1
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Horton JS, Taylor TB. Mutation bias and adaptation in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37943288 DOI: 10.1099/mic.0.001404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Genetic mutation, which provides the raw material for evolutionary adaptation, is largely a stochastic force. However, there is ample evidence showing that mutations can also exhibit strong biases, with some mutation types and certain genomic positions mutating more often than others. It is becoming increasingly clear that mutational bias can play a role in determining adaptive outcomes in bacteria in both the laboratory and the clinic. As such, understanding the causes and consequences of mutation bias can help microbiologists to anticipate and predict adaptive outcomes. In this review, we provide an overview of the mechanisms and features of the bacterial genome that cause mutational biases to occur. We then describe the environmental triggers that drive these mechanisms to be more potent and outline the adaptive scenarios where mutation bias can synergize with natural selection to define evolutionary outcomes. We conclude by describing how understanding mutagenic genomic features can help microbiologists predict areas sensitive to mutational bias, and finish by outlining future work that will help us achieve more accurate evolutionary forecasts.
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Affiliation(s)
- James S Horton
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
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2
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Ait Saada A, Guo W, Costa AB, Yang J, Wang J, Lobachev K. Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions. Nucleic Acids Res 2023; 51:3722-3734. [PMID: 36919609 PMCID: PMC10164571 DOI: 10.1093/nar/gkad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
DNA inverted repeats (IRs) are widespread across many eukaryotic genomes. Their ability to form stable hairpin/cruciform secondary structures is causative in triggering chromosome instability leading to several human diseases. Distance and sequence divergence between IRs are inversely correlated with their ability to induce gross chromosomal rearrangements (GCRs) because of a lesser probability of secondary structure formation and chromosomal breakage. In this study, we demonstrate that structural parameters that normally constrain the instability of IRs are overcome when the repeats interact in single-stranded DNA (ssDNA). We established a system in budding yeast whereby >73 kb of ssDNA can be formed in cdc13-707fs mutants. We found that in ssDNA, 12 bp or 30 kb spaced Alu-IRs show similarly high levels of GCRs, while heterology only beyond 25% suppresses IR-induced instability. Mechanistically, rearrangements arise after cis-interaction of IRs leading to a DNA fold-back and the formation of a dicentric chromosome, which requires Rad52/Rad59 for IR annealing as well as Rad1-Rad10, Slx4, Msh2/Msh3 and Saw1 proteins for nonhomologous tail removal. Importantly, using structural characteristics rendering IRs permissive to DNA fold-back in yeast, we found that ssDNA regions mapped in cancer genomes contain a substantial number of potentially interacting and unstable IRs.
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Affiliation(s)
- Anissia Ait Saada
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Wenying Guo
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alex B Costa
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jiaxin Yang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Kirill S Lobachev
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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3
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Casas-Delucchi CS, Daza-Martin M, Williams SL, Coster G. The mechanism of replication stalling and recovery within repetitive DNA. Nat Commun 2022; 13:3953. [PMID: 35853874 PMCID: PMC9296464 DOI: 10.1038/s41467-022-31657-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/27/2022] [Indexed: 11/09/2022] Open
Abstract
Accurate chromosomal DNA replication is essential to maintain genomic stability. Genetic evidence suggests that certain repetitive sequences impair replication, yet the underlying mechanism is poorly defined. Replication could be directly inhibited by the DNA template or indirectly, for example by DNA-bound proteins. Here, we reconstitute replication of mono-, di- and trinucleotide repeats in vitro using eukaryotic replisomes assembled from purified proteins. We find that structure-prone repeats are sufficient to impair replication. Whilst template unwinding is unaffected, leading strand synthesis is inhibited, leading to fork uncoupling. Synthesis through hairpin-forming repeats is rescued by replisome-intrinsic mechanisms, whereas synthesis of quadruplex-forming repeats requires an extrinsic accessory helicase. DNA-induced fork stalling is mechanistically similar to that induced by leading strand DNA lesions, highlighting structure-prone repeats as an important potential source of replication stress. Thus, we propose that our understanding of the cellular response to replication stress may also be applied to DNA-induced replication stalling.
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Affiliation(s)
- Corella S Casas-Delucchi
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Manuel Daza-Martin
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Sophie L Williams
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Gideon Coster
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
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4
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Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022; 23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.
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Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Correspondence:
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5
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Svetec Miklenić M, Svetec IK. Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer. Int J Mol Sci 2021; 22:2840. [PMID: 33799581 PMCID: PMC7999016 DOI: 10.3390/ijms22062840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause.
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Affiliation(s)
| | - Ivan Krešimir Svetec
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia;
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6
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Guiblet WM, Cremona MA, Harris RS, Chen D, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Res 2021; 49:1497-1516. [PMID: 33450015 PMCID: PMC7897504 DOI: 10.1093/nar/gkaa1269] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/14/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Approximately 13% of the human genome can fold into non-canonical (non-B) DNA structures (e.g. G-quadruplexes, Z-DNA, etc.), which have been implicated in vital cellular processes. Non-B DNA also hinders replication, increasing errors and facilitating mutagenesis, yet its contribution to genome-wide variation in mutation rates remains unexplored. Here, we conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within noncoding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms. Functional data analysis at single-base resolution demonstrated that substitution frequencies are usually elevated at non-B DNA, with patterns specific to each non-B DNA type. Mirror, direct and inverted repeats have higher substitution frequencies in spacers than in repeat arms, whereas G-quadruplexes, particularly stable ones, have higher substitution frequencies in loops than in stems. Several non-B DNA types also affect substitution frequencies in their flanking regions. Finally, non-B DNA explains more variation than any other predictor in multiple regression models for diversity or divergence at 1-Megabase scale. Thus, non-B DNA substantially contributes to variation in substitution frequencies at small and large scales. Our results highlight the role of non-B DNA in germline mutagenesis with implications to evolution and genetic diseases.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, UniversityPark, PA 16802, USA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Operations and Decision Systems, Université Laval, Canada
- CHU de Québec – Université Laval Research Center, Canada
| | - Robert S Harris
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Di Chen
- Intercollege Graduate Degree Program in Genetics, Huck Institutes of the Life Sciences, Penn State University, UniversityPark, PA 16802, USA
| | - Kristin A Eckert
- Department of Pathology, Penn State University, College of Medicine, Hershey, PA 17033, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
- EMbeDS, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
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7
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Ortolá B, Cordero T, Hu X, Daròs JA. Intron-assisted, viroid-based production of insecticidal circular double-stranded RNA in Escherichia coli. RNA Biol 2021; 18:1846-1857. [PMID: 33472518 PMCID: PMC8582998 DOI: 10.1080/15476286.2021.1872962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
RNA interference (RNAi) is a natural mechanism for protecting against harmful genetic elements and regulating gene expression, which can be artificially triggered by the delivery of homologous double-stranded RNA (dsRNA). This mechanism can be exploited as a highly specific and environmentally friendly pest control strategy. To this aim, systems for producing large amounts of recombinant dsRNA are necessary. We describe a system to efficiently produce large amounts of circular dsRNA in Escherichia coli and demonstrate the efficient insecticidal activity of these molecules against Western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte), a highly damaging pest of corn crops. In our system, the two strands of the dsRNA are expressed in E. coli embedded within the very stable scaffold of Eggplant latent viroid (ELVd), a small circular non-coding RNA. Stability in E. coli of the corresponding plasmids with long inverted repeats was achieved by using a cDNA coding for a group-I autocatalytic intron from Tetrahymena thermophila as a spacer. RNA circularization and large-scale accumulation in E. coli cells was facilitated by co-expression of eggplant tRNA ligase, the enzyme that ligates ELVd during replication in the host plant. The inserted intron efficiently self-spliced from the RNA product during transcription. Circular RNAs containing a dsRNA moiety homologous to smooth septate junction 1 (DvSSJ1) gene exhibited excellent insecticide activity against WCR larvae. Finally, we show that the viroid scaffold can be separated from the final circular dsRNA product using a second T. thermophila self-splicing intron in a permuted form.
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Affiliation(s)
- Beltrán Ortolá
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de Valencia), Valencia, Spain
| | - Teresa Cordero
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de Valencia), Valencia, Spain
| | - Xu Hu
- Corteva Agriscience, Johnston, Iowa, USA
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de Valencia), Valencia, Spain
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8
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Svetec Miklenić M, Gatalica N, Matanović A, Žunar B, Štafa A, Lisnić B, Svetec IK. Size-dependent antirecombinogenic effect of short spacers on palindrome recombinogenicity. DNA Repair (Amst) 2020; 90:102848. [PMID: 32388488 DOI: 10.1016/j.dnarep.2020.102848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 03/21/2020] [Accepted: 03/28/2020] [Indexed: 01/01/2023]
Abstract
Palindromic sequences in DNA can instigate genetic recombination and genome instability, which can result in devastating conditions such as the Emmanuel syndrome. Palindrome recombinogenicity increases with its size and sequence similarity between palindrome arms, while quasipalindromes with long spacers are less recombinogenic. However, the minimal spacer length, which could reduce or abolish palindrome recombinogenicity in the eukaryotic genome, was never determined. Therefore, we constructed a series of palindromes containing spacers of lengths ranging from 0 (perfect palindrome) to 10 bp and tested their recombinogenicity in yeast Saccharomyces cerevisiae. We found that a 7 bp spacer significantly reduces 126 bp palindrome recombinogenicity, while a 10 bp spacer completely stabilizes palindromes up to 150 bp long. Additionally, we showed that palindrome stimulated recombination rate is not dependent on Mus81 and Yen1 endonucleases. We also compared the recombinogenicity of a perfect 126 bp palindrome and a corresponding quasipalindrome consisting of the same palindrome arms with a stabilising 10 bp spacer in sgs1Δ and rad27Δ backgrounds, since both Sgs1 helicase and Rad27 endonuclease are implicated in preventing hairpin formation at palindromic sequences during replication.
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Affiliation(s)
- Marina Svetec Miklenić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Nikolina Gatalica
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Angela Matanović
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Bojan Žunar
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Anamarija Štafa
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Berislav Lisnić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ivan Krešimir Svetec
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
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9
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Gellon L, Kaushal S, Cebrián J, Lahiri M, Mirkin SM, Freudenreich CH. Mrc1 and Tof1 prevent fragility and instability at long CAG repeats by their fork stabilizing function. Nucleic Acids Res 2019; 47:794-805. [PMID: 30476303 PMCID: PMC6344861 DOI: 10.1093/nar/gky1195] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/13/2018] [Indexed: 12/14/2022] Open
Abstract
Fork stabilization at DNA impediments is key to maintaining replication fork integrity and preventing chromosome breaks. Mrc1 and Tof1 are two known stabilizers that travel with the replication fork. In addition to a structural role, Mrc1 has a DNA damage checkpoint function. Using a yeast model system, we analyzed the role of Mrc1 and Tof1 at expanded CAG repeats of medium and long lengths, which are known to stall replication forks and cause trinucleotide expansion diseases such as Huntington's disease and myotonic dystrophy. We demonstrate that the fork stabilizer but not the checkpoint activation function of Mrc1 is key for preventing DNA breakage and death of cells containing expanded CAG tracts. In contrast, both Mrc1 functions are important in preventing repeat length instability. Mrc1 has a general fork protector role that is evident at forks traversing both repetitive and non-repetitive DNA, though it becomes crucial at long CAG repeat lengths. In contrast, the role of Tof1 in preventing fork breakage is specific to long CAG tracts of 85 or more repeats. Our results indicate that long CAG repeats have a particular need for Tof1 and highlight the importance of fork stabilizers in maintaining fork integrity during replication of structure-forming repeats.
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Affiliation(s)
- Lionel Gellon
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Simran Kaushal
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Jorge Cebrián
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Mayurika Lahiri
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
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10
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Aygun N, Altungoz O. MYCN is amplified during S phase, and c‑myb is involved in controlling MYCN expression and amplification in MYCN‑amplified neuroblastoma cell lines. Mol Med Rep 2018; 19:345-361. [PMID: 30483774 PMCID: PMC6297758 DOI: 10.3892/mmr.2018.9686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 10/03/2018] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma derived from primitive sympathetic neural precursors is a common type of solid tumor in infants. MYCN proto-oncogene bHLH transcription factor (MYCN) amplification and 1p36 deletion are important factors associated with the poor prognosis of neuroblastoma. Expression levels of MYCN and c-MYB proto-oncogene transcription factor (c-myb) decline during the differentiation of neuroblastoma cells; E2F transcription factor 1 (E2F1) activates the MYCN promoter. However, the underlying mechanism of MYCN overexpression and amplification requires further investigation. In the present study, potential c-Myb target genes, and the effect of c-myb RNA interference (RNAi) on MYCN expression and amplification were investigated in MYCN-amplified neuroblastoma cell lines. The mRNA expression levels and MYCN gene copy number in five neuroblastoma cell lines were determined by quantitative polymerase chain reaction. In addition, variations in potential target gene expression and MYCN gene copy number between pre- and post-c-myb RNAi treatment groups in MYCN-amplified Kelly, IMR32, SIMA and MHH-NB-11 cell lines, normalized to those of non-MYCN-amplified SH-SY5Y, were examined. To determine the associations between gene expression levels and chromosomal aberrations, MYCN amplification and 1p36 alterations in interphases/metaphases were analyzed using fluorescence in situ hybridization. Statistical analyses revealed correlations between 1p36 alterations and the expression of c-myb, MYB proto-oncogene like 2 (B-myb) and cyclin dependent kinase inhibitor 1A (p21). Additionally, the results of the present study also demonstrated that c-myb may be associated with E2F1 and L3MBTL1 histone methyl-lysine binding protein (L3MBTL1) expression, and that E2F1 may contribute to MYCN, B-myb, p21 and chromatin licensing and DNA replication factor 1 (hCdt1) expression, but to the repression of geminin (GMNN). On c-myb RNAi treatment, L3MBTL1 expression was silenced, while GMNN was upregulated, indicating G2/M arrest. In addition, MYCN gene copy number increased following treatment with c-myb RNAi. Notably, the present study also reported a 43.545% sequence identity between upstream of MYCN and Drosophila melanogaster amplification control element 3, suggesting that expression and/or amplification mechanisms of developmentally-regulated genes may be evolutionarily conserved. In conclusion, c-myb may be associated with regulating MYCN expression and amplification. c-myb, B-myb and p21 may also serve a role against chromosome 1p aberrations. Together, it was concluded that MYCN gene is amplified during S phase, potentially via a replication-based mechanism.
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Affiliation(s)
- Nevim Aygun
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Oguz Altungoz
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
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11
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Le TT, Furukohri A, Tatsumi-Akiyama M, Maki H. Collision with duplex DNA renders Escherichia coli DNA polymerase III holoenzyme susceptible to DNA polymerase IV-mediated polymerase switching on the sliding clamp. Sci Rep 2017; 7:12755. [PMID: 29038530 PMCID: PMC5643309 DOI: 10.1038/s41598-017-13080-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/18/2017] [Indexed: 11/12/2022] Open
Abstract
Organisms possess multiple DNA polymerases (Pols) and use each for a different purpose. One of the five Pols in Escherichia coli, DNA polymerase IV (Pol IV), encoded by the dinB gene, is known to participate in lesion bypass at certain DNA adducts. To understand how cells choose Pols when the replication fork encounters an obstacle on template DNA, the process of polymerase exchange from the primary replicative enzyme DNA polymerase III (Pol III) to Pol IV was studied in vitro. Replicating Pol III forming a tight holoenzyme (Pol III HE) with the sliding clamp was challenged by Pol IV on a primed ssDNA template carrying a short inverted repeat. A rapid and lesion-independent switch from Pol III to Pol IV occurred when Pol III HE encountered a hairpin stem duplex, implying that the loss of Pol III-ssDNA contact induces switching to Pol IV. Supporting this idea, mutant Pol III with an increased affinity for ssDNA was more resistant to Pol IV than wild-type Pol III was. We observed that an exchange between Pol III and Pol IV also occurred when Pol III HE collided with primer/template duplex. Our data suggest that Pol III-ssDNA interaction may modulate the susceptibility of Pol III HE to Pol IV-mediated polymerase exchange.
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Affiliation(s)
- Thanh Thi Le
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Asako Furukohri
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| | - Masahiro Tatsumi-Akiyama
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hisaji Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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12
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El Kafsi H, Loux V, Mariadassou M, Blin C, Chiapello H, Abraham AL, Maguin E, van de Guchte M. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Sci Rep 2017; 7:44331. [PMID: 28281695 PMCID: PMC5345009 DOI: 10.1038/srep44331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/07/2017] [Indexed: 12/29/2022] Open
Abstract
The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a non-manipulated circular bacterial chromosome, at the replication terminus. This intriguing observation prompted us to investigate if similar IRs could be found in other bacteria. IRs with sizes varying from 38 to 76 kbp were found at the replication terminus of all 5 L. delbrueckii ssp. bulgaricus chromosomes analysed, but in none of 1373 other chromosomes. They represent the first naturally occurring very large IRs detected in circular bacterial genomes. A comparison of the L. bulgaricus replication terminus regions and the corresponding regions without IR in 5 L. delbrueckii ssp. lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells. We postulate that the L. delbrueckii ssp. bulgaricus-specific IRs in different strains derive from a single ancestral IR of at least 93 kbp.
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Affiliation(s)
- Hela El Kafsi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Valentin Loux
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Camille Blin
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Hélène Chiapello
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Anne-Laure Abraham
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuelle Maguin
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Maarten van de Guchte
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Gadaleta MC, Das MM, Tanizawa H, Chang YT, Noma KI, Nakamura TM, Noguchi E. Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres. PLoS Genet 2016; 12:e1005943. [PMID: 26990647 PMCID: PMC4798670 DOI: 10.1371/journal.pgen.1005943] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/25/2016] [Indexed: 01/09/2023] Open
Abstract
Genomic instability associated with DNA replication stress is linked to cancer and genetic pathologies in humans. If not properly regulated, replication stress, such as fork stalling and collapse, can be induced at natural replication impediments present throughout the genome. The fork protection complex (FPC) is thought to play a critical role in stabilizing stalled replication forks at several known replication barriers including eukaryotic rDNA genes and the fission yeast mating-type locus. However, little is known about the role of the FPC at other natural impediments including telomeres. Telomeres are considered to be difficult to replicate due to the presence of repetitive GT-rich sequences and telomere-binding proteins. However, the regulatory mechanism that ensures telomere replication is not fully understood. Here, we report the role of the fission yeast Swi1Timeless, a subunit of the FPC, in telomere replication. Loss of Swi1 causes telomere shortening in a telomerase-independent manner. Our epistasis analyses suggest that heterochromatin and telomere-binding proteins are not major impediments for telomere replication in the absence of Swi1. Instead, repetitive DNA sequences impair telomere integrity in swi1Δ mutant cells, leading to the loss of repeat DNA. In the absence of Swi1, telomere shortening is accompanied with an increased recruitment of Rad52 recombinase and more frequent amplification of telomere/subtelomeres, reminiscent of tumor cells that utilize the alternative lengthening of telomeres pathway (ALT) to maintain telomeres. These results suggest that Swi1 ensures telomere replication by suppressing recombination and repeat instability at telomeres. Our studies may also be relevant in understanding the potential role of Swi1Timeless in regulation of telomere stability in cancer cells. In every round of the cell cycle, cells must accurately replicate their full genetic information. This process is highly regulated, as defects during DNA replication cause genomic instability, leading to various genetic disorders including cancers. To thwart these problems, cells carry an array of complex mechanisms to deal with various obstacles found across the genome that can hamper DNA replication and cause DNA damage. Understanding how these mechanisms are regulated and orchestrated is of paramount importance in the field. In this report, we describe how Swi1, a Timeless-related protein in fission yeast, regulates efficient replication of telomeres, which are considered to be difficult to replicate due to the presence of repetitive DNA and telomere-binding proteins. We show that Swi1 prevents telomere damage and maintains telomere length by protecting integrity of telomeric repeats. Swi1-mediated telomere maintenance is independent of telomerase activity, and loss of Swi1 causes hyper-activation of recombination-based telomere maintenance, which generates heterogeneous telomeres. Similar telomerase-independent and recombination-dependent mechanism is utilized by approximately 15% of human cancers, linking telomere replication defects with cancer development. Thus, our study may be relevant in understanding the role of telomere replication defects in the development of cancers in humans.
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Affiliation(s)
- Mariana C. Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Mukund M. Das
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Hideki Tanizawa
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Ya-Ting Chang
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Ken-ichi Noma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Toru M. Nakamura
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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