Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily

Abstract

We present the BPIFAn/BPIFBn systematic nomenclature for the PLUNC (palate lung and nasal epithelium clone)/PSP (parotid secretory protein)/BSP30 (bovine salivary protein 30)/SMGB (submandibular gland protein B) family of proteins, based on an adaptation of the SPLUNCn (short PLUNCn)/LPLUNCn (large PLUNCn) nomenclature. The nomenclature is applied to a set of 102 sequences which we believe represent the current reliable data for BPIFA/BPIFB proteins across all species, including marsupials and birds. The nomenclature will be implemented by the HGNC (HUGO Gene Nomenclature Committee).

Figure 1. Phylogenetic tree of the 102 proteins in the collection described in the text

The tree was constructed using clustalw and displayed using ITOL. The names of proteins are of the style X {Y}. For proteins that are described in the literature, X is the common name generally used there. For proteins derived from BLAST searches for this work the proteins are identified by NCBI gi accession number. Y is the systematic name established by inspection of the tree, and further justified by the analysis in Figure 2. Branches joining proteins within the same family are in the same colour. A range of similar hues is used for the subfamilies of BPIFA2. For one domain BPIFA proteins, colours at the red end of the spectrum are used, whereas the blue end is used for the two domain BPIFB proteins. Species included in this figure: chicken (Gallus gallus), chimp (Pan troglodytes), chinchilla (Chinchilla lanigera), cow (Bos taurus), dog (Canis familiaris), hamster (Mesocricetus auratus), horse (Equus caballus), human (Homo sapiens), marmoset (Callithrix jacchus), mouse (Mus musculus), opossum (Monodelphis domestica), orangutan (Pongo abelii), panda (Ailuropoda melanoleuca), pig (Sus scrofa), platypus (Ornithorhynchus anatinus), rabbit (Oryctolagus cuniculus), rat (Rattus norvegicus), rhesus monkey (Macaca mulatta), xenopus (Xenopus silurana), zebra finch (Taeniopygia guttata). Note that in order to maintain a reasonable size to this collection of sequences, a 90% maximum pairwise identity was imposed during its assembly (see main text for details). Therefore if a protein is not shown for a particular species it does not necessarily imply its absence from that species. This is particularly the case for the well conserved BPIFB3 and BPIF4 families.

Figure 2. Pairwise identities of sequences from Figure 1, aligned against the representative sequence from each BPIF family, as described in the text

Filled green circles show the pairwise identity with the representative from the family to which the sequence has been assigned (the cognate representative). Filled red circles show the pairwise identity to the representative sequences from the other families. Open green circles show the pairwise identity of a protein from a subfamily (such as mouse BPIFA2E) to the representative of the family of which the subfamily is a part (thus to human BPIFA2 in the case of mouse BPIFA2E). Crosses are used in place of circles for non-eutherian proteins and for mouse vomeromodulin. If an assignment is robust then the green circle should be substantially to the right of the red circles. The dashed ovals identify the non-cognate representative giving rise to pairwise identities above 30%.