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Proposed Guidelines for a Unified Nomenclature and Phylogenetic Analysis of Type III Hop Effector Proteins in the Plant Pathogen Pseudomonas syringae

April 2005 , Volume 18 , Number  4
Pages  275 - 282

Magdalen Lindeberg , 1 John Stavrinides , 2 Jeffrey H. Chang , 3 James R. Alfano , 4 Alan Collmer , 1 Jeffery L. Dangl , 3 Jean T. Greenberg , 5 John W. Mansfield , 6 and David S. Guttman 2

1Department of Plant Pathology, Cornell University, Ithaca, NY 14853, U.S.A.; 2Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada; 3Department of Biology and Curriculum in Genetics, University of North Carolina, Chapel Hill, 27599-3280, U.S.A.; 4The Plant Science Initiative and the Department of Plant Pathology, University of Nebraska, Lincoln 68588-0660, U.S.A.; 5The University of Chicago, Department of Molecular Genetics and Cell Biology, 1103 East 57th Street, Erman Biology Center, Chicago 60637 IL, U.S.A.; 6Department of Agricultural Sciences, Imperial College London, Wye Campus, Wye, Ashford, Kent, TN25 5AH, U.K.

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Accepted 10 December 2004.

Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system (TTSS). Recent availability of complete genome sequences for a number of P. syringae pathovars has led to a significant increase in the rate of effector discovery. However, lack of a systematic nomenclature has resulted in multiple names being assigned to the same Hop, unrelated Hops designated by the same alphabetic character, and failure of name choices to reflect consistent standards of experimental confirmation or phylogenetic relatedness. Therefore, specific experimental and bioinformatic criteria are proposed for proteins to be designated as Hops. A generic Hop name structure, HopXY#pv strain, also is proposed, wherein family membership is indicated by the alphabetic characters, subgroup membership numerically, and source pathovar and strain in subscript. Guidelines are provided for phylogenetic characterization and name selection for Hops that are novel, related to previously characterized Hops, chimeras, pseudogenes, truncations, or nonexpressed alleles. Phylogenetic analyses of previously characterized Hops are described, the results of which have been used to guide their integration into the proposed nomenclature.