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Kozmin SG, Rogozin IB, Moore EA, Abney M, Schaaper RM, Pavlov YI. Comment on "A commensal strain of Staphylococcus epidermidis protects against skin neoplasia" by Nakatsuji et al. SCIENCE ADVANCES 2019; 5:eaaw3915. [PMID: 31535021 PMCID: PMC6739109 DOI: 10.1126/sciadv.aaw3915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
A recent article in Science Advances described the striking discovery that the commensal Staphylococcus epidermidis strain MO34 displays antimicrobial and antitumor activities by producing a small molecule, identified as the nucleobase analog 6-N-hydroxylaminopurine (6-HAP). However, in contradiction to the literature, the authors claimed that 6-HAP is nonmutagenic and proposed that the toxic effect of 6-HAP results from its ability to inhibit, in its base form, DNA synthesis. To resolve the discrepancy, we proved by genetic experiments with bacteria and yeast that extracts of MO34 do contain a mutagenic compound whose effects are identical to chemically synthesized 6-HAP. The MO34 extract induced the same mutation spectrum as authentic 6-HAP. Notably, the toxic and mutagenic effects of both synthetic and MO34-derived 6-HAP depended on conversion to the corresponding nucleotide. The nucleobase 6-HAP does not inhibit DNA synthesis in vitro, and we conclude that 6-HAP exerts its biological activity when incorporated into DNA.
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Affiliation(s)
- Stanislav G. Kozmin
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth A. Moore
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mariah Abney
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- University of Nebraska at Omaha, Omaha, NE, USA
| | - Roel M. Schaaper
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Departments of Microbiology and Pathology, Biochemistry and Molecular Biology, Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
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2
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Westergard L, True HL. Extracellular environment modulates the formation and propagation of particular amyloid structures. Mol Microbiol 2014; 92:698-715. [PMID: 24628771 DOI: 10.1111/mmi.12579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 11/27/2022]
Abstract
Amyloidogenic proteins, including prions, assemble into multiple forms of structurally distinct fibres. The [PSI(+)] prion, endogenous to the yeast Saccharomyces cerevisiae, is a dominantly inherited, epigenetic modifier of phenotypes. [PSI(+)] formation relies on the coexistence of another prion, [RNQ(+)]. Here, in order to better define the role of amyloid diversity on cellular phenotypes, we investigated how physiological and environmental changes impact the generation and propagation of diverse protein conformations from a single polypeptide. Utilizing the yeast model system, we defined extracellular factors that influence the formation of a spectrum of alternative self-propagating amyloid structures of the Sup35 protein, called [PSI(+)] variants. Strikingly, exposure to specific stressful environments dramatically altered the variants of [PSI(+)] that formed de novo. Additionally, we found that stress also influenced the association between the [PSI(+)] and [RNQ(+)] prions in a way that it superceded their typical relationship. Furthermore, changing the growth environment modified both the biochemical properties and [PSI(+)]-inducing capabilities of the [RNQ(+)] template. These data suggest that the cellular environment contributes to both the generation and the selective propagation of specific amyloid structures, providing insight into a key feature that impacts phenotypic diversity in yeast and the cross-species transmission barriers characteristic of prion diseases.
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Affiliation(s)
- Laura Westergard
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
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Lada AG, Stepchenkova EI, Waisertreiger ISR, Noskov VN, Dhar A, Eudy JD, Boissy RJ, Hirano M, Rogozin IB, Pavlov YI. Genome-wide mutation avalanches induced in diploid yeast cells by a base analog or an APOBEC deaminase. PLoS Genet 2013; 9:e1003736. [PMID: 24039593 PMCID: PMC3764175 DOI: 10.1371/journal.pgen.1003736] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/05/2013] [Indexed: 11/23/2022] Open
Abstract
Genetic information should be accurately transmitted from cell to cell; conversely, the adaptation in evolution and disease is fueled by mutations. In the case of cancer development, multiple genetic changes happen in somatic diploid cells. Most classic studies of the molecular mechanisms of mutagenesis have been performed in haploids. We demonstrate that the parameters of the mutation process are different in diploid cell populations. The genomes of drug-resistant mutants induced in yeast diploids by base analog 6-hydroxylaminopurine (HAP) or AID/APOBEC cytosine deaminase PmCDA1 from lamprey carried a stunning load of thousands of unselected mutations. Haploid mutants contained almost an order of magnitude fewer mutations. To explain this, we propose that the distribution of induced mutation rates in the cell population is uneven. The mutants in diploids with coincidental mutations in the two copies of the reporter gene arise from a fraction of cells that are transiently hypersensitive to the mutagenic action of a given mutagen. The progeny of such cells were never recovered in haploids due to the lethality caused by the inactivation of single-copy essential genes in cells with too many induced mutations. In diploid cells, the progeny of hypersensitive cells survived, but their genomes were saturated by heterozygous mutations. The reason for the hypermutability of cells could be transient faults of the mutation prevention pathways, like sanitization of nucleotide pools for HAP or an elevated expression of the PmCDA1 gene or the temporary inability of the destruction of the deaminase. The hypothesis on spikes of mutability may explain the sudden acquisition of multiple mutational changes during evolution and carcinogenesis.
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Affiliation(s)
- Artem G. Lada
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Elena I. Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Saint Petersburg Branch of Vavilov Institute of General Genetics, St. Petersburg, Russia
- Department of Genetics, Saint Petersburg University, St. Petersburg, Russia
| | - Irina S. R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Vladimir N. Noskov
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Alok Dhar
- Department of Genetics, Cell Biology and Anatomy and Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - James D. Eudy
- Department of Genetics, Cell Biology and Anatomy and Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Robert J. Boissy
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Masayuki Hirano
- Emory Vaccine Center, Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Genetics, Saint Petersburg University, St. Petersburg, Russia
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Waisertreiger ISR, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI. Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:699-724. [PMID: 23055184 PMCID: PMC3893020 DOI: 10.1002/em.21735] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/13/2012] [Accepted: 08/15/2012] [Indexed: 06/01/2023]
Abstract
The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ϵ, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair.
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Affiliation(s)
- Irina S.-R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Victoria G. Liston
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Miriam R. Menezes
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Hyun-Min Kim
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Elena I. Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Saint Petersburg Branch of Vavilov Institute of General Genetics, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Igor B. Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, U.S.A
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Youri. I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
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An effective method for detection and analysis of DNA damage induced by heavy-ion beams. Biosci Biotechnol Biochem 2007; 71:2864-9. [PMID: 17986762 DOI: 10.1271/bbb.70571] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have developed an efficient system to detect and analyze DNA mutations induced by heavy-ion beams in Arabiopsis thaliana. In this system, a stable transgenic Arabidopsis line that constitutively expresses a yellow fluorescent protein (YFP) by a single-copy gene at a genomic locus was constructed and irradiated with heavy-ion beams. The YFP gene is a target of mutagenesis, and its loss of function or expression can easily be detected by the disappearance of YFP signals in planta under microscopy. With this system, a (12)C(6+)-induced mutant with single deletion and multiple base changes was isolated.
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Matuo Y, Nishijima S, Hase Y, Sakamoto A, Tanaka A, Shimizu K. Specificity of mutations induced by carbon ions in budding yeast Saccharomyces cerevisiae. Mutat Res 2006; 602:7-13. [PMID: 16949109 DOI: 10.1016/j.mrfmmm.2006.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 06/27/2006] [Accepted: 07/13/2006] [Indexed: 05/11/2023]
Abstract
To investigate the nature of mutations induced by accelerated ions in eukaryotic cells, the effects of carbon-ion irradiation were compared with those of gamma-ray irradiation in the budding yeast Saccharomyces cerevisiae. The mutational effect and specificity of carbon-ion beams were studied in the URA3 gene of the yeast. Our experiments showed that the carbon ions generated more than 10 times the number of mutations induced by gamma-rays, and that the types of base changes induced by carbon ions include transversions (68.7%), transitions (13.7%) and deletions/insertions (17.6%). The transversions were mainly G:C-->T:A, and all the transitions were G:C-->A:T. In comparison with the surrounding sequence context of mutational base sites, the C residues in the 5'-AC(A/T)-3' sequence were found to be easily changed. Large deletions and duplications were not observed, whereas ion-induced mutations in Arabidopsis thaliana were mainly short deletions and rearrangements. The remarkable feature of yeast mutations induced by carbon ions was that the mutation sites were localized near the linker regions of nucleosomes, whereas mutations induced by gamma-ray irradiation were located uniformly throughout the gene.
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Affiliation(s)
- Youichirou Matuo
- Graduate School of Engineering, Osaka University, Yamada-oka 2-1, Suita, Osaka 565-0871, Japan
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Liebman SW, Bagriantsev SN, Derkatch IL. Biochemical and genetic methods for characterization of [PIN+] prions in yeast. Methods 2006; 39:23-34. [PMID: 16793281 DOI: 10.1016/j.ymeth.2006.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Accepted: 04/24/2006] [Indexed: 10/24/2022] Open
Abstract
The glutamine- and asparagine-rich Rnq1p protein in Saccharomyces cerevisiae can exist in the cell as a soluble monomer or in one of several aggregated, infectious, prion forms called [PIN(+)]. Interest in [PIN(+)] is heightened by its ability to promote the conversion of other proteins into a prion or an aggregated amyloid state. However, little is known about the function of Rnq1p, which makes it difficult to assay the phenotypes associated with its normal vs. prion forms. In this chapter, we describe methods used to detect [PIN(+)] and distinguish between different variations of the prion. Genetic methods are based on the ability of the [PIN(+)] prion to facilitate the appearance of another yeast prion, [PSI(+)], which has an easily detectable phenotype. Biochemical methods exploit the fact that the [PIN(+)] prion exists in the yeast cytosol in the form of large aggregates, composed of SDS-stable subparticles. Sucrose gradient centrifugation, agarose SDS electrophoresis and GFP fusions are used to distinguish between aggregates and subparticles from different [PIN(+)] variants.
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Affiliation(s)
- Susan W Liebman
- Department of Biological Sciences, Laboratory for Molecular Biology, University of Illinois, Chicago, IL 60607, USA
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Williams TM, Fabbri RM, Reeves JW, Crouse GF. A new reversion assay for measuring all possible base pair substitutions in Saccharomyces cerevisiae. Genetics 2005; 170:1423-6. [PMID: 15911571 PMCID: PMC1451166 DOI: 10.1534/genetics.105.042697] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A TRP5-based reversion system that allows the rates of all possible base pair substitutions to be measured when the TRP5 locus is in both orientations relative to a defined origin of replication has been developed. This system should be useful for a wide variety of mutation and repair studies in yeast.
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Affiliation(s)
| | | | | | - Gray F. Crouse
- Corresponding author: Department of Biology, Emory University, 1510 Clifton Rd., Atlanta, GA 30322-1100. E-mail:
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Abstract
To determine whether replicational mutagenesis in the yeast genome is influenced by the positions of active origins, a reporter gene was placed in two orientations at multiple locations within a 39,000 bp region of chromosome III possessing two strong origins. The frequency of mutations resulting from misincorporation of adenine opposite 8-hydroxyguanine in one strand and 6-hydroxylaminopurine opposite cytosine in the other strand differed by 3- to 10-fold, depending on the gene orientation and its distance from the origins. The observed patterns indicate that active origins establish a strand bias for mutations that is maintained over thousands of base pairs and results from lower nucleotide selectivity and/or less efficient proofreading or mismatch repair during leading strand DNA replication.
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Affiliation(s)
- Youri I Pavlov
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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Current Awareness. Yeast 2001. [DOI: 10.1002/yea.686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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