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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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Sakamoto AN, Kaya H, Endo M. Deletion of TLS polymerases promotes homologous recombination in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2018; 13:e1483673. [PMID: 29944437 PMCID: PMC6128680 DOI: 10.1080/15592324.2018.1483673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Unrepaired DNA damage hinders the maintenance of genome integrity because it blocks the catalytic activity of replicase. The stalled replication fork can be processed through either translesion synthesis (TLS) with specific polymerases, or replication using the undamaged template. To investigate how TLS activities are regulated and how the stalled replication fork is processed in plants, reversion frequencies and homologous recombination (HR) frequencies were analyzed using GUS-based substrates. The HR frequencies in plants deficient in DNA polymerase ζ (Pol ζ) or Rev1 were higher than that in wildtype plants under normal conditions, and were significantly increased by ultraviolet light irradiation. Heat shock protein (HSP) 90 is known to be involved in various stress responses. To examine the role of HSP90 in the regulation of damage tolerance, we analyzed reversion frequencies and HR frequencies in plants grown in the presence of a HSP inhibitor, geldanamycin (GDA). Reversion frequency was lower in GDA-treated plants than in mock-treated plants. Though the HR frequency was higher in GDA-treated wildtype plants than in mock-treated plants, no significant difference was detected in Rev1-deficient plants. In yeast, TLS polymerases interacted with each other or with a replication clump component, proliferating cell nuclear antigen (PCNA). HSP90 interacted with REV1 or REV7 in Nicotiana benthamiana cells. These results suggest that HSP90 interacts with TLS polymerase(s), which promotes error-prone TLS in plants.
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Affiliation(s)
- A. N. Sakamoto
- Department of Radiation-Applied Biology Research, National Institutes for Quantum and Radiological Science and Technology (QST), Takasaki, Gumma, Japan
- CONTACT A. N. Sakamoto Department of Radiation-Applied Biology Research, National Institutes for Quantum and Radiological Science and Technology (QST), Watanuki-machi 1233, Takasaki, Gumma 370-1292, Japan
| | - H. Kaya
- Plant Molecular Biology and Virology, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, Japan
| | - M. Endo
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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Wicker T, Yu Y, Haberer G, Mayer KFX, Marri PR, Rounsley S, Chen M, Zuccolo A, Panaud O, Wing RA, Roffler S. DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nat Commun 2016; 7:12790. [PMID: 27599761 PMCID: PMC5023962 DOI: 10.1038/ncomms12790] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/02/2016] [Indexed: 12/16/2022] Open
Abstract
DNA (class 2) transposons are mobile genetic elements which move within their ‘host' genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions. Most importantly, we find this phenomenon also in maize, wheat and barley. Thus, these findings suggest that DNA transposon activity is a major evolutionary force in grasses which provide the basis of most food consumed by humankind. DNA transposons are numerous in plant genomes. Here, Wicker et al. analyse transposon polymorphisms in rice and other grasses and show that sequences flanking excision sites contain up to 10 times more mutations than average, suggesting transposons are a major factor shaping the evolution of grass genomes.
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Affiliation(s)
- Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | | | | | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101 China
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR5096 UPVD/CNRS, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.,International Rice Research Institute, Los Baños, 4031 Laguna, Philippines.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
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