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Grin IR, Petrova DV, Endutkin AV, Ma C, Yu B, Li H, Zharkov DO. Base Excision DNA Repair in Plants: Arabidopsis and Beyond. Int J Mol Sci 2023; 24:14746. [PMID: 37834194 PMCID: PMC10573277 DOI: 10.3390/ijms241914746] [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: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.
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Affiliation(s)
- Inga R. Grin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Daria V. Petrova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
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Han Q, Hung YH, Zhang C, Bartels A, Rea M, Yang H, Park C, Zhang XQ, Fischer RL, Xiao W, Hsieh TF. Loss of linker histone H1 in the maternal genome influences DEMETER-mediated demethylation and affects the endosperm DNA methylation landscape. FRONTIERS IN PLANT SCIENCE 2022; 13:1070397. [PMID: 36618671 PMCID: PMC9813442 DOI: 10.3389/fpls.2022.1070397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of the female gamete companion cell establishes gene imprinting in the endosperm and is essential for seed viability. DME demethylates small and genic-flanking transposons as well as intergenic and heterochromatin sequences, but how DME is recruited to these loci remains unknown. H1.2 was identified as a DME-interacting protein in a yeast two-hybrid screen, and maternal genome H1 loss affects DNA methylation and expression of selected imprinted genes in the endosperm. Yet, the extent to which H1 influences DME demethylation and gene imprinting in the Arabidopsis endosperm has not been investigated. Here, we showed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-bound heterochromatins are barriers for DME demethylation. Loss of H1 in the maternal genome has a very limited effect on gene transcription or gene imprinting regulation in the endosperm; however, it variably influences euchromatin TE methylation and causes a slight hypermethylation and a reduced expression in selected imprinted genes. We conclude that loss of maternal H1 indirectly influences DME-mediated demethylation and endosperm DNA methylation landscape but does not appear to affect endosperm gene transcription and overall imprinting regulation.
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Affiliation(s)
- Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Yu-Hung Hung
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Changqing Zhang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Matthew Rea
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Hanwen Yang
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Christine Park
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Xiang-Qian Zhang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
- College of Food Science and Engineering, Foshan University, Foshan, China
| | - Robert L. Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
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Torgasheva NA, Diatlova EA, Grin IR, Endutkin AV, Mechetin GV, Vokhtantsev IP, Yudkina AV, Zharkov DO. Noncatalytic Domains in DNA Glycosylases. Int J Mol Sci 2022; 23:ijms23137286. [PMID: 35806289 PMCID: PMC9266487 DOI: 10.3390/ijms23137286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Many proteins consist of two or more structural domains: separate parts that have a defined structure and function. For example, in enzymes, the catalytic activity is often localized in a core fragment, while other domains or disordered parts of the same protein participate in a number of regulatory processes. This situation is often observed in many DNA glycosylases, the proteins that remove damaged nucleobases thus initiating base excision DNA repair. This review covers the present knowledge about the functions and evolution of such noncatalytic parts in DNA glycosylases, mostly concerned with the human enzymes but also considering some unique members of this group coming from plants and prokaryotes.
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Affiliation(s)
- Natalia A. Torgasheva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Evgeniia A. Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
| | - Inga R. Grin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Ivan P. Vokhtantsev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
| | - Anna V. Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
- Correspondence:
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