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

Magdalen Lindeberg, John Stavrinides, Jeffrey H. Chang, James R Alfano, Alan Collmer, Jeffery L. Dangl, Jean T. Greenberg, John W. Mansfield, David S. Guttman

Research output: Contribution to journalReview article

107 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)275-282
Number of pages8
JournalMolecular Plant-Microbe Interactions
Volume18
Issue number4
DOIs
StatePublished - Apr 1 2005

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Pseudomonas syringae
Humulus
Plant Proteins
hops
Pathogens
Terminology
plant pathogens
Names
Guidelines
phylogeny
Proteins
proteins
type III secretion system
Pseudogenes
pseudogenes
chimerism
Plant Cells
Bioinformatics
Computational Biology
bioinformatics

ASJC Scopus subject areas

  • Physiology
  • Agronomy and Crop Science

Cite this

Proposed guidelines for a unified nomenclature and phylogenetic analysis of type III hop effector proteins in the plant pathogen Pseudomonas syringae. / Lindeberg, Magdalen; Stavrinides, John; Chang, Jeffrey H.; Alfano, James R; Collmer, Alan; Dangl, Jeffery L.; Greenberg, Jean T.; Mansfield, John W.; Guttman, David S.

In: Molecular Plant-Microbe Interactions, Vol. 18, No. 4, 01.04.2005, p. 275-282.

Research output: Contribution to journalReview article

Lindeberg, Magdalen ; Stavrinides, John ; Chang, Jeffrey H. ; Alfano, James R ; Collmer, Alan ; Dangl, Jeffery L. ; Greenberg, Jean T. ; Mansfield, John W. ; Guttman, David S. / Proposed guidelines for a unified nomenclature and phylogenetic analysis of type III hop effector proteins in the plant pathogen Pseudomonas syringae. In: Molecular Plant-Microbe Interactions. 2005 ; Vol. 18, No. 4. pp. 275-282.
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