating ~5100 strains, each of which is barcoded and overexpresses a specific ORF, a set we termed “barFLEX.” Additional synthetic genetic array allows the barFLEX collection to be moved into different genetic backgrounds. As a proof-of-principle, we describe the properties of the barFLEX overexpression collection and its application in synthetic dosage lethality studies under different environmental conditions.
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Abstract
The maintenance of genome stability is critical for survival, and its failure is often associated with tumorigenesis. The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand cross-links (ICLs), and a germline defect in the pathway results in FA, a cancer predisposition syndrome driven by genome instability. Central to this pathway is the monoubiquitination of FANCD2, which coordinates multiple DNA repair activities required for the resolution of ICLs. Recent studies have demonstrated how the FA pathway coordinates three critical DNA repair processes, including nucleolytic incision, translesion DNA synthesis (TLS), and homologous recombination (HR). Here, we review recent advances in our understanding of the downstream ICL repair steps initiated by ubiquitin-mediated FA pathway activation.
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Schlecht U, St Onge RP, Walther T, François JM, Davis RW. Cationic amphiphilic drugs are potent inhibitors of yeast sporulation. PLoS One 2012; 7:e42853. [PMID: 22905177 PMCID: PMC3414501 DOI: 10.1371/journal.pone.0042853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 07/12/2012] [Indexed: 11/18/2022] Open
Abstract
Meiosis is a highly regulated developmental process that occurs in all eukaryotes that engage in sexual reproduction. Previous epidemiological work shows that male and female infertility is rising and environmental factors, including pollutants such as organic solvents, are thought to play a role in this phenomenon. To better understand how organic compounds interfere with meiotic development, the model organism Saccharomyces cerevisiae was exposed to 446 bioactive molecules while undergoing meiotic development, and sporulation efficiency was quantified employing two different high-throughput assays. 12 chemicals were identified that strongly inhibited spore formation but did not interfere with vegetative growth. Many of these chemicals are known to bind to monoamine-receptors in higher eukaryotes and are cationic amphiphilic drugs. A detailed analysis of one of these drugs, tripelennamine, revealed that it induces sporulation-specific cytotoxicity and a strong inhibition of meiotic M phase. The drug, however, only mildly interfered with pre-meiotic DNA synthesis and the early meiotic transcriptional program. Chemical-genomic screening identified genes involved in autophagy as hypersensitive to tripelennamine. In addition, we found that growing and sporulating yeast cells heterozygous for the aminophospholipid translocase, NEO1, are haploinsufficient in the presence of the drug.
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Affiliation(s)
- Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America.
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Abstract
A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We describe a high-throughput strategy based on the method Tn-seq that can be applied to any genetically manipulatable microorganism. By screening 17 in vitro and two in vivo (carriage and infection) conditions for the pathogen Streptococcus pneumoniae, we create a resource consisting of >1800 interactions that is rich in new genotype–phenotype relationships. We describe genes that are involved in differential carbon source utilization in the host, as well as genes that are involved both in virulence and in resistance against specific in vitro stresses, thereby revealing selection pressures that the pathogen experiences in vivo. We reveal the secondary response to an antibiotic, including a dual role efflux pump also involved in resistance to pH stress. Through genetic-interaction mapping and gene-expression analysis we define the mechanism of attenuation and the regulatory relationship between a two-component system and a core biosynthetic pathway specific to microorganisms. Thus, we have generated a resource that provides detailed insight into the biology and virulence of S. pneumoniae and provided a road map for similar discovery in other microorganisms.
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Affiliation(s)
- Tim van Opijnen
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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