Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH
Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD i...
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| Format: | Article |
| Language: | English |
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The Biophysical Society of Japan
2020-10-01
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| Series: | Biophysics and Physicobiology |
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| Online Access: | https://doi.org/10.2142/biophysico.BSJ-2020010 |
| _version_ | 1818530681625509888 |
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| author | Ryuma Sato Yoshiharu Mori Risa Matsui Noriaki Okimoto Junpei Yamamoto Makoto Taiji |
| author_facet | Ryuma Sato Yoshiharu Mori Risa Matsui Noriaki Okimoto Junpei Yamamoto Makoto Taiji |
| author_sort | Ryuma Sato |
| collection | DOAJ |
| description | Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD. |
| first_indexed | 2024-12-11T17:22:47Z |
| format | Article |
| id | doaj.art-86be6f80f6bd48ad9bd86bd78061c963 |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-12-11T17:22:47Z |
| publishDate | 2020-10-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-86be6f80f6bd48ad9bd86bd78061c9632022-12-22T00:57:04ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792020-10-011710.2142/biophysico.BSJ-2020010Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASHRyuma Sato0Yoshiharu Mori1Risa Matsui2Noriaki Okimoto3Junpei Yamamoto4Makoto Taiji5Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, JapanSchool of Pharmacy, Kitasato University, Minato-ku, Tokyo 108-8641, JapanGraduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, JapanCenter for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, JapanGraduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, JapanCenter for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, JapanFollowing the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD.https://doi.org/10.2142/biophysico.BSJ-2020010electron transferelectronic coupling matrix elementssalt bridgedna binding |
| spellingShingle | Ryuma Sato Yoshiharu Mori Risa Matsui Noriaki Okimoto Junpei Yamamoto Makoto Taiji Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH Biophysics and Physicobiology electron transfer electronic coupling matrix elements salt bridge dna binding |
| title | Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH |
| title_full | Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH |
| title_fullStr | Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH |
| title_full_unstemmed | Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH |
| title_short | Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH |
| title_sort | theoretical insights into the dna repair function of arabidopsis thaliana cryptochrome dash |
| topic | electron transfer electronic coupling matrix elements salt bridge dna binding |
| url | https://doi.org/10.2142/biophysico.BSJ-2020010 |
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