CyanoLyase - Pelican ANR project
CyanoLyase is a manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases.
Phycobilin lyases are enzymes that bind chromophores (phycobilins) to specific cysteinyl sites of phycobiliproteins (PBPs; Scheer and Zhao, 2008). PBPs are pigmented proteins organized in hexamers [(αβ)3]2 and constituting the bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae (Sidler, 1994). PBP aggregates also constitute a minor antenna system in cryptophytes (Glazer & Wedemayer, 1995) and in the atypical cyanobacterium Acaryochloris (Marquardt et al., 1997).
There are four main types of PBPs: allophycocyanin (APC), phycocyanin (PC), phycoerythrocyanin (PEC) and phycoerythrin (PE), with many marine Synechococcus spp. having two distinct types of PE (PEI and PEII; Six et al., 2007). The only PBP present in low light-adapted ecotypes of the marine cyanobacterium Prochlorococcus is a modified PE called PEIII (Hess et al., 1996), whereas high light-adapted ecotypes possess only a degenerated β-PEIII subunit.
The phycobilin composition of most PBPs is highly variable, since in both cyanobacteria and red algae, they bind from one to three out of four possible phycobilin types: phycocyanobilin (PCB), phycoerythrobilin (PEB), phycourobilin (PUB) and phycoviolobilin (PVB), which are isomers with distinct spectral properties. An even larger variety of phycobilins exists in cryptophytes (Glazer & Wedemayer, 1995).
Although a number of phycobilin lyases have been biochemically characterized and one 3D structure is even available (Kuzin et al., 2007; Kupka et al., 2010; Schluchter et al., 2010), phycobilin lyases are multi-domain enzymes which are often poorly annotated by automatic gene annotation pipelines. CyanoLyase is therefore aimed at facilitating annotation of these lyases using different tools, including Blast to find similarities of query sequences with manually curated sequences of the database and Protomata learner (Coste & Kerbellec, 2005a & 2005b) to identify conserved motifs in lyase families.
Bretaudeau A, Coste F, Humily F, Garczarek L, Le Corguillé G, Six L, Ratin M, Collin O, Schluchter WA & Partensky F. 2012. CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. Nucleic Acids Research. 10.1093/nar/gks1091 (Database issue 2013).
This database was developed by Anthony Bretaudeau (GenOuest Bioinformatics Platform, Rennes, France) under the scientific management of Frédéric Partensky (Station biologique de Roscoff, France). The complete list of participants can be seen in the "About us". This work was done in the framework of the Pelican project (contract with the "Agence Nationale pour la Recherche" N° ANR-09-PCS-GENM-030).