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Weiss T, Kumar J, Chen C, Guo S, Schlegel O, Lutterman J, Ling K, Zhang F. Dual activities of an X-family DNA polymerase regulate CRISPR-induced insertional mutagenesis across species. Nat Commun 2024; 15:6293. [PMID: 39060288 PMCID: PMC11282277 DOI: 10.1038/s41467-024-50676-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The canonical non-homologous end joining (c-NHEJ) repair pathway, generally viewed as stochastic, has recently been shown to produce predictable outcomes in CRISPR-Cas9 mutagenesis. This predictability, mainly in 1-bp insertions and small deletions, has led to the development of in-silico prediction programs for various animal species. However, the predictability of CRISPR-induced mutation profiles across species remained elusive. Comparing CRISPR-Cas9 repair outcomes between human and plant species reveals significant differences in 1-bp insertion profiles. The high predictability observed in human cells links to the template-dependent activity of human Polλ. Yet plant Polλ exhibits dual activities, generating 1-bp insertions through both templated and non-templated manners. Polλ knockout in plants leads to deletion-only mutations, while its overexpression enhances 1-bp insertion rates. Two conserved motifs are identified to modulate plant Polλ's dual activities. These findings unveil the mechanism behind species-specific CRISPR-Cas9-induced insertion profiles and offer strategies for predictable, precise genome editing through c-NHEJ.
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Affiliation(s)
- Trevor Weiss
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shengsong Guo
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Oliver Schlegel
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Lutterman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA.
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA.
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de Pater S, Kamoen L, van Schendel R, Hooykaas PJJ, Tijsterman M. Profiling Cas9- and Cas12a-induced mutagenesis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39052360 DOI: 10.1111/tpj.16943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
With the advancement of CRISPR technologies, a comprehensive understanding of repair mechanisms following double-strand break (DSB) formation is important for improving the precision and efficiency of genetic modifications. In plant genetics, two Cas nucleases are widely used, i.e. Cas9 and Cas12a, which differ with respect to PAM sequence composition, position of the DSB relative to the PAM, and DSB-end configuration (blunt vs. staggered). The latter difference has led to speculations about different options for repair and recombination. Here, we provide detailed repair profiles for LbCas12a in Arabidopsis thaliana, using identical experimental settings previously reported for Cas9-induced DSBs, thus allowing for a quantitative comparison of both nucleases. For both enzymes, non-homologous end-joining (NHEJ) produces 70% of mutations, whereas polymerase theta-mediated end-joining (TMEJ) generates 30%, indicating that DSB-end configuration does not dictate repair pathway choice. Relevant for genome engineering approaches aimed at integrating exogenous DNA, we found that Cas12a similarly stimulates the integration of T-DNA molecules as does Cas9. Long-read sequencing of both Cas9 and Cas12a repair outcomes further revealed a previously underappreciated degree of DNA loss upon TMEJ. The most notable disparity between Cas9 and Cas12a repair profiles is caused by how NHEJ acts on DSB ends with short overhangs: non-symmetric Cas9 cleavage produce 1 bp insertions, which we here show to depend on polymerase Lambda, whereas staggered Cas12a DSBs are not subjected to fill-in synthesis. We conclude that Cas9 and Cas12a are equally effective for genome engineering purposes, offering flexibility in nuclease choice based on the availability of compatible PAM sequences.
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Affiliation(s)
- Sylvia de Pater
- Department of Plant Sciences, Institute of Biology, Leiden University, Leiden, BE, 2333, the Netherlands
| | - Lycka Kamoen
- Department of Plant Sciences, Institute of Biology, Leiden University, Leiden, BE, 2333, the Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, RC, 2300, the Netherlands
| | - Paul J J Hooykaas
- Department of Plant Sciences, Institute of Biology, Leiden University, Leiden, BE, 2333, the Netherlands
| | - Marcel Tijsterman
- Department of Plant Sciences, Institute of Biology, Leiden University, Leiden, BE, 2333, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, RC, 2300, the Netherlands
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3
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Morales-Ruiz T, Beltrán-Melero C, Ortega-Paredes D, Luna-Morillo JA, Martínez-Macías MI, Roldán-Arjona T, Ariza RR, Córdoba-Cañero D. The enzymatic properties of Arabidopsis thaliana DNA polymerase λ suggest a role in base excision repair. PLANT MOLECULAR BIOLOGY 2024; 114:3. [PMID: 38217735 PMCID: PMC10787897 DOI: 10.1007/s11103-023-01407-8] [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] [Received: 07/28/2023] [Accepted: 11/27/2023] [Indexed: 01/15/2024]
Abstract
Base excision repair (BER) generates gapped DNA intermediates containing a 5'-terminal 2-deoxyribose-5-phosphate (5'-dRP) group. In mammalian cells, gap filling and dRP removal are catalyzed by Pol β, which belongs to the X family of DNA polymerases. In higher plants, the only member of the X family of DNA polymerases is Pol λ. Although it is generally believed that plant Pol λ participates in BER, there is limited experimental evidence for this hypothesis. Here we have characterized the biochemical properties of Arabidopsis thaliana Pol λ (AtPol λ) in a BER context, using a variety of DNA repair intermediates. We have found that AtPol λ performs gap filling inserting the correct nucleotide, and that the rate of nucleotide incorporation is higher in substrates containing a C in the template strand. Gap filling catalyzed by AtPol λ is most efficient with a phosphate at the 5'-end of the gap and is not inhibited by the presence of a 5'-dRP mimic. We also show that AtPol λ possesses an intrinsic dRP lyase activity that is reduced by mutations at two lysine residues in its 8-kDa domain, one of which is present in Pol λ exclusively and not in any Pol β homolog. Importantly, we also found that the dRP lyase activity of AtPol λ allows efficient completion of uracil repair in a reconstituted short-patch BER reaction. These results suggest that AtPol λ plays an important role in plant BER.
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Affiliation(s)
- T Morales-Ruiz
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - C Beltrán-Melero
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - D Ortega-Paredes
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - J A Luna-Morillo
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - M I Martínez-Macías
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - T Roldán-Arjona
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - R R Ariza
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - D Córdoba-Cañero
- Department of Genetics, University of Córdoba, Córdoba, Spain.
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Reina Sofía University Hospital, Córdoba, Spain.
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Thomson G, Dickinson L, Jacob Y. Genomic consequences associated with Agrobacterium-mediated transformation of plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:342-363. [PMID: 37831618 PMCID: PMC10841553 DOI: 10.1111/tpj.16496] [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] [Received: 08/11/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Attenuated strains of the naturally occurring plant pathogen Agrobacterium tumefaciens can transfer virtually any DNA sequence of interest to model plants and crops. This has made Agrobacterium-mediated transformation (AMT) one of the most commonly used tools in agricultural biotechnology. Understanding AMT, and its functional consequences, is of fundamental importance given that it sits at the intersection of many fundamental fields of study, including plant-microbe interactions, DNA repair/genome stability, and epigenetic regulation of gene expression. Despite extensive research and use of AMT over the last 40 years, the extent of genomic disruption associated with integrating exogenous DNA into plant genomes using this method remains underappreciated. However, new technologies like long-read sequencing make this disruption more apparent, complementing previous findings from multiple research groups that have tackled this question in the past. In this review, we cover progress on the molecular mechanisms involved in Agrobacterium-mediated DNA integration into plant genomes. We also discuss localized mutations at the site of insertion and describe the structure of these DNA insertions, which can range from single copy insertions to large concatemers, consisting of complex DNA originating from different sources. Finally, we discuss the prevalence of large-scale genomic rearrangements associated with the integration of DNA during AMT with examples. Understanding the intended and unintended effects of AMT on genome stability is critical to all plant researchers who use this methodology to generate new genetic variants.
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Affiliation(s)
- Geoffrey Thomson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Lauren Dickinson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
- Yale Cancer Center, Yale School of Medicine; New Haven, Connecticut 06511, USA
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5
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García-Medel PL, Peralta-Castro A, Baruch-Torres N, Fuentes-Pascacio A, Pedroza-García JA, Cruz-Ramirez A, Brieba LG. Arabidopsis thaliana PrimPol is a primase and lesion bypass DNA polymerase with the biochemical characteristics to cope with DNA damage in the nucleus, mitochondria, and chloroplast. Sci Rep 2021; 11:20582. [PMID: 34663822 PMCID: PMC8523556 DOI: 10.1038/s41598-021-00151-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/07/2021] [Indexed: 11/09/2022] Open
Abstract
PrimPol is a novel Primase–Polymerase that synthesizes RNA and DNA primers de novo and extents from these primers as a DNA polymerase. Animal PrimPol is involved in nuclear and mitochondrial DNA replication by virtue of its translesion DNA synthesis (TLS) and repriming activities. Here we report that the plant model Arabidopsis thaliana encodes a functional PrimPol (AtPrimPol). AtPrimPol is a low fidelity and a TLS polymerase capable to bypass DNA lesions, like thymine glycol and abasic sites, by incorporating directly across these lesions or by skipping them. AtPrimPol is also an efficient primase that preferentially recognizes the single-stranded 3′-GTCG-5′ DNA sequence, where the 3′-G is cryptic. AtPrimPol is the first DNA polymerase that localizes in three cellular compartments: nucleus, mitochondria, and chloroplast. In vitro, AtPrimPol synthesizes primers that are extended by the plant organellar DNA polymerases and this reaction is regulated by organellar single-stranded binding proteins. Given the constant exposure of plants to endogenous and exogenous DNA-damaging agents and the enzymatic capabilities of lesion bypass and re-priming of AtPrimPol, we postulate a predominant role of this enzyme in avoiding replication fork collapse in all three plant genomes, both as a primase and as a TLS polymerase.
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Affiliation(s)
- Paola L García-Medel
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Antolín Peralta-Castro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico.,Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Alma Fuentes-Pascacio
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - José A Pedroza-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Alfredo Cruz-Ramirez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico.
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6
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Čermák T. Sequence modification on demand: search and replace tools for precise gene editing in plants. Transgenic Res 2021; 30:353-379. [PMID: 34086167 DOI: 10.1007/s11248-021-00253-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/05/2021] [Indexed: 12/26/2022]
Abstract
Until recently, our ability to generate allelic diversity in plants was limited to introduction of variants from domesticated and wild species by breeding via uncontrolled recombination or the use of chemical and physical mutagens-processes that are lengthy and costly or lack specificity, respectively. Gene editing provides a faster and more precise way to create new variation, although its application in plants has been dominated by the creation of short insertion and deletion mutations leading to loss of gene function, mostly due to the dependence of editing outcomes on DNA repair pathway choices intrinsic to higher eukaryotes. Other types of edits such as point mutations and precise and pre-designed targeted sequence insertions have rarely been implemented, despite providing means to modulate the expression of target genes or to engineer the function and stability of their protein products. Several advancements have been developed in recent years to facilitate custom editing by regulation of repair pathway choices or by taking advantage of alternative types of DNA repair. We have seen the advent of novel gene editing tools that are independent of DNA double-strand break repair, and methods completely independent of host DNA repair processes are being increasingly explored. With the aim to provide a comprehensive review of the state-of-the-art methodology for allele replacement in plants, I discuss the adoption of these improvements for plant genome engineering.
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Van Vu T, Thi Hai Doan D, Kim J, Sung YW, Thi Tran M, Song YJ, Das S, Kim J. CRISPR/Cas-based precision genome editing via microhomology-mediated end joining. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:230-239. [PMID: 33047464 PMCID: PMC7868975 DOI: 10.1111/pbi.13490] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 10/03/2020] [Indexed: 05/05/2023]
Abstract
Gene editing and/or allele introgression with absolute precision and control appear to be the ultimate goals of genetic engineering. Precision genome editing in plants has been developed through various approaches, including oligonucleotide-directed mutagenesis (ODM), base editing, prime editing and especially homologous recombination (HR)-based gene targeting. With the advent of CRISPR/Cas for the targeted generation of DNA breaks (single-stranded breaks (SSBs) or double-stranded breaks (DSBs)), a substantial advancement in HR-mediated precise editing frequencies has been achieved. Nonetheless, further research needs to be performed for commercially viable applications of precise genome editing; hence, an alternative innovative method for genome editing may be required. Within this scope, we summarize recent progress regarding precision genome editing mediated by microhomology-mediated end joining (MMEJ) and discuss their potential applications in crop improvement.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteKm 02, Pham Van Dong RoadCo Nhue 1, Bac Tu Liem, Hanoi11917Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- Division of Life ScienceGyeongsang National University501 Jinju‐daeroJinju52828Republic of Korea
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8
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The Dark Side of UV-Induced DNA Lesion Repair. Genes (Basel) 2020; 11:genes11121450. [PMID: 33276692 PMCID: PMC7761550 DOI: 10.3390/genes11121450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others on plant genetic material. The energy of UV light is sufficient to induce mutations in DNA. Some examples of DNA damage induced by UV are pyrimidine dimers, oxidized nucleotides as well as single and double-strand breaks. When exposed to light, plants can repair major UV-induced DNA lesions, i.e., pyrimidine dimers using photoreactivation. However, this highly efficient light-dependent DNA repair system is ineffective in dim light or at night. Moreover, it is helpless when it comes to the repair of DNA lesions other than pyrimidine dimers. In this review, we have focused on how plants cope with deleterious DNA damage that cannot be repaired by photoreactivation. The current understanding of light-independent mechanisms, classified as dark DNA repair, indispensable for the maintenance of plant genetic material integrity has been presented.
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Du Y, Hase Y, Satoh K, Shikazono N. Characterization of gamma irradiation-induced mutations in Arabidopsis mutants deficient in non-homologous end joining. JOURNAL OF RADIATION RESEARCH 2020; 61:639-647. [PMID: 32766789 PMCID: PMC7482170 DOI: 10.1093/jrr/rraa059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/01/2020] [Accepted: 07/14/2020] [Indexed: 05/03/2023]
Abstract
To investigate the involvement of the non-homologous end joining (NHEJ) pathway in plant mutagenesis by ionizing radiation, we conducted a genome-wide characterization of the mutations induced by gamma rays in NHEJ-deficient Arabidopsis mutants (AtKu70-/- and AtLig4-/-). Although both mutants were more sensitive to gamma rays than the wild-type control, the AtKu70-/- mutant was slightly more sensitive than the AtLig4-/- mutant. Single-base substitutions (SBSs) were the predominant mutations in the wild-type control, whereas deletions (≥2 bp) and complex-type mutations [i.e. more than two SBSs or short insertion and deletions (InDels) separated by fewer than 10 bp] were frequently induced in the mutants. Single-base deletions were the most frequent deletions in the wild-type control, whereas the most common deletions in the mutants were 11-30 bp. The apparent microhomology at the rejoined sites of deletions peaked at 2 bp in the wild-type control, but was 3-4 bp in the mutants. This suggests the involvement of alternative end joining and single-strand annealing pathways involving increased microhomology for rejoining DNA ends. Complex-type mutations comprising short InDels were frequently detected in the mutants, but not in the wild-type control. Accordingly, NHEJ is more precise than the backup pathways, and is the main pathway for rejoining the broken DNA ends induced by ionizing radiation in plants.
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Affiliation(s)
- Yan Du
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Yoshihiro Hase
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
- Corresponding author. Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan. Tel: +81-27-346-9032; Fax: +81-27-346-9688;
| | - Katsuya Satoh
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Naoya Shikazono
- Kansai Photon Science Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
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Abstract
Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10–15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication.
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11
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Roldán-Arjona T, Ariza RR, Córdoba-Cañero D. DNA Base Excision Repair in Plants: An Unfolding Story With Familiar and Novel Characters. FRONTIERS IN PLANT SCIENCE 2019; 10:1055. [PMID: 31543887 PMCID: PMC6728418 DOI: 10.3389/fpls.2019.01055] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
Base excision repair (BER) is a critical genome defense pathway that deals with a broad range of non-voluminous DNA lesions induced by endogenous or exogenous genotoxic agents. BER is a complex process initiated by the excision of the damaged base, proceeds through a sequence of reactions that generate various DNA intermediates, and culminates with restoration of the original DNA structure. BER has been extensively studied in microbial and animal systems, but knowledge in plants has lagged behind until recently. Results obtained so far indicate that plants share many BER factors with other organisms, but also possess some unique features and combinations. Plant BER plays an important role in preserving genome integrity through removal of damaged bases. However, it performs additional important functions, such as the replacement of the naturally modified base 5-methylcytosine with cytosine in a plant-specific pathway for active DNA demethylation.
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Affiliation(s)
- Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Rafael R. Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Dolores Córdoba-Cañero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
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12
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Sakamoto AN. Translesion Synthesis in Plants: Ultraviolet Resistance and Beyond. FRONTIERS IN PLANT SCIENCE 2019; 10:1208. [PMID: 31649692 PMCID: PMC6794406 DOI: 10.3389/fpls.2019.01208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/03/2019] [Indexed: 05/06/2023]
Abstract
Plant genomes sustain various forms of DNA damage that stall replication forks. Translesion synthesis (TLS) is one of the pathways to overcome stalled replication in which specific polymerases (TLS polymerase) perform bypass synthesis across DNA damage. This article gives a brief overview of plant TLS polymerases. In Arabidopsis, DNA polymerase (Pol) ζ, η, κ, θ, and λ and Reversionless1 (Rev1) are shown to be involved in the TLS. For example, AtPolη bypasses ultraviolet (UV)-induced cyclobutane pyrimidine dimers in vitro. Disruption of AtPolζ or AtPolη increases root stem cell death after UV irradiation. These results suggest that AtPolζ and ATPolη bypass UV-induced damage, prevent replication arrest, and allow damaged cells to survive and grow. In general, TLS polymerases have low fidelity and often induce mutations. Accordingly, disruption of AtPolζ or AtRev1 reduces somatic mutation frequency, whereas disruption of AtPolη elevates it, suggesting that plants have both mutagenic and less mutagenic TLS activities. The stalled replication fork can be resolved by a strand switch pathway involving a DNA helicase Rad5. Disruption of both AtPolζ and AtRAD5a shows synergistic or additive effects in the sensitivity to DNA-damaging agents. Moreover, AtPolζ or AtRev1 disruption elevates homologous recombination frequencies in somatic tissues. These results suggest that the Rad5-dependent pathway and TLS are parallel. Plants grown in the presence of heat shock protein 90 (HSP90) inhibitor showed lower mutation frequencies, suggesting that HSP90 regulates mutagenic TLS in plants. Hypersensitivities of TLS-deficient plants to γ-ray and/or crosslink damage suggest that plant TLS polymerases have multiple roles, as reported in other organisms.
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Baruch-Torres N, Brieba LG. Plant organellar DNA polymerases are replicative and translesion DNA synthesis polymerases. Nucleic Acids Res 2017; 45:10751-10763. [PMID: 28977655 PMCID: PMC5737093 DOI: 10.1093/nar/gkx744] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/14/2017] [Indexed: 02/01/2023] Open
Abstract
Genomes acquire lesions that can block the replication fork and some lesions must be bypassed to allow survival. The nuclear genome of flowering plants encodes two family-A DNA polymerases (DNAPs), the result of a duplication event, that are the sole DNAPs in plant organelles. These DNAPs, dubbed Plant Organellar Polymerases (POPs), resemble the Klenow fragment of bacterial DNAP I and are not related to metazoan and fungal mitochondrial DNAPs. Herein we report that replicative POPs from the plant model Arabidopsis thaliana (AtPolI) efficiently bypass one the most insidious DNA lesions, an apurinic/apyrimidinic (AP) site. AtPolIs accomplish lesion bypass with high catalytic efficiency during nucleotide insertion and extension. Lesion bypass depends on two unique polymerization domain insertions evolutionarily unrelated to the insertions responsible for lesion bypass by DNAP θ, an analogous lesion bypass polymerase. AtPolIs exhibit an insertion fidelity that ranks between the fidelity of replicative and lesion bypass DNAPs, moderate 3′-5′ exonuclease activity and strong strand-displacement. AtPolIs are the first known example of a family-A DNAP evolved to function in both DNA replication and lesion bypass. The lesion bypass capabilities of POPs may be required to prevent replication fork collapse in plant organelles.
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Affiliation(s)
- Noe Baruch-Torres
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821 Irapuato Guanajuato, México
| | - Luis G Brieba
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821 Irapuato Guanajuato, México
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Sihi S, Maiti S, Bakshi S, Nayak A, Chaudhuri S, Sengupta DN. Understanding the role of DNA polymerase λ gene in different growth and developmental stages of Oryza sativa L. indica rice cultivars. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 120:156-168. [PMID: 29031161 DOI: 10.1016/j.plaphy.2017.09.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 06/07/2023]
Abstract
DNA polymerase λ (Pol λ) is the only member of DNA polymerase family X present in plants. The enzyme is ddNTP sensitive as it contains the conserved C-terminal Pol β domain. The 1.1 kb partial coding sequence isolated spanned the whole 3' regions of the gene containing functionally important domains of the Pol λ gene. Comparative in silico studies from both indica and japonica cultivars involving homology modelling showed that the model for the partial Pol λ gene was stable and acceptable. The alignment of both the protein models showed a RMS value of 0.783. Apart from this, expression of Pol λ and its relative activity is studied during different development stages of three different indica rice cultivars (IR29, Nonabokra and N22). Enhanced accumulation and higher activity of Pol λ during the early seedling stage was detected. Higher expression and activity were observed in the anthers, which was probably necessary for DNA repair during microspore formation. However, during the maturation stage of seed development and plant growth, expression and the activity of Pol λ decreased due to slow metabolic activity and a reduced rate of cell division respectively. Furthermore, the expression and activity of Pol λ were found to be higher in IR29 in comparison to Nonabokra and N22. IR29 is a rice cultivar susceptible to environmental stresses and hence it encounters higher DNA damages. The enhanced presence and activity of the Pol λ enzyme in IR29 with respect to the other two cultivars, which are more tolerant to the environmental stresses during various developmental stages, is therefore explainable.
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Affiliation(s)
- Sayantani Sihi
- Division of Plant Biology, Bose Institute, 93/1 A.P.C. Road, Kolkata 700009, India
| | - Soumitra Maiti
- Division of Plant Biology, Bose Institute, 93/1 A.P.C. Road, Kolkata 700009, India
| | - Sankar Bakshi
- Vidyasagar College for Women, 39 Sankar Ghosh Lane Kolkata 700006, India
| | - Arup Nayak
- Division of Plant Biology, Bose Institute, 93/1 A.P.C. Road, Kolkata 700009, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India
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PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses. PLoS One 2017; 12:e0180478. [PMID: 28678890 PMCID: PMC5498030 DOI: 10.1371/journal.pone.0180478] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/15/2017] [Indexed: 01/04/2023] Open
Abstract
Eukaryotic protein phosphatase 4 (PP4) is a PP2A-type protein phosphatase that is part of a conserved complex with regulatory factors PSY2 and PP4R2. Various lines of Arabidopsis thaliana with mutated PP4 subunit genes were constructed to study the so far completely unknown functions of PP4 in plants. Mutants with knocked out putative functional homolog of the PSY2 LIKE (PSY2L) gene were dwarf and bushy, while plants with knocked out PP4R2 LIKE (PP4R2L) looked very similar to WT. The psy2l seedlings had short roots with disorganized morphology and impaired meristem. Seedling growth was sensitive to the genotoxin cisplatin. Global transcript analysis (RNA-seq) of seedlings and rosette leaves revealed several groups of genes, shared between both types of tissues, strongly influenced by knocked out PSY2L. Receptor kinases, CRINKLY3 and WAG1, important for growth and development, were down-regulated 3–7 times. EUKARYOTIC ELONGATION FACTOR5A1 was down-regulated 4–6 fold. Analysis of hormone sensitive genes indicated that abscisic acid levels were high, while auxin, cytokinin and gibberellic acid levels were low in psy2l. Expression of specific transcription factors involved in regulation of anthocyanin synthesis were strongly elevated, e.g. the master regulator PAP1, and intriguingly TT8, which is otherwise mainly expressed in seeds. The psy2l mutants accumulated anthocyanins under conditions where WT did not, pointing to PSY2L as a possible upstream negative regulator of PAP1 and TT8. Expression of the sugar-phosphate transporter GPT2, important for cellular sugar and phosphate homeostasis, was enhanced 7–8 times. Several DNA damage response genes, including the cell cycle inhibitor gene WEE1, were up-regulated in psy2l. The activation of DNA repair signaling genes, in combination with phenotypic traits showing aberrant root meristem and sensitivity to the genotoxic cisplatin, substantiate the involvement of Arabidopsis PSY2L in maintenance of genome integrity.
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Biedermann S, Harashima H, Chen P, Heese M, Bouyer D, Sofroni K, Schnittger A. The retinoblastoma homolog RBR1 mediates localization of the repair protein RAD51 to DNA lesions in Arabidopsis. EMBO J 2017; 36:1279-1297. [PMID: 28320735 PMCID: PMC5412766 DOI: 10.15252/embj.201694571] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 11/13/2022] Open
Abstract
The retinoblastoma protein (Rb), which typically functions as a transcriptional repressor of E2F‐regulated genes, represents a major control hub of the cell cycle. Here, we show that loss of the Arabidopsis Rb homolog RETINOBLASTOMA‐RELATED 1 (RBR1) leads to cell death, especially upon exposure to genotoxic drugs such as the environmental toxin aluminum. While cell death can be suppressed by reduced cell‐proliferation rates, rbr1 mutant cells exhibit elevated levels of DNA lesions, indicating a direct role of RBR1 in the DNA‐damage response (DDR). Consistent with its role as a transcriptional repressor, we find that RBR1 directly binds to and represses key DDR genes such as RADIATION SENSITIVE 51 (RAD51), leaving it unclear why rbr1 mutants are hypersensitive to DNA damage. However, we find that RBR1 is also required for RAD51 localization to DNA lesions. We further show that RBR1 is itself targeted to DNA break sites in a CDKB1 activity‐dependent manner and partially co‐localizes with RAD51 at damage sites. Taken together, these results implicate RBR1 in the assembly of DNA‐bound repair complexes, in addition to its canonical function as a transcriptional regulator.
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Affiliation(s)
- Sascha Biedermann
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France.,Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | | | - Poyu Chen
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Maren Heese
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Daniel Bouyer
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U 1024, Paris, France
| | - Kostika Sofroni
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France .,Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
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