Proposed guidelines for a unified nomenclature and phylogenetic analysis of type III Hop effector proteins in the plant pathogen Pseudomonas syringae

• Published in: Molecular plant-microbe interactions Vol. 18; no. 4; pp. 275 - 282
• Main Authors: Lindeberg, M, Stavrinides, J, Chang, J.H, Alfano, J.R, Collmer, A, Dangl, J.L, Greenberg, J.T, Mansfield, J.W, Guttman, D.S
• Format: Journal Article
• Language: English
• Published: St Paul, MN APS Press 01.04.2005; American Phytopathological Society; The American Phytopathological Society
• Subjects: bacterial outer membrane proteins; Bacterial plant pathogens; bacterial proteins; Bacterial Proteins - classification; Bacterial Proteins - genetics; Biological and medical sciences; biological nomenclature; Fundamental and applied biological sciences. Psychology; Guidelines as Topic; Likelihood Functions; literature reviews; Phylogeny; Phytopathology. Animal pests. Plant and forest protection; plant pathogenic bacteria; Pseudomonas syringae; Pseudomonas syringae - genetics; Terminology as Topic; Type III secretion system; Pseudomonadales; Plant; Microbiology; Plant pathogen; Pseudomonas syringae; Nomenclature; Bacteria; Pseudomonadaceae; Phylogeny; Protein
• ISSN: 0894-0282; 1943-7706
• DOI: 10.1094/mpmi-18-0275

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.