Generic Hop Name Structure:

Subgroup

While orthology and paralogy relationships of Hops within a family are generally ignored due to the confounding effects of horizontal gene transfer, homology families are further divided when the level of amino acid similarity is sufficiently high and the phylogenetic structure for these subgroups is strong. Although there is no way to determine from sequence if these subgroups are functionally distinct, they represent distinct and strongly supported evolutionary lineages. Subgroup membership is indicated by the numerical designation following the alphabetic characters. The subgroup designation "1" should be assigned even in cases where the homology family is not subdivided, in order to facilitate possible future expansion of the family when additional members are identified.
For instructions for determining family and subgroup membership see protocol for phylogenetic analysis.

Source

Pathovar and strain of the source bacterium are to be indicated in the subscript. This format is generally consistent with ASM guidelines for gene naming wherein genotypic designations are indicated by three letter locus symbols, functionally related loci distinguished by capital letters, and subscripts used to distinguish genes from different organisms and strains. Pathovar abbreviations such as Pma and Pto follow the recommendations of Vivian and Mansfield 1993, and the update by D.S. Guttman (pathovar abbreviations). Although strain designations have not been routinely included in past Avr and Hop name assignments, the anticipated sequencing of multiple strains from single pathovars necessitates their inclusion in the new nomenclature.

Pre-requisites: Confirm that the protein in question meets one or more of the criteria required for Hop naming (see criteria for Hop name assignment) Determine whether the protein in question is similar to a previously characterized Hop family and subgroup (see protocol for phylogenetic analysis)

Name a confirmed Hop lacking similarity to any known Hop family:

1. Select next available alphabetic character (see Hop name list)
2. Add a subgroup designation of "1"
3. Add source pathovar and strain (see list of pathovar abbreviations)

Name a Hop that is a member of an established family AND subgroup:

1. Confirm membership in an existing family and subgroup (see protocol for phylogenetic analysis). Note that if homology is being used as the only criterion for Hop naming, the sequence must also have an N-terminal consensus translocation motif as described in criteria for Hop name assignment
2. Assign the alphabetic character and number of the family and subgroup of which it is a member, followed by the appropriate pathovar and strain designation

Examples:

• A member of the HopXY1 family and subgroup identified in Pto DC3000 would be named HopXY1 Pto DC3000.
• If a member of the HopXY1 family and subgroup had previously been identified in Pto DC3000, the newly identified Hop would be named HopXY1-2 Pto DC3000.

Name a Hop that is a member of a NOVEL subgroup within an established family:

1. Evaluate relationship to existing families and subgroups and confirm that the computed genetic distance exceeds that within established subgroups (see protocol for phylogenetic analysis)
2. Assign the alphabetic character of the family followed by the next available subgroup number (see Hop name list) and appropriate source pathovar and strain

Chimeras - As a general rule, Hops for which a contiguous stretch > 40% of the coding region is unique or derived from an unrelated Hop should be considered chimeras. All chimeras thus far identified are composed of a region similar to a previously named Hop and a novel coding sequence. These have been assigned a unique alphabetic designation. If Hops are identified that appear to be chimeras composed of two previously characterized Hops, it is recommended that they be named using the alphabetic characters of both parents (e.g. a chimera Hop composed of regions from HopABpv strain and HopXYpv strain would be named HopAB-XYpv strain).

Pseudogenes - Non-expressed homologs of characterized Hop families can be named according to the convention for bacterial pseudogenes wherein the gene name is preceded by the Greek letter "psi" (e.g. yhopXY1pv strain).

Non-secreted/translocated Hop alleles - Homologs that are expressed but neither secreted nor translocated, can be named after the Hop family and subgroup to which they are homologous followed by an asterisk (e.g. HopXY1 * pv strain). Experimental confirmation of this phenotype is strongly encouraged, as not all Hops have an obvious N-terminal secretion/translocation domain.

Gene disruptions - Homologs of previously characterized hop genes that are truncated by a frameshift or premature stop codon can be indicated by addition of a single quotation mark to the hop gene name (i.e. hopXY'pv strain). If a disrupted gene fails to be expressed, a "psi" (y) can also be added to reflect pseudogene status. Insertions by mobile genetic elements can be indicated with a double colon followed by the name of the inserted element (i.e. hopXY::IS10pv strain).

Hop chaperones - Three Hop chaperones have been experimentally confirmed and named with the designation Shc (specific Hop chaperone) followed by the letter of the first Hop for which they were shown to be a chaperone. This designation was chosen to parallel the Yersinia spp. term Syc (specific Yersinia chaperone). Acceptable evidence for chaperone activity includes any method that directly demonstrates association of the chaperone and its cognate Hop, such as affinity chromatography, immunoblotting, yeast two-hybrid experiments, or crystal structure. In addition, a decrease in Hrp-dependent secretion of the chaperoned protein should be evident upon mutagenesis of the chaperone gene.