Molecular Evolution of the Photolyase–Blue-Light Photoreceptor Family
Abstract
The photolyase-blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases, and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts, respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence between eubacteria and eukaryotes.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The LUCA lineage contained photolyase.
“Phylogenetic analyses indicate that photolyase was present in the lineage of the Last Universal Common Ancestor (LUCA) and that the observed paraphyletic distribution across the three domains is due to widespread gene loss (Heijde et al. 2010;Kanai et al. 1997).”
From Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor (2018) · cites this paper as Kanai et al. 1997
Cites
Crystal Structure of DNA Photolyase from Escherichia coli
Park, H.-W., Kim, S., Sancar, A., & Deisenhofer, J. (1995) · Science · doi:10.1126/science.7604260 · Cited by 585 · see citing works
A plant gene for photolyase: an enzyme catalyzing the repair of UV‐light‐induced DNA damage
Batschauer, A. (1993) · The Plant Journal · doi:10.1046/j.1365-313x.1993.04040705.x · Cited by 116 · see citing works
Adachi, J., & Hasegawa, M. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00160510 · Cited by 94 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The cryb mutation identifies cryptochrome as a circadian photoreceptor in Drosophila
Stanewsky, R., Kaneko, M., Emery, P., Beretta, B., Wager-Smith, K., Kay, S. A., Rosbash, M., & Hall, J. C. (1998) · Cell · doi:10.1016/s0092-8674(00)81638-4 · Cited by 968 · see citing works
Emery, P., So, W. V., Kaneko, M., Hall, J. C., & Rosbash, M. (1998) · Cell · doi:10.1016/s0092-8674(00)81637-2 · Cited by 912 · see citing works
Lin (2005) · Genome biology · doi:10.1186/gb-2005-6-5-220 · Cited by 351 · see citing works
Enzyme plus light therapy to repair DNA damage in ultraviolet-B-irradiated human skin
Stege, H., Roza, L., Vink, A. A., Grewe, M., Ruzicka, T., Grether-Beck, S., & Krutmann, J. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.030528897 · Cited by 292 · see citing works
Cryptochromes—a potential magnetoreceptor: what do we know and what do we want to know?
Liedvogel, M., & Mouritsen, H. (2010) · Journal of The Royal Society Interface · doi:10.1098/rsif.2009.0411.focus · Cited by 231 · see citing works
Light-driven DNA repair by photolyases
Essen, L. O., & Klar, T. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-005-5447-y · Cited by 200 · see citing works
Photolyase: Dynamics and electron-transfer mechanisms of DNA repair
Zhang, M., Wang, L., & Zhong, D. (2017) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2017.08.007 · Cited by 115 · see citing works
Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor
Cantine, M. D., & Fournier, G. P. (2018) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-017-9542-5 · Cited by 54 · see citing works
Ueda, T., Kato, A., Kuramitsu, S., Terasawa, H., & Shimada, I. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m507972200 · Cited by 48 · see citing works
Fukushiro, M., Takeuchi, T., Takeuchi, Y., Hur, S.-P., Sugama, N., Takemura, A., Kubo, Y., Okano, K., & Okano, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028643 · Cited by 47 · see citing works
Effect of xenogenic repair enzymes on photoimmunology and photocarcinogenesis
Stege, H. (2001) · Journal of Photochemistry and Photobiology B: Biology · doi:10.1016/s1011-1344(01)00246-9 · Cited by 38 · see citing works
- Authors
- Kanai, S., Kikuno, R., Toh, H., Ryo, H., & Todo, T.
- Affiliations
- Biomolecular Engineering Research Institute (Japan) (JP)
- The University of Osaka (JP)
- Kyoto University (JP)
- ORCID
- Todo, Takeshi
- Venue
- Journal of Molecular Evolution
- Published
- 1997-11
- Volume
- 45
- Issue
- 5
- Pages
- 535-548
- ISSN
- 0022-2844 (ISSN-L)
- OpenAlex
- W2364878906
- Cited by
- 158
- References
- 3
- Citations by year
- 2026: 2 · 2024: 4 · 2023: 3 · 2022: 1 · 2021: 3 · 2020: 5 · 2019: 4 · 2018: 5 · 2017: 7 · 2016: 4 · 2015: 2 · 2014: 8 · 2013: 3 · 2012: 3
- FWCI
- 10.54
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Journal of Molecular Evolution (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Light effects on plants
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Photosynthetic Processes and Mechanisms
- Keywords
- (6-4) photolyase, blue-light photoreceptor, photoreactivation, functional divergence, gene duplication, phylogenetic analysis
- MeSH terms
- Amino Acid Sequence, Animals, Deoxyribodipyrimidine Photo-Lyase, Molecular Sequence Data, Photoreceptor Cells, Phylogeny, Sequence Alignment, Sequence Homology, Amino Acid, Evolution, Molecular
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
