1
|
An ML, Miao JL. Genetic and Molecular Characterization of a Dash Cryptochrome Homologous Gene from Antarctic Diatom Phaeodactylum tricornutum ICE-H. Mol Biol 2022. [DOI: 10.1134/s0026893322060024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
2
|
Sato R, Mori Y, Matsui R, Okimoto N, Yamamoto J, Taiji M. Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH. Biophys Physicobiol 2020; 17:113-124. [PMID: 33194514 PMCID: PMC7610064 DOI: 10.2142/biophysico.bsj-2020010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/28/2020] [Indexed: 12/01/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Ryuma Sato
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
| | - Yoshiharu Mori
- School of Pharmacy, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Risa Matsui
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Noriaki Okimoto
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Makoto Taiji
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
| |
Collapse
|
3
|
Resilience and self-regulation processes of microalgae under UV radiation stress. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2019.100322] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
4
|
Terai Y, Sato R, Yumiba T, Harada R, Shimizu K, Toga T, Ishikawa-Fujiwara T, Todo T, Iwai S, Shigeta Y, Yamamoto J. Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities. Nucleic Acids Res 2019; 46:6761-6772. [PMID: 29762762 PMCID: PMC6061865 DOI: 10.1093/nar/gky364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/24/2018] [Indexed: 12/28/2022] Open
Abstract
(6–4) Photolyases ((6–4)PLs) are flavoenzymes that repair the carcinogenic UV-induced DNA damage, pyrimidine(6–4)pyrimidone photoproducts ((6–4)PPs), in a light-dependent manner. Although the reaction mechanism of DNA photorepair by (6–4)PLs has been intensively investigated, the molecular mechanism of the lesion recognition remains obscure. We show that a well-conserved arginine residue in Xenopus laevis (6–4)PL (Xl64) participates in DNA binding, through Coulomb and CH–π interactions. Fragment molecular orbital calculations estimated attractive interaction energies of –80–100 kcal mol–1 for the Coulomb interaction and –6 kcal mol–1 for the CH–π interaction, and the loss of either of them significantly reduced the affinity for (6–4)PP-containing oligonucleotides, as well as the quantum yield of DNA photorepair. From experimental and theoretical observations, we formulated a DNA binding model of (6–4)PLs. Based on the binding model, we mutated this Arg in Xl64 to His, which is well conserved among the animal cryptochromes (CRYs), and found that the CRY-type mutant exhibited reduced affinity for the (6–4)PP-containing oligonucleotides, implying the possible molecular origin of the functional diversity of the photolyase/cryptochrome superfamily.
Collapse
Affiliation(s)
- Yuma Terai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Ryuma Sato
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takahiro Yumiba
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Kohei Shimizu
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Tatsuya Toga
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Tomoko Ishikawa-Fujiwara
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Todo
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
5
|
Terashima M, Ohashi K, Takasuka TE, Kojima H, Fukui M. Antarctic heterotrophic bacterium Hymenobacter nivis P3 T displays light-enhanced growth and expresses putative photoactive proteins. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:227-235. [PMID: 30298689 DOI: 10.1111/1758-2229.12702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
Hymenobacter nivis P3T is a heterotrophic bacterium isolated from Antarctic red snow generated by algal blooms. Despite being non-photosynthetic, H. nivis was dominantly found in the red snow environment that is exposed to high light and UV irradiation, suggesting that this species can flourish under such harsh conditions. In order to further understand the adaptive strategies on the snow surface environment of Antarctica, the genome of H. nivis P3T was sequenced and analyzed, which identified genes putatively encoding for light-reactive proteins such as proteorhodopsin, phytochrome, photolyase and several copies of cryptochromes. Culture-based experiments revealed that H. nivis P3T growth was significantly enhanced under light conditions, while dark conditions had increased extracellular polymeric substances. Furthermore, the expression of several putative light-reactive proteins was determined by proteomic analysis. These results indicate that H. nivis P3T is able to potentially utilize light, which may explain its dominance on the red snow surface environment of Antarctica. ORIGINALITY-SIGNIFICANCE STATEMENT: The role of proteorhodopsin in heterotrophic bacteria is not well-characterized, as only a handful of proteorhodopsin-harbouring isolates were shown to have a light-enhanced phenotype through culture-based experiments to date. This is the first study that demonstrates light-stimulated growth and protein expression evidence of photoactive proteins for a non-marine psychrophile and for a member of the genus Hymenobacter. It is also the first study that provides comprehensive proteome information for this genus. This study presents significant results in understanding the adaptive mechanism of a heterotrophic non-photosynthetic bacterium thriving on the snow surface environment of Antarctica as well as demonstrating the role of light-utilization in promoting growth, possibly through proteorhodopsin.
Collapse
Affiliation(s)
- Mia Terashima
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, 060-0819, Japan
| | - Keisuke Ohashi
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, 060-0819, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, 060-0819, Japan
| |
Collapse
|
6
|
Sato R, Kitoh-Nishioka H, Ando K, Yamato T. Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited. J Phys Chem B 2018; 122:6912-6921. [PMID: 29890068 DOI: 10.1021/acs.jpcb.8b04333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photoinduced electron transfer (ET) reaction of cyclobutane pyrimidine dimer (CPD) photolyase plays an essential role in its DNA repair reaction, and the molecular mechanism of the ET reaction has attracted a large number of experimental and theoretical studies. We investigated the quantum mechanical nature of their ET reactions, characterized by multiple ET pathways of the CPD photolyase derived from Anacystis nidulans. Using the generalized Mulliken-Hush (GMH) method and the bridge green function (GF) methods, we estimated the electronic coupling matrix element, TDA, to be 36 ± 30 cm-1 from the donor (FADH-) to the acceptor (CPD). The estimated ET time was 386 ps, in good agreement with the experimental value (250 ps) in the literature. Furthermore, we performed the molecular dynamics (MD) simulations and ab initio molecular orbital (MO) calculations, and explored the electron tunneling pathway. We examined 20 different structures during the MD trajectory and quantitatively evaluated the electron tunneling currents for each of them. As a result, we demonstrated that the ET route via Asn349 was the dominant pathway among the five major routes via (Adenine/Asn349), (Adenine/Glu283), (Adenine/Glu283/Asn349/Met353), (Met353/Asn349), and (Asn349), indicating that Asn349 is an essential amino acid residue in the ET reaction.
Collapse
Affiliation(s)
- Ryuma Sato
- Department of Physics, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8602 , Japan
| | - Hirotaka Kitoh-Nishioka
- Center for Computational Sciences , University of Tsukuba 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Koji Ando
- Department of Information and Sciences , Tokyo Woman's Christian University , 2-6-1 Zempukuji, Suginami-ku , Tokyo 167-8585 , Japan
| | - Takahisa Yamato
- Department of Physics, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8602 , Japan.,Institute of Genetics and Molecular and Cellular Biology , University of Strasbourg , 1 rue Laurent Fries Parc d'Innovation 67404 Illkirch, Cedex, France
| |
Collapse
|