Photolyase is a
phylogenetically old enzyme which is present and functional in many species, from the
bacteria to the
fungi to
plants and to the
animals. Photolyase is particularly important in repairing UV induced damage in plants. The photolyase mechanism is no longer working in humans and other placental mammals who instead rely on the less efficient
nucleotide excision repair mechanism, although they do retain many
cryptochromes. Freezing stress in the annual wheat
Triticum aestivum and in its perennial relative
Thinopyrum intermedium is accompanied by large increases in expression of DNA photolyases. Photolyases are
flavoproteins and contain two light-harvesting
cofactors. Many photolyases have an
N-terminal domain that binds a second cofactor. All photolyases contain the two-electron-reduced
FADH−; they are divided into two main classes based on the second cofactor, which may be either the
pterin methenyltetrahydrofolate (MTHF) in
folate photolyases or the
deazaflavin 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) in
deazaflavin photolyases. Although only FAD is required for catalytic activity, the second cofactor significantly accelerates reaction rate in low-light conditions. The enzyme acts by
electron transfer in which the reduced flavin FADH− is activated by light energy and acts as an electron donor to break the pyrimidine dimer. On the basis of sequence similarities DNA photolyases can be grouped into a few classes: • Class 1 CPD photolyases are enzymes that process cyclobutane pyrimidine dimer (CPD) lesions from Gram-negative and Gram-positive bacteria, as well as the halophilic
archaea Halobacterium halobium. • Class 2 CPD photolyases also process CPD lesions. They are found in plants like the thale cress
Arabidopsis thaliana and the
rice. • The plant and fungi cryptochromes are similar to Class 1 CPDs. They are blue light photoreceptors that mediate blue light-induced gene expression and modulation of
circadian rhythms. • Class 3 CPD lyases make up a sister group to the plant cryptochromes, which in turn are a sister group to class 1 CPDs. • The Cry-DASH group are CPD lyases highly specific for single-stranded DNA. Members include
Vibrio cholerae, X1Cry from
Xenopus laevis, and AtCry3 from
Arabidopsis thaliana. DASH was initially named after
Drosophila,
Arabidopsis,
Synechocystis, and
Human, four taxa initially thought to carry this family of lyases. The categorization has since changed. The "Cry" part of their name was due to initial assumptions that they were cryptochromes. • Eukaryotic
(6-4)DNA photolyases form a group with animal cryptochromes that control circadian rhythms. They are found in diverse species including
Drosophila and humans. The cryptochromes have their own detailed grouping. • Bacterial 6-4 lyases (), also known as the FeS-BCP group, form their own outgroup relative to all photolyases. The non-class 2 branch of CPDs tend to be grouped into class 1 in some systems such as PRINTS (PR00147). Although the members of the smaller groups are agreed upon, the phylogeny can vary greatly among authors due to differences in methodology, leading to some confusion with authors who try to fit everything (sparing FeS-BCP) into a two-class classification. The cryptochromes form a
polyphyletic group including photolyases that have lost their DNA repair activity and instead control circadian rhythms. == Application==