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dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors.

Kim YM, Choi J, Lee HY, Lee GW, Lee YH, Choi D - Database (Oxford) (2014)

Bottom Line: Cryptochromes have conserved domain architectures with two distinct domains, an N-terminal photolyase-related domain and a C-terminal domain.Although the molecular function and domain architecture of cryptochromes are conserved, their molecular mechanisms differ between plants and animals.Thus, cryptochromes are one of the best candidates for comparative and evolutionary studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea and Center for Fungal Genetic Resources and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-742, Korea.

ABSTRACT
Cryptochromes are flavoproteins that play a central role in the circadian oscillations of all living organisms except archaea. Cryptochromes are clustered into three subfamilies: plant-type cryptochromes, animal-type cryptochromes and cryptochrome-DASH proteins. These subfamilies are composed of photolyase/cryptochrome superfamily with 6-4 photolyase and cyclobutane pyrimidine dimer photolyase. Cryptochromes have conserved domain architectures with two distinct domains, an N-terminal photolyase-related domain and a C-terminal domain. Although the molecular function and domain architecture of cryptochromes are conserved, their molecular mechanisms differ between plants and animals. Thus, cryptochromes are one of the best candidates for comparative and evolutionary studies. Here, we have developed a Web-based platform for comparative and evolutionary studies of cryptochromes, dbCRY (http://www.dbcryptochrome.org/). A pipeline built upon the consensus domain profile was applied to 1438 genomes and identified 1309 genes. To support comparative and evolutionary genomics studies, the Web interface provides diverse functions such as (i) browsing by species, (ii) protein domain analysis, (iii) multiple sequence alignment, (iv) homology search and (v) extended analysis opportunities through the implementation of 'Favorite Browser' powered by the Comparative Fungal Genomics Platform 2.0 (CFGP 2.0; http://cfgp.snu.ac.kr/). dbCRY would serve as a standardized and systematic solution for cryptochrome genomics studies. Database URL: http://www.dbcryptochrome.org/

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(A) The pipeline for the identification of cryptochrome-encoding genes. To construct the pipeline, expert-curated protein sequences annotated as cryptochrome or DNA photolyase were collected from UniprotKB/SwissProt and analyzed by InterPro scan. Cryptochrome genes were identified from 1458 genomes belonging to 1406 species and classified into five subfamilies. The identified 1309 genes were archived in the database. (B) The box plot represents a normalized number of cryptochrome/photolyase genes per genome.
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bau037-F1: (A) The pipeline for the identification of cryptochrome-encoding genes. To construct the pipeline, expert-curated protein sequences annotated as cryptochrome or DNA photolyase were collected from UniprotKB/SwissProt and analyzed by InterPro scan. Cryptochrome genes were identified from 1458 genomes belonging to 1406 species and classified into five subfamilies. The identified 1309 genes were archived in the database. (B) The box plot represents a normalized number of cryptochrome/photolyase genes per genome.

Mentions: To identify putative genes that encode photolyases or cryptochromes, five subfamilies were defined based on previous research (9, 15), and protein domain profiling was performed (Table 1). To determine the domain profiles for each class, all protein sequences from UniprotKB/SwissProt (16) that are annotated as DNA photolyase, cryptochrome or CRY-DASH proteins were retrieved. Retrieved proteins were turned out to have three essential domains for cryptochromes, which include IPR005101 [DNA photolyase, flavin adenine dinucleotide (FAD)-binding/cryptochrome, C-terminal], IPR006050 (DNA photolyase, N-terminal) and IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold). To identify putative genes that encode cryptochromes, >7.5 million protein sequences from 1438 genomes in bacteria, archaea, oomycetes, fungi, plants and animals were screened. A total of 1309 protein sequences that had all three essential cryptochrome domains were identified. By identifying the presence and absence of additional domains, these 1309 protein sequences were further classified into five subfamilies: animal-type cryptochromes, CRY-DASH proteins, CPD photolyase class I, CPD photolyase class II and plant-type cryptochromes (Figure 1).Table 1.


dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors.

Kim YM, Choi J, Lee HY, Lee GW, Lee YH, Choi D - Database (Oxford) (2014)

(A) The pipeline for the identification of cryptochrome-encoding genes. To construct the pipeline, expert-curated protein sequences annotated as cryptochrome or DNA photolyase were collected from UniprotKB/SwissProt and analyzed by InterPro scan. Cryptochrome genes were identified from 1458 genomes belonging to 1406 species and classified into five subfamilies. The identified 1309 genes were archived in the database. (B) The box plot represents a normalized number of cryptochrome/photolyase genes per genome.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016680&req=5

bau037-F1: (A) The pipeline for the identification of cryptochrome-encoding genes. To construct the pipeline, expert-curated protein sequences annotated as cryptochrome or DNA photolyase were collected from UniprotKB/SwissProt and analyzed by InterPro scan. Cryptochrome genes were identified from 1458 genomes belonging to 1406 species and classified into five subfamilies. The identified 1309 genes were archived in the database. (B) The box plot represents a normalized number of cryptochrome/photolyase genes per genome.
Mentions: To identify putative genes that encode photolyases or cryptochromes, five subfamilies were defined based on previous research (9, 15), and protein domain profiling was performed (Table 1). To determine the domain profiles for each class, all protein sequences from UniprotKB/SwissProt (16) that are annotated as DNA photolyase, cryptochrome or CRY-DASH proteins were retrieved. Retrieved proteins were turned out to have three essential domains for cryptochromes, which include IPR005101 [DNA photolyase, flavin adenine dinucleotide (FAD)-binding/cryptochrome, C-terminal], IPR006050 (DNA photolyase, N-terminal) and IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold). To identify putative genes that encode cryptochromes, >7.5 million protein sequences from 1438 genomes in bacteria, archaea, oomycetes, fungi, plants and animals were screened. A total of 1309 protein sequences that had all three essential cryptochrome domains were identified. By identifying the presence and absence of additional domains, these 1309 protein sequences were further classified into five subfamilies: animal-type cryptochromes, CRY-DASH proteins, CPD photolyase class I, CPD photolyase class II and plant-type cryptochromes (Figure 1).Table 1.

Bottom Line: Cryptochromes have conserved domain architectures with two distinct domains, an N-terminal photolyase-related domain and a C-terminal domain.Although the molecular function and domain architecture of cryptochromes are conserved, their molecular mechanisms differ between plants and animals.Thus, cryptochromes are one of the best candidates for comparative and evolutionary studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea and Center for Fungal Genetic Resources and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-742, Korea.

ABSTRACT
Cryptochromes are flavoproteins that play a central role in the circadian oscillations of all living organisms except archaea. Cryptochromes are clustered into three subfamilies: plant-type cryptochromes, animal-type cryptochromes and cryptochrome-DASH proteins. These subfamilies are composed of photolyase/cryptochrome superfamily with 6-4 photolyase and cyclobutane pyrimidine dimer photolyase. Cryptochromes have conserved domain architectures with two distinct domains, an N-terminal photolyase-related domain and a C-terminal domain. Although the molecular function and domain architecture of cryptochromes are conserved, their molecular mechanisms differ between plants and animals. Thus, cryptochromes are one of the best candidates for comparative and evolutionary studies. Here, we have developed a Web-based platform for comparative and evolutionary studies of cryptochromes, dbCRY (http://www.dbcryptochrome.org/). A pipeline built upon the consensus domain profile was applied to 1438 genomes and identified 1309 genes. To support comparative and evolutionary genomics studies, the Web interface provides diverse functions such as (i) browsing by species, (ii) protein domain analysis, (iii) multiple sequence alignment, (iv) homology search and (v) extended analysis opportunities through the implementation of 'Favorite Browser' powered by the Comparative Fungal Genomics Platform 2.0 (CFGP 2.0; http://cfgp.snu.ac.kr/). dbCRY would serve as a standardized and systematic solution for cryptochrome genomics studies. Database URL: http://www.dbcryptochrome.org/

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