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P. syringae Hop Identification and Nomenclature Home Page

Hop effector proteins represent the most rapidly growing class of virulence factors in P. syringae pathovars. Given the number of Hops thusfar identified, and the non-standard nomenclature by which they have been named, recent efforts have focused on assembly of a single database of Hops identified in P. syringae pathovars, and development of standardized criteria for Hop identification and nomenclature.

Hop Databases (9-10-09: Helpers and discontinued Hops moved to independent databases)

Hop database
T3SS helper database
Discontinued Hops and helpers

Hop database alphabetized by former names

New Hop Nomenclature:

Criteria for effector identification and procedures for selection of appropriate names is now published. Please cite the following paper in all references to the new nomenclature:

Magdalen Lindeberg, John Stavrinides, Jeffrey H. Chang, James R. Alfano, Alan Collmer, Jeffery L. Dangl, Jean T. Greenberg, John W. Mansfield, and David S. Guttman. 2005. Unified nomenclature and phylogenetic analysis of extracellular proteins delivered by the type III secretion system of the plant pathogenic bacterium Pseudomonas syringae. 2005. MPMI 18:275-282. text MPMI online extras: Table 1, Table 2, Table 3, errata (for regularly updated and corrected versions of Table 1, go to the main Hop database)

Specific issues related to Hop identification and nomenclature are discussed in detail under the links below (also given in the menu at the top of the page):

Acceptable criteria for Hop name assignment

    1. Phylogenetic membership in an established Hop family
    2. Confirmed HrpL-dependence and a consensus translocation pattern
    3. Hrp-dependent (TTSS) secretion into the cell milieu or translocation into the plant cell with evidence of expression
    4. Avirulence phenotype or hypersensitive response
Rules for name selection Generic name structure: HopXY#pv strain
    1. Family indicated by alphabetic character(s)
    2. Subgroup (closely related members within a family) indicated numerically
    3. Source pathovar and strain indicated in subscript

Name structures are also discussed for Hop pseudogenes, non-secreted alleles, truncations, and chaperones

Phylogenetic Analysis

Protocol for using free and publically available software (ClustalW and MEGA) to determine whether protein sequences fall into existing Hop families and subgroups

Hop name list

  • Hop names already assigned are listed at this link
  • Once an alphabetic character combination has been used, it CANNOT be applied to Hops in a different family.
  • NAME ASSIGNMENTS FOR NEWLY DISCOVERED HOPS ARE NOT OFFICIAL UNTIL PUBLIC RELEASE OF THE SEQUENCE IN GENBANK.

Guide to Terminology

The variety of names given to proteins secreted by the Hrp system and described in the effector database reflect the phenotype, source strain and priority. Explanations for the various names are given below:

Hop (Hrp outer protein): Applies generically to all proteins secreted/translocated by the Hrp system of P. syringae and other plant pathogens with similar Hrp systems (e.g., Erwinia and Pantoea spp).

Avr (Avirulence protein): Denotes a protein found through the avirulence phenotype it confers on a P. syringae strain in appropriate test plants. A shortcoming of the Avr designation is that the implied avirulence phenotype is not always shared by homologs in other pathovars and strains. However, many Avr names are deeply imbedded in the literature, and so it has been left to the original lab of discovery to decide whether a given Avr family should be incorporated into the new noemnclatural system

Hrp (Hypersensitive response and pathogenicity): Most mutations in the TTSS machinery abolish the ability of P. syringae to elicit the "HR" in nonhosts or to be pathogenic in hosts. HrpA (the Hrp pilus subunit) represents a TTSS substrate that retains its original designation because of its Hrp phenotype and/or association with the Hrp system.

Effector: A term for virulence proteins injected into host cells by a TTSS, which is broadly applicable to various plant and animal pathogens.

Helper Protein: A term of convenience referring to extracellular accessory proteins (such as HrpA) plus other TTSS substrates (such as harpins) whose primary function is likely to be the translocation of true effectors through host barriers. Also called translocators.

Harpins: Presumed helper proteins that are secreted by the TTSS in more abundance than true effectors, appear to interact with plant cell walls and membranes, are glycine-rich and devoid of cysteine, and possess a heat-stable ability to elicit the hypersensitive response when infiltrated into the intercellular (apoplastic) spaces of plant leaves.

TTSS: Type III secretion pathway, also referred to as the Hrp pathway in P. syringae pathovars. Secretion or translocation through this pathway is considered the defining characteristic for P. syringae effector proteins