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Criteria for Hop Name Assignment

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The term Hop applies generically to proteins that are secreted and/or translocated by the TTSS of P. syringae and related plant pathogens.Most are EFFECTORS, with their primary function being inside the host cell. Others are likely to be TRANSLOCATORS or HELPERS, assisting the delivery of true effectors across host cell barriers. This nomenclature system does not distinguish between effectors and translocators. All proteins traveling the TTSS pathway will be classified as Hops.

The following criteria have been designed to ease the experimental burden required for Hop naming, while minimizing the generation of artifactual Hops and Hop families that are not expressed or secreted. In order for newly identified proteins to receive a Hop designation, ONE OF THE FOLLOWING CRITERIA MUST BE MET:

A. Phylogenetic Membership in an established Hop family in combination with a consensus translocation motif

If >60% of a new protein's sequence can be aligned (e<10-5) with one or more members of a Hop family previously characterized using criteria B, C, or D, the new protein can be given a name reflecting this relationship. However, more in-depth phylogenetic analyses are encouraged for a more accurate assessment of family and subgroup membership (see protocol for phylogenetic analysis). The additional requirement of an N-terminal secretion/translocation sequence (see criterion B below) is included so that Hop names will be limited to plausible TTSS substrates. If a protein or gene is found to be homologous to a previously identified Hop family, but upon testing, does not meet any of the three experimental criteria, the name should be modified to conform to the guidelines for pseudogenes and non-secreted/translocated homologs (see Rules for Name Selection).

B. Confirmed HrpL-dependence and a consensus translocation motif

Hop identification has typically proceeded with a rapid discovery phase followed by a slow phase of experimental confirmation, leading to a situation where proteins are published as "TTSS effector candidates", with experimental confirmation and final naming delayed for a year or more. To allow naming to proceed at a faster rate and eliminate the need to name candidate Hops, proteins will be considered eligible for the Hop designation if HrpL-dependence is experimentally demonstrated and a consensus N-terminal targeting pattern is present. Based on the findings of previous investigations, the consensus N-terminal targeting pattern is defined here as having:

  1. > 10% Ser in the first 50 amino acids
  2. Ile, Leu, Val or Pro in the third or fourth position
  3. no Asp or Glu residues in the first 12 amino acids

It is expected that effectors named using criterion C will eventually be tested for Type III-dependent secretion and/or translocation.

For more information on the identification of a consensus translocation motif, see Guttman et al, 2002, Petnicki-Ocwieja et al, 2002, Greenberg and Vinatzer, 2003

C. Hrp-dependent (TTSS) Secretion and/or Translocation and Evidence of Expression

Passage through the TTSS is the defining characteristic of Hop proteins; however, evidence of expression is also required to avoid the proliferation of Hop families that have been computationally identified and translocated under artificial conditions, but for which there may be no actual expression.

Evidence of expression includes bioinformatic or experimental evidence supporting expression of at least one member of the Hop family in question. Evidence of expression should also include assessment of the presence of an upstream Hrp box.
(see Innes et al. 1993 (J. Bacteriol. 175:4089), Shen and Keen, 1993 ( J. Bacteriol. 175:5916), Xiao and Hutcheson, 1994 (J. Bacteriol. 176:3089), Fouts et al. 2002)

Accepted methods for demonstrating translocation include showing that AvrRpt2 or Cya can be translocated into the cell interior in a Hrp-dependent manner, when fused to either the N-terminal portion of the candidate protein or to the full ORF of the candidate being tested
(see Mudgett, et al, 2000, Guttman, et al, 2001, Schechter, et al 2004).

Accepted methods for evaluating secretion include use of Western blots to detect epitope tagged proteins in the culture supernatant
(see Petnicki-Ocwieja, et al 2002).

D. Avirulence Phenotype

Proteins shown to induce an avirulence reaction on plant hosts when expressed in heterologous strains of P. syringae will be considered Hops. However, subsequent demonstration of secretion or translocation is encouraged, given that proteins such as AvrD, which direct the production of low molecular-weight elicitors, are active in bacterial cells but may not be TTSS substrates.













Magdalen Lindeberg
PPI Project Coordinator
Plant Pathology and Plant-Microbe Biology
Cornell University