PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature
|Author(s)||Gueguen Yannick1, Garnier Julien1, Robert Lorenne1, Lefranc Marie-Paule2, Mougenot Isabelle3, De Lorgeril Julien1, Janech Michael1, Gross Paul S.4, Warr Gregory W.4, Cuthbertson Brandon4, Barracco Margherita A.5, Bulet Philippe6, Aumelas André7, Yang Yinshan7, Bo Dong8, Xiang Jianhai8, Tassanakajon Anchalee9, Piquemal Piquemal10, Bachere Evelyne1|
|Affiliation(s)||1 : Ifremer, Univ Montpellier 2, CNRS, F-34095 Montpellier 6, France.
2 : Univ Montpellier 2, LIGM, Inst France, UPR 1142,CNRS, F-34396 Montpellier, France.
3 : Univ Montpellier 2, CNRS, UMR 5506, LIRMM, F-34392 Montpellier 5, France.
4 : Med Univ S Carolina, Dept Biochem & Mol Biol, Charleston, SC 29425 USA.
5 : Univ Fed Santa Catarina, Dept Biol Celular Embriol & Genet, Florianopolis, SC, Brazil.
6 : Atheris Labs, CH-1233 Geneva, Switzerland.
7 : Univ Montpellier 1, Ctr Biochim Struct, F-34060 Montpellier 2, France.
8 : Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China.
9 : Chulalongkorn Univ, Dept Biochem, Fac Sci, Shrimp Mol Biol & Genom Lab, Bangkok 10330, Thailand.
10 : Univ Montpellier 2, Skuld Tech Co, F-34095 Montpellier 5, France.
|Source||Developmental & Comparative Immunology (0145-305X) (Elsevier), 2006 , Vol. 30 , N. 3 , P. 283-288|
|WOS© Times Cited||112|
|Keyword(s)||Nomenclature, Sequence database, Crustacea, Antimicrobial peptide, Penaeid shrimp, Penaeidin|
|Abstract||Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.|