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Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes. Microorganisms 2023; 11:microorganisms11010229. [PMID: 36677521 PMCID: PMC9862619 DOI: 10.3390/microorganisms11010229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of deletions in the viral genome. In this work, we performed a statistical analysis of deletions. Specifically, we analyzed correlations between deletions in the SARS-CoV-2 genome and repetitive elements and documented a significant association of deletions with runs of identical (poly-) nucleotides and direct repeats. Our analyses of deletions in the accessory genes of SARS-CoV-2 suggested that there may be a hypervariability in ORF7A and ORF8 that is not associated with repetitive elements. Such recurrent search in a "sequence space" of accessory genes (that might be driven by natural selection) did not yet cause increased viability of the SARS-CoV-2 variants. However, deletions in the accessory genes may ultimately produce new variants that are more successful compared to the viral strains with the conventional architecture of the SARS-CoV-2 accessory genes.
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2
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Rogozin IB, Charyyeva A, Sidorenko IA, Babenko VN, Yurchenko V. Frequent Recombination Events in Leishmania donovani: Mining Population Data. Pathogens 2020; 9:pathogens9070572. [PMID: 32679679 PMCID: PMC7400496 DOI: 10.3390/pathogens9070572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/24/2020] [Accepted: 07/13/2020] [Indexed: 11/21/2022] Open
Abstract
The Leishmania donovani species complex consists of all L. donovani and L. infantum strains mainly responsible for visceral leishmaniasis (VL). It was suggested that genome rearrangements in Leishmania spp. occur very often, thus enabling parasites to adapt to the different environmental conditions. Some of these rearrangements may be directly linked to the virulence or explain the reduced efficacy of antimonial drugs in some isolates. In the current study, we focused on a large-scale analysis of putative gene conversion events using publicly available datasets. Previous population study of L. donovani suggested that population variability of L. donovani is relatively low, however the authors used masking procedures and strict read selection criteria. We decided to re-analyze DNA-seq data without masking sequences, because we were interested in the most dynamic fraction of the genome. The majority of samples have an excess of putative gene conversion/recombination events in the noncoding regions, however we found an overall excess of putative intrachromosomal gene conversion/recombination in the protein coding genes, compared to putative interchromosomal gene conversion/recombination events.
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Affiliation(s)
- Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA;
| | - Arzuv Charyyeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Ivan A. Sidorenko
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (I.A.S.); (V.N.B.)
| | - Vladimir N. Babenko
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (I.A.S.); (V.N.B.)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
- Correspondence:
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3
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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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Postnikova O, Poliakov E, Golestaneh N, Rogozin IB, Redmond TM. Stable Intronic Sequences and Exon Skipping Events in the Human RPE65 Gene: Analysis of Expression in Retinal Pigment Epithelium Cells and Cell Culture Models. Front Genet 2019; 10:634. [PMID: 31379919 PMCID: PMC6658614 DOI: 10.3389/fgene.2019.00634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/17/2019] [Indexed: 12/04/2022] Open
Abstract
Currently, there is much interest in intronic sequence-containing long non-coding RNAs and the role of intronic transcription in regulation of cellular metabolism and fate. Several stable intronic sequence RNAs (sisRNAs) were recently implicated in regulation of parental genes. To investigate transcription from introns of the RPE65 gene, we analyzed RNA-seq and Nanopore sequencing data from different cell models of human retinal pigment epithelium (RPE) and native bovine RPE. We discovered putative stable poly-adenylated transcripts with sequences corresponding to intronic regions of the RPE65 gene in the cytoplasm of RPE cells. These stable intronic sequences could be important for RPE65 transcription, splicing or translation. We also analyzed alternative splicing events in RPE65. Frequent exon skipping events involving exons 2, 3, and 7 were detected. The rate of these events was much higher in human RPE cell cultures compared with native RPE , consistent with lack of translation of RPE65 mRNA in cell cultures.
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Affiliation(s)
- Olga Postnikova
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, NIH, Bethesda, MD, United States
| | - Eugenia Poliakov
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, NIH, Bethesda, MD, United States
| | - Nady Golestaneh
- Departments of Ophthalmology, Neurology, Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, United States
| | - T Michael Redmond
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, NIH, Bethesda, MD, United States
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Roche-Lima A, Carrasquillo-Carrión K, Gómez-Moreno R, Cruz JM, Velázquez-Morales DM, Rogozin IB, Baerga-Ortiz A. The Presence of Genotoxic and/or Pro-inflammatory Bacterial Genes in Gut Metagenomic Databases and Their Possible Link With Inflammatory Bowel Diseases. Front Genet 2018; 9:116. [PMID: 29692798 PMCID: PMC5902703 DOI: 10.3389/fgene.2018.00116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/22/2018] [Indexed: 01/19/2023] Open
Abstract
Background: The human gut microbiota is a dynamic community of microorganisms that mediate important biochemical processes. Differences in the gut microbial composition have been associated with inflammatory bowel diseases (IBD) and other intestinal disorders. In this study, we quantified and compared the frequencies of eight genotoxic and/or pro-inflammatory bacterial genes found in metagenomic Whole Genome Sequences (mWGSs) of samples from individuals with IBD vs. a cohort of healthy human subjects. Methods: The eight selected gene sequences were clbN, clbB, cif, cnf-1, usp, tcpC from Escherichia coli, gelE from Enterococcus faecalis and murB from Akkermansia muciniphila. We also included the sequences for the conserved murB genes from E. coli and E. faecalis as markers for the presence of Enterobacteriaceae or Enterococci in the samples. The gene sequences were chosen based on their previously reported ability to disrupt normal cellular processes to either promote inflammation or to cause DNA damage in cultured cells or animal models, which could be linked to a role in IBD. The selected sequences were searched in three different mWGS datasets accessed through the Human Microbiome Project (HMP): a healthy cohort (N = 251), a Crohn's disease cohort (N = 60) and an ulcerative colitis cohort (N = 17). Results: Firstly, the sequences for the murB housekeeping genes from Enterobacteriaceae and Enterococci were more frequently found in the IBD cohorts (32% E. coli in IBD vs. 12% in healthy; 13% E. faecalis in IBD vs. 3% in healthy) than in the healthy cohort, confirming earlier reports of a higher presence of both of these taxa in IBD. For some of the sequences in our study, especially usp and gelE, their frequency was even more sharply increased in the IBD cohorts than in the healthy cohort, suggesting an association with IBD that is not easily explained by the increased presence of E. coli or E. faecalis in those samples. Conclusion: Our results suggest a significant association between the presence of some of these genotoxic or pro-inflammatory gene sequences and IBDs. In addition, these results illustrate the power and limitations of the HMP database in the detection of possible clinical correlations for individual bacterial genes.
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Affiliation(s)
- Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Kelvin Carrasquillo-Carrión
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Ramón Gómez-Moreno
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico.,Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Juan M Cruz
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Dayanara M Velázquez-Morales
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Igor B Rogozin
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD, United States
| | - Abel Baerga-Ortiz
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico.,Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
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Dahal BK, Kadyrova LY, Delfino KR, Rogozin IB, Gujar V, Lobachev KS, Kadyrov FA. Involvement of DNA mismatch repair in the maintenance of heterochromatic DNA stability in Saccharomyces cerevisiae. PLoS Genet 2017; 13:e1007074. [PMID: 29069084 PMCID: PMC5673234 DOI: 10.1371/journal.pgen.1007074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 11/06/2017] [Accepted: 10/15/2017] [Indexed: 11/30/2022] Open
Abstract
Heterochromatin contains a significant part of nuclear DNA. Little is known about the mechanisms that govern heterochromatic DNA stability. We show here that in the yeast Saccharomyces cerevisiae (i) DNA mismatch repair (MMR) is required for the maintenance of heterochromatic DNA stability, (ii) MutLα (Mlh1-Pms1 heterodimer), MutSα (Msh2-Msh6 heterodimer), MutSβ (Msh2-Msh3 heterodimer), and Exo1 are involved in MMR at heterochromatin, (iii) Exo1-independent MMR at heterochromatin frequently leads to the formation of Pol ζ-dependent mutations, (iv) MMR cooperates with the proofreading activity of Pol ε and the histone acetyltransferase Rtt109 in the maintenance of heterochromatic DNA stability, (v) repair of base-base mismatches at heterochromatin is less efficient than repair of base-base mismatches at euchromatin, and (vi) the efficiency of repair of 1-nt insertion/deletion loops at heterochromatin is similar to the efficiency of repair of 1-nt insertion/deletion loops at euchromatin. Eukaryotic mismatch repair is an important intracellular process that defends DNA against mutations. Inactivation of mismatch repair in human cells strongly increases the risk of cancer initiation and development. Although significant progress has been made in understanding mismatch repair at euchromatin, mismatch repair at heterochromatin is not well understood. Baker’s yeast is a key model organism to study mismatch repair. We determined that in baker’s yeast (1) mismatch repair protects heterochromatic DNA from mutations, (2) the MutLα, MutSα, MutSβ, and Exo1 proteins play important roles in mismatch repair at heterochromatin, (3) Exo1-independent mismatch repair at heterochromatin is an error-prone process; (4) mismatch repair cooperates with two other intracellular processes to protect the stability of heterochromatic DNA; and (5) the efficiency of repair of base-base mismatches at heterochromatin is lower than the efficiency of repair of base-base mismatches at euchromatin, but the efficiency of 1-nt insertion/deletion loop repair at heterochromatin is similar to the efficiency of 1-nt insertion/deletion loop repair at euchromatin.
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Affiliation(s)
- Basanta K. Dahal
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States of America
| | - Lyudmila Y. Kadyrova
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States of America
| | - Kristin R. Delfino
- Center for Clinical Research, Southern Illinois University School of Medicine, Springfield, IL, United States of America
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America
| | - Vaibhavi Gujar
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States of America
| | - Kirill S. Lobachev
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Farid A. Kadyrov
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States of America
- * E-mail:
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7
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Cheung PPH, Rogozin IB, Choy KT, Ng HY, Peiris JSM, Yen HL. Comparative mutational analyses of influenza A viruses. RNA (NEW YORK, N.Y.) 2015; 21:36-47. [PMID: 25404565 PMCID: PMC4274636 DOI: 10.1261/rna.045369.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The error-prone RNA-dependent RNA polymerase (RdRP) and external selective pressures are the driving forces for RNA viral diversity. When confounded by selective pressures, it is difficult to assess if influenza A viruses (IAV) that have a wide host range possess comparable or distinct spontaneous mutational frequency in their RdRPs. We used in-depth bioinformatics analyses to assess the spontaneous mutational frequencies of two RdRPs derived from human seasonal (A/Wuhan/359/95; Wuhan) and H5N1 (A/Vietnam/1203/04; VN1203) viruses using the mini-genome system with a common firefly luciferase reporter serving as the template. High-fidelity reverse transcriptase was applied to generate high-quality mutational spectra which allowed us to assess and compare the mutational frequencies and mutable motifs along a target sequence of the two RdRPs of two different subtypes. We observed correlated mutational spectra (τ correlation P < 0.0001), comparable mutational frequencies (H3N2:5.8 ± 0.9; H5N1:6.0 ± 0.5), and discovered a highly mutable motif "(A)AAG" for both Wuhan and VN1203 RdRPs. Results were then confirmed with two recombinant A/Puerto Rico/8/34 (PR8) viruses that possess RdRP derived from Wuhan or VN1203 (RG-PR8×Wuhan(PB2, PB1, PA, NP) and RG-PR8×VN1203(PB2, PB1, PA, NP)). Applying novel bioinformatics analysis on influenza mutational spectra, we provide a platform for a comprehensive analysis of the spontaneous mutation spectra for an RNA virus.
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Affiliation(s)
- Peter Pak-Hang Cheung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894-6075, USA
| | - Ka-Tim Choy
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Hoi Yee Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Joseph Sriyal Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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8
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Poliakov E, Koonin EV, Rogozin IB. Impairment of translation in neurons as a putative causative factor for autism. Biol Direct 2014; 9:16. [PMID: 25011470 PMCID: PMC4099083 DOI: 10.1186/1745-6150-9-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/01/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions associated with ASD on mRNA stability, splicing enhancers and silencers, and codon usage. PRESENTATION OF THE HYPOTHESIS We hypothesize that subtle impairment of translation, resulting in dosage imbalance of neuron-specific proteins, contributes to the etiology of ASD synergistically with environmental neurotoxins. TESTING THE HYPOTHESIS A statistically significant shift from optimal to suboptimal codons caused by rare synonymous substitutions associated with ASD was detected whereas no effect on other analyzed characteristics of transcripts was identified. This result suggests that the impact of rare codons on the translation of genes involved in neuron development, even if slight in magnitude, could contribute to the pathogenesis of ASD in the presence of an aggressive chemical background. This hypothesis could be tested by further analysis of ASD-associated mutations, direct biochemical characterization of their effects, and assessment of in vivo effects on animal models. IMPLICATIONS OF THE HYPOTHESIS It seems likely that the synergistic action of environmental hazards with genetic variations that in themselves have limited or no deleterious effects but are potentiated by the environmental factors is a general principle that underlies the alarming increase in the ASD prevalence. REVIEWERS This article was reviewed by Andrey Rzhetsky, Neil R. Smalheiser, and Shamil R. Sunyaev.
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Affiliation(s)
- Eugenia Poliakov
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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9
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Mitochondrial DNA and microsatellite markers evidence a different pattern of hybridization in red-legged partridge (Alectoris rufa) populations from NW Italy. EUR J WILDLIFE RES 2012. [DOI: 10.1007/s10344-012-0686-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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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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Hashimoto K, Rogozin IB, Panchenko AR. Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases. Hum Mutat 2012; 33:1566-75. [PMID: 22753356 PMCID: PMC3465464 DOI: 10.1002/humu.22145] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 01/16/2023]
Abstract
Aberrant activation of receptor tyrosine kinases (RTKs) is a common feature of many cancer cells. It was previously suggested that the mechanisms of kinase activation in cancer might be linked to transitions between active and inactive states. Here, we estimate the effects of single and double cancer mutations on the stability of active and inactive states of the kinase domains from different RTKs. We show that singleton cancer mutations destabilize active and inactive states; however, inactive states are destabilized more than the active ones, leading to kinase activation. We show that there exists a relationship between the estimate of oncogenic potential of cancer mutation and kinase activation. Namely, more frequent mutations have a higher activating effect, which might allow us to predict the activating effect of the mutations from the mutation spectra. Independent evolutionary analysis of mutation spectra complements this observation and finds the same frequency threshold defining mutation hotspots. We analyze double mutations and report a positive epistasis and additional advantage of doublets with respect to cancer cell fitness. The activation mechanisms of double mutations differ from those of single mutations and double mutation spectrum is found to be dissimilar to the mutation spectrum of singletons.
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Affiliation(s)
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna R. Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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12
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Lada AG, Waisertreiger ISR, Grabow CE, Prakash A, Borgstahl GEO, Rogozin IB, Pavlov YI. Replication protein A (RPA) hampers the processive action of APOBEC3G cytosine deaminase on single-stranded DNA. PLoS One 2011; 6:e24848. [PMID: 21935481 PMCID: PMC3174200 DOI: 10.1371/journal.pone.0024848] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 08/19/2011] [Indexed: 11/25/2022] Open
Abstract
Background Editing deaminases have a pivotal role in cellular physiology. A notable member of this superfamily, APOBEC3G (A3G), restricts retroviruses, and Activation Induced Deaminase (AID) generates antibody diversity by localized deamination of cytosines in DNA. Unconstrained deaminase activity can cause genome-wide mutagenesis and cancer. The mechanisms that protect the genomic DNA from the undesired action of deaminases are unknown. Using the in vitro deamination assays and expression of A3G in yeast, we show that replication protein A (RPA), the eukaryotic single-stranded DNA (ssDNA) binding protein, severely inhibits the deamination activity and processivity of A3G. Principal Findings/Methodology We found that mutations induced by A3G in the yeast genomic reporter are changes of a single nucleotide. This is unexpected because of the known property of A3G to catalyze multiple deaminations upon one substrate encounter event in vitro. The addition of recombinant RPA to the oligonucleotide deamination assay severely inhibited A3G activity. Additionally, we reveal the inverse correlation between RPA concentration and the number of deaminations induced by A3G in vitro on long ssDNA regions. This resembles the “hit and run” single base substitution events observed in yeast. Significance Our data suggest that RPA is a plausible antimutator factor limiting the activity and processivity of editing deaminases in the model yeast system. Because of the similar antagonism of yeast RPA and human RPA with A3G in vitro, we propose that RPA plays a role in the protection of the human genome cell from A3G and other deaminases when they are inadvertently diverged from their natural targets. We propose a model where RPA serves as one of the guardians of the genome that protects ssDNA from the destructive processive activity of deaminases by non-specific steric hindrance.
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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
| | - Irina S.-R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Corinn E. Grabow
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Aishwarya Prakash
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, 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
- Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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13
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Aksenova A, Volkov K, Maceluch J, Pursell ZF, Rogozin IB, Kunkel TA, Pavlov YI, Johansson E. Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε. PLoS Genet 2010; 6:e1001209. [PMID: 21124948 PMCID: PMC2987839 DOI: 10.1371/journal.pgen.1001209] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 10/15/2010] [Indexed: 01/31/2023] Open
Abstract
Yeast DNA polymerase ε (Pol ε) is a highly accurate and processive enzyme that participates in nuclear DNA replication of the leading strand template. In addition to a large subunit (Pol2) harboring the polymerase and proofreading exonuclease active sites, Pol ε also has one essential subunit (Dpb2) and two smaller, non-essential subunits (Dpb3 and Dpb4) whose functions are not fully understood. To probe the functions of Dpb3 and Dpb4, here we investigate the consequences of their absence on the biochemical properties of Pol ε in vitro and on genome stability in vivo. The fidelity of DNA synthesis in vitro by purified Pol2/Dpb2, i.e. lacking Dpb3 and Dpb4, is comparable to the four-subunit Pol ε holoenzyme. Nonetheless, deletion of DPB3 and DPB4 elevates spontaneous frameshift and base substitution rates in vivo, to the same extent as the loss of Pol ε proofreading activity in a pol2-4 strain. In contrast to pol2-4, however, the dpb3Δdpb4Δ does not lead to a synergistic increase of mutation rates with defects in DNA mismatch repair. The increased mutation rate in dpb3Δdpb4Δ strains is partly dependent on REV3, as well as the proofreading capacity of Pol δ. Finally, biochemical studies demonstrate that the absence of Dpb3 and Dpb4 destabilizes the interaction between Pol ε and the template DNA during processive DNA synthesis and during processive 3′ to 5′exonucleolytic degradation of DNA. Collectively, these data suggest a model wherein Dpb3 and Dpb4 do not directly influence replication fidelity per se, but rather contribute to normal replication fork progression. In their absence, a defective replisome may more frequently leave gaps on the leading strand that are eventually filled by Pol ζ or Pol δ, in a post-replication process that generates errors not corrected by the DNA mismatch repair system. The high fidelity of DNA replication is safeguarded by the accuracy of nucleotide selection by DNA polymerases, proofreading activity of the replicative polymerases, and the DNA mismatch repair system. Errors made by replicative polymerases are corrected by mismatch repair, and inactivation of the mismatch repair system results in a multiplicative increase in error rates when combined with a proofreading deficient allele of a replicative polymerase. In this study, we demonstrate that the deletion of two non-essential genes encoding for two subunits of Pol ε give an increased mutation rate due to increased synthesis by the error-prone DNA polymerase ζ. Surprisingly, there was no multiplicative increase in error rates when the mismatch repair system was inactivated. We propose that the deletion of DPB3 and DPB4 gives a defective replisome, which in turn gives increased synthesis, in part, by Pol ζ during an error-prone post-replication process that is not efficiently repaired by the mismatch repair system.
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Affiliation(s)
- Anna Aksenova
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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14
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Resch AM, Ogurtsov AY, Rogozin IB, Shabalina SA, Koonin EV. Evolution of alternative and constitutive regions of mammalian 5'UTRs. BMC Genomics 2009; 10:162. [PMID: 19371439 PMCID: PMC2674463 DOI: 10.1186/1471-2164-10-162] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Accepted: 04/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) in protein-coding sequences has emerged as an important mechanism of regulation and diversification of animal gene function. By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5'-untranslated regions (5'UTRs) of mammalian genes are not well characterized. RESULTS We evaluated the abundance, conservation and evolution of putative regulatory control elements, namely, upstream start codons (uAUGs) and open reading frames (uORFs), in the 5'UTRs of human and mouse genes impacted by alternative events. For genes with alternative 5'UTRs, the fraction of alternative sequences (those present in a subset of the transcripts) is much greater than that in the corresponding coding sequence, conceivably, because 5'UTRs are not bound by constraints on protein structure that limit AS in coding regions. Alternative regions of mammalian 5'UTRs evolve faster and are subject to a weaker purifying selection than constitutive portions. This relatively weak selection results in over-abundance of uAUGs and uORFs in the alternative regions of 5'UTRs compared to constitutive regions. Nevertheless, even in alternative regions, uORFs evolve under a stronger selection than the rest of the sequences, indicating that some of the uORFs are conserved regulatory elements; some of the non-conserved uORFs could be involved in species-specific regulation. CONCLUSION The findings on the evolution and selection in alternative and constitutive regions presented here are consistent with the hypothesis that alternative events, namely, AS and ATI, in 5'UTRs of mammalian genes are likely to contribute to the regulation of translation.
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Affiliation(s)
- Alissa M Resch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
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15
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Xiao Z, Ray M, Jiang C, Clark AB, Rogozin IB, Diaz M. Known components of the immunoglobulin A:T mutational machinery are intact in Burkitt lymphoma cell lines with G:C bias. Mol Immunol 2007; 44:2659-66. [PMID: 17240451 PMCID: PMC1868521 DOI: 10.1016/j.molimm.2006.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 12/10/2006] [Indexed: 12/14/2022]
Abstract
The basis for mutations at A:T base pairs in immunoglobulin hypermutation and defining how AID interacts with the DNA of the immunoglobulin locus are major aspects of the immunoglobulin mutator mechanism where questions remain unanswered. Here, we examined the pattern of mutations generated in mice deficient in various DNA repair proteins implicated in A:T mutation and found a previously unappreciated bias at G:C base pairs in spectra from mice simultaneously deficient in DNA mismatch repair and uracil DNA glycosylase. This suggests a strand-biased DNA transaction for AID delivery which is then masked by the mechanism that introduces A:T mutations. Additionally, we asked if any of the known components of the A:T mutation machinery underscore the basis for the paucity of A:T mutations in the Burkitt lymphoma cell lines, Ramos and BL2. Ramos and BL2 cells were proficient in MSH2/MSH6-mediated mismatch repair, and express high levels of wild-type, full-length DNA polymerase eta. In addition, Ramos cells have high levels of uracil DNA glycosylase protein and are proficient in base excision repair. These results suggest that Burkitt lymphoma cell lines may be deficient in an unidentified factor that recruits the machinery necessary for A:T mutation or that AID-mediated cytosine deamination in these cells may be processed by conventional base excision repair truncating somatic hypermutation at the G:C phase. Either scenario suggests that cytosine deamination by AID is not enough to trigger A:T mutation, and that additional unidentified factors are required for full spectrum hypermutation in vivo.
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Affiliation(s)
- Zheng Xiao
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, D3-01, 111 TW Alexander Drive, Research Triangle Park NC 27709
| | - Madhumita Ray
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, D3-01, 111 TW Alexander Drive, Research Triangle Park NC 27709
| | - Chuancang Jiang
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, D3-01, 111 TW Alexander Drive, Research Triangle Park NC 27709
| | - Alan B. Clark
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, D3-01, 111 TW Alexander Drive, Research Triangle Park NC 27709
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Libray of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Marilyn Diaz
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, D3-01, 111 TW Alexander Drive, Research Triangle Park NC 27709
- * Corresponding author: , Phone Number: 919-541-4740, Fax: 919-541-7593
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16
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Mayorov VI, Rogozin IB, Adkison LR, Gearhart PJ. DNA polymerase eta contributes to strand bias of mutations of A versus T in immunoglobulin genes. THE JOURNAL OF IMMUNOLOGY 2005; 174:7781-6. [PMID: 15944281 DOI: 10.4049/jimmunol.174.12.7781] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
DNA polymerase (pol) eta participates in hypermutation of A:T bases in Ig genes because humans deficient for the polymerase have fewer substitutions of these bases. To determine whether polymerase eta is also responsible for the well-known preference for mutations of A vs T on the nontranscribed strand, we sequenced variable regions from three patients with xeroderma pigmentosum variant (XP-V) disease, who lack polymerase eta. The frequency of mutations in the intronic region downstream of rearranged J(H)4 gene segments was similar between XP-V and control clones; however, there were fewer mutations of A:T bases and correspondingly more substitutions of C:G bases in the XP-V clones (p < 10(-7)). There was significantly less of a bias for mutations of A compared with T nucleotides in the XP-V clones compared with control clones, whereas the frequencies for mutations of C and G were identical in both groups. An analysis of mutations in the WA sequence motif suggests that polymerase eta generates more mutations of A than T on the nontranscribed strand. This in vivo data from polymerase eta-deficient B cells correlates well with the in vitro specificity of the enzyme. Because polymerase eta inserts more mutations opposite template T than template A, it would generate more substitutions of A on the newly synthesized strand.
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Affiliation(s)
- Vladimir I Mayorov
- Department of Basic Medical Sciences, Mercer University School of Medicine, Macon, GA 31207, USA
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17
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Mayorov VI, Rogozin IB, Adkison LR, Frahm C, Kunkel TA, Pavlov YI. Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes. BMC Immunol 2005; 6:10. [PMID: 15949042 PMCID: PMC1180437 DOI: 10.1186/1471-2172-6-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2005] [Accepted: 06/10/2005] [Indexed: 12/02/2022] Open
Abstract
Background Antibody genes are diversified by somatic hypermutation (SHM), gene conversion and class-switch recombination. All three processes are initiated by the activation-induced deaminase (AID). According to a DNA deamination model of SHM, AID converts cytosine to uracil in DNA sequences. The initial deamination of cytosine leads to mutation and recombination in pathways involving replication, DNA mismatch repair and possibly base excision repair. The DNA sequence context of mutation hotspots at G-C pairs during SHM is DGYW/WRCH (G-C is a hotspot position, R = A/G, Y = T/C, W = A/T, D = A/G/T). Results To investigate the mechanisms of AID-induced mutagenesis in a model system, we studied the genetic consequences of AID expression in yeast. We constructed a yeast vector with an artificially synthesized human AID gene insert using codons common to highly expressed yeast genes. We found that expression of the artificial hAIDSc gene was moderately mutagenic in a wild-type strain and highly mutagenic in an ung1 uracil-DNA glycosylase-deficient strain. A majority of mutations were at G-C pairs. In the ung1 strain, C-G to T-A transitions were found almost exclusively, while a mixture of transitions with 12% transversions was characteristic in the wild-type strain. In the ung1 strain mutations that could have originated from deamination of the transcribed stand were found more frequently. In the wild-type strain, the strand bias was reversed. DGYW/WRCH motifs were preferential sites of mutations. Conclusion The results are consistent with the hypothesis that AID-mediated deamination of DNA is a major cause of mutations at G-C base pairs in immunoglobulin genes during SHM. The sequence contexts of mutations in yeast induced by AID and those of somatic mutations at G-C pairs in immunoglobulin genes are significantly similar. This indicates that the intrinsic substrate specificity of AID itself is a primary determinant of mutational hotspots at G-C base pairs during SHM.
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Affiliation(s)
| | - Igor B Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda MD 20894, USA
- Institute of Cytology and Genetics SD RAS, Novosibirsk 630090, Russia
| | | | - Christin Frahm
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
| | - Thomas A Kunkel
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
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18
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Glazko GV, Koonin EV, Rogozin IB. Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection. ACTA ACUST UNITED AC 2004; 1679:95-106. [PMID: 15297143 DOI: 10.1016/j.bbaexp.2004.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Revised: 04/28/2004] [Accepted: 05/14/2004] [Indexed: 01/13/2023]
Abstract
We present a classification analysis of the mutation spectra of the p53 gene and construct maps of hotspots for the germline (Li-Fraumein syndrome), different types of tumors and their derived cell lines. While spectra from solid tumors share common hotspots with the germline spectrum, they also contain unique sets of somatic hotspots that are not observed in the germline. All these hotspots correspond to amino acid replacements in the DNA-binding interface of p53. The mutation spectra of lymphomas and cell lines derived from lymphomas and lung cancers contained few hotspots compared to solid tumors. Thus, the distribution of hotspots in the p53 gene appears to depend on the tumor type and cell growth conditions; this specificity is missed by the bulk hotspot analysis. A negative correlation was detected between the amino acid replacement propensity in tumors and evolutionary variability: the hotspots are located in the positions that are highly conserved in p53 and its paralogs, p63 and p73. In all the mutation spectra, substitutions leading to amino acid replacements strongly dominate over silent substitutions, indicating that functional sites evolving under strong purifying selection are subject to intensive positive selection in p53-dependent tumors. These results are compatible with the gain-of-function concept of the role of p53 in tumorigenesis.
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Affiliation(s)
- Galina V Glazko
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
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19
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Poltoratsky VP, Wilson SH, Kunkel TA, Pavlov YI. Recombinogenic Phenotype of Human Activation-Induced Cytosine Deaminase. THE JOURNAL OF IMMUNOLOGY 2004; 172:4308-13. [PMID: 15034045 DOI: 10.4049/jimmunol.172.7.4308] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Class switch recombination, gene conversion, and somatic hypermutation that diversify rearranged Ig genes to produce various classes of high affinity Abs are dependent on the enzyme activation-induced cytosine deaminase (AID). Evidence suggests that somatic hypermutation is due to error-prone DNA repair that is initiated by AID-mediated deamination of cytosine in DNA, whereas the mechanism by which AID controls recombination remains to be elucidated. In this study, using a yeast model system, we have observed AID-dependent recombination. Expression of human AID in wild-type yeast is mutagenic for G-C to A-T transitions, and as expected, this mutagenesis is increased upon inactivation of uracil-DNA glycosylase. AID expression also strongly induces intragenic mitotic recombination, but only in a strain possessing uracil-DNA glycosylase. Thus, the initial step of base excision repair is required for AID-dependent recombination and is a branch point for either hypermutagenesis or recombination.
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Affiliation(s)
- Vladimir P Poltoratsky
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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20
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Shcherbakova PV, Pavlov YI, Chilkova O, Rogozin IB, Johansson E, Kunkel TA. Unique error signature of the four-subunit yeast DNA polymerase epsilon. J Biol Chem 2003; 278:43770-80. [PMID: 12882968 DOI: 10.1074/jbc.m306893200] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have purified wild type and exonuclease-deficient four-subunit DNA polymerase epsilon (Pol epsilon) complex from Saccharomyces cerevisiae and analyzed the fidelity of DNA synthesis by the two enzymes. Wild type Pol epsilon synthesizes DNA accurately, generating single-base substitutions and deletions at average error rates of </=2 x 10-5 and </=5 x 10-7, respectively. Pol epsilon lacking 3' --> 5' exonuclease activity is less accurate to a degree suggesting that wild type Pol epsilon proofreads at least 92% of base substitution errors and at least 99% of frameshift errors made by the polymerase. Surprisingly the base substitution fidelity of exonuclease-deficient Pol epsilon is severalfold lower than that of proofreading-deficient forms of other replicative polymerases. Moreover the spectrum of errors shows a feature not seen with other A, B, C, or X family polymerases: a high proportion of transversions resulting from T.dTTP, T.dCTP, and C.dTTP mispairs. This unique error specificity and amino acid sequence alignments suggest that the structure of the polymerase active site of Pol epsilon differs from those of other B family members. We observed both similarities and differences between the spectrum of substitutions generated by proofreading-deficient Pol epsilon in vitro and substitutions occurring in vivo in a yeast strain defective in Pol epsilon proofreading and DNA mismatch repair. We discuss the implications of these findings for the role of Pol epsilon polymerase activity in DNA replication.
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Affiliation(s)
- Polina V Shcherbakova
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, North Carolina 27709, USA
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21
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Rogozin IB, Pavlov YI. Theoretical analysis of mutation hotspots and their DNA sequence context specificity. Mutat Res 2003; 544:65-85. [PMID: 12888108 DOI: 10.1016/s1383-5742(03)00032-2] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mutation frequencies vary significantly along nucleotide sequences such that mutations often concentrate at certain positions called hotspots. Mutation hotspots in DNA reflect intrinsic properties of the mutation process, such as sequence specificity, that manifests itself at the level of interaction between mutagens, DNA, and the action of the repair and replication machineries. The hotspots might also reflect structural and functional features of the respective DNA sequences. When mutations in a gene are identified using a particular experimental system, resulting hotspots could reflect the properties of the gene product and the mutant selection scheme. Analysis of the nucleotide sequence context of hotspots can provide information on the molecular mechanisms of mutagenesis. However, the determinants of mutation frequency and specificity are complex, and there are many analytical methods for their study. Here we review computational approaches for analyzing mutation spectra (distribution of mutations along the target genes) that include many mutable (detectable) positions. The following methods are reviewed: derivation of a consensus sequence, application of regression approaches to correlate nucleotide sequence features with mutation frequency, mutation hotspot prediction, analysis of oligonucleotide composition of regions containing mutations, pairwise comparison of mutation spectra, analysis of multiple spectra, and analysis of "context-free" characteristics. The advantages and pitfalls of these methods are discussed and illustrated by examples from the literature. The most reliable analyses were obtained when several methods were combined and information from theoretical analysis and experimental observations was considered simultaneously. Simple, robust approaches should be used with small samples of mutations, whereas combinations of simple and complex approaches may be required for large samples. We discuss several well-documented studies where analysis of mutation spectra has substantially contributed to the current understanding of molecular mechanisms of mutagenesis. The nucleotide sequence context of mutational hotspots is a fingerprint of interactions between DNA and DNA repair, replication, and modification enzymes, and the analysis of hotspot context provides evidence of such interactions.
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Affiliation(s)
- Igor B Rogozin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, Russia
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22
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Abstract
The last decade has witnessed a remarkable increase in the number of mutations identified both in human disease-related genes and mutation reporter genes including those in mammalian cells and transgenic animals. This has led to the curation of a number of computerised databases, which make mutation data freely available for analysis. A primary interest of both the clinical researcher and the genetic toxicologist is determination of location and types of mutation within a gene of interest. Collections of mutation data observed for a disease-related gene or, for a gene exposed to a particular chemical, permits discovery of regions of sequence along the gene prone to mutagenesis and may provide clues to the origin of a mutation. The principal tool for visualising the distribution pattern of mutant data along a gene is the mutation spectrum: the distribution and frequency of mutations along a nucleotide sequence. In genetic toxicology, the current wealth of mutation data available allows us to construct many mutation spectra of interest to investigate the mutagenic mechanisms and mutational sites for one or a group of mutagens. Using the multivariate statistical methods principal components analysis (PCA) and cluster analysis (CA) we have tested the ability of these methods to establish the underlying patterns within and between 60 UV-induced, mitomycin C-induced and spontaneous mutations in the supF gene. The spectra were derived from human, monkey and mouse cells including both repair efficient and repair deficient cell lines. We demonstrate and support the successful application of multivariate statistical methods for exploring large sets of mutation spectra to reveal underlying patterns, groupings and similarities. The methods clearly demonstrate how different patterns of spontaneous and UV-induced supF mutation spectra can result from variation in plasmid, culture medium, species origin of cell line and whether mutations arose in vivo or in vitro.
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Affiliation(s)
- P D Lewis
- Bioinformatics Group, Centre for Molecular and Genetic Toxicology, School of Biological Sciences, University of Wales Swansea, UK.
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23
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Abstract
Several lines of research are now converging towards an integrated understanding of mutational mechanisms and their evolutionary implications. Experimentally, crystal structures reveal the effect of sequence context on polymerase fidelity; large-scale sequencing projects generate vast amounts of sequence polymorphism data; and locus-specific databases are being constructed. Computationally, software and analytical tools have been developed to analyze mutational data, to identify mutational hot spots, and to compare the signatures of mutagenic agents.
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Affiliation(s)
- M Zavolan
- Laboratory of Computational Genomics, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
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24
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Abstract
The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis.
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Affiliation(s)
- I Rogozin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, Russia.
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25
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Abstract
Threshold dose/concentration values, such as the lowest effective dose, minimum effective dose or the lowest effective concentration (LED, MED or LEC, respectively) are in use as an alternative to the mutagen potency measures based on the 'rate' measurements (e.g., the slope of the initial part of the dose-response curve). In this respect, several statistical procedures for the corresponding so-called 'dose finding' were proposed during the last decades. However, most of them disregard the discrete nature of responses such as the plate colony count in the Ames Salmonella assay. When the plate counts agree with the Poisson assumption, two procedures considered here seem to be appropriate for the dose finding. One is based on the stepwise collapsing of the homogeneous control and dose counts; another consists of constructing the confidence limits for the mutation induction factor (MIF). When the dose and control counts are non-overlapping, the simple 'visual' non-parametric estimation of LED is possible. Applicability and validity of the methods is demonstrated with the two data sets on the mutagenicity of the beta-carboline alkaloid, harmine, and one of the oxidation products of apomorphine.
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Affiliation(s)
- N N Khromov-Borisov
- Departamento de Biofísica e Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil.
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26
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Picada JN, Khromov-Borisov NN, Henriques JA. Deletogenic activity of 1,2:7,8-diepoxyoctane in the Salmonella typhimurium tester strain TA102. Mutat Res 1999; 437:165-73. [PMID: 10556620 DOI: 10.1016/s1383-5742(99)00082-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
1,2:7,8-Diepoxyoctane (DEO), whose deletogenic activity was first demonstrated in ad-3 system of Neurospora crassa and then in different species, has been tested in Salmonella typhimurium tester strain TA102 (hisG428(Ochre)). It was confirmed that it is a direct acting mutagen and was found that its activity is stimulated with the S9 mix. Obtained His(+) revertants were screened on their response to the histidine analog, N-(2-thiazolyl)-DL-alanine (ThiAla). Thirty-two percent of spontaneous and 52% of DEO-induced revertants were resistant to the analog while no resistance was observed among those induced with 4-nitroquinoline-N-oxide (4NQO). Resistance to ThiAla was interpreted as due to small deletions surrounding the target TAA codon in hisG428(Ochre). Thus, at least two simple test-systems, ad-3 of N. crassa and hisG428(Ochre) of S. typhimurium, gave compatible results and might be useful in searching of deletogens.
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Affiliation(s)
- J N Picada
- Departamento de Biofsica, GENOTOX-Laboratório de Genotoxicidade/Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Bloco IV, Prdio 43.421, Caixa Postal 15.005, Campus do Vale/UFRGS, CEP 91501-970, Porto Alegre, RS, Brazil
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