LIGAND-BINDING DOMAINS IN VITELLOGENIN RECEPTORS AND OTHER LDL-RECEPTOR FAMILY MEMBERS SHARE A COMMON ANCESTRAL ORDERING OF CYSTEINE-RICH REPEATS

Insect vitellogenin and yolk protein receptors (VgR/YPR) are newly dis covered members of the low-density lipoprotein receptor (LDLR) family, which is characterized by a highly conserved arrangement of repetitiv e modular elements homologous to functionally unrelated proteins. The insect VgR/YPRs are unique in having two clusters of complement-type c ysteine-rich (class A) repeats or modules, with five modules in the fi rst cluster and seven iu the second cluster, unlike classical LDLRs wh ich have a single seven-module cluster, vertebrate VgRs and very low d ensity lipoprotein receptors (VLDLR) which have a single eight-module cluster, and LDLR-related proteins (LRPs) and megalins which have four clusters of 2-7, 8, 10, and 11 modules. Alignment of clusters across subfamilies by conventional alignment programs is problematic because of the repetitive nature of the component modules which may have under gone rearrangements, duplications, and deletions during evolution. To circumvent this problem, we ''fingerprinted'' each class A module in t he different clusters by identifying those amino acids that are both r elatively conserved and relatively unique within the cluster. Inter cl uster reciprocal comparisons of fingerprints and aligned sequences all owed us to distinguish four cohorts of modules reflecting shared recen t ancestry. All but two of the 57 modules examined could be assigned t o one of these four cohorts designated A, B, C, and D. Alignment of cl usters based on modular cohorts revealed that all clusters are derived from a single primordial cluster of at least seven modules with a con sensus arrangement of CDCADBC. All extant clusters examined are consis tent with this consensus, though none matches it perfectly. This analy sis also revealed that the eight-module clusters in vertebrate VgRs, i nsect VgR/YPRs, and LRP/megalins are not directly homologous with one another. Assignment of modules to cohorts permitted us to properly ali gn 32 class A clusters from all four LDLR subfamilies for phylogenetic analysis. The results revealed that smaller one-cluster and two-clust er members of the family did not originate from the breakup of a large two-cluster or four-cluster receptor. Similarly, the LRP/megalins did not arise from the duplication of a two-cluster insect VgR/YPR-like p rogenitor. Rather, it appears that the multicluster receptors were ind ependently constructed from the same single-cluster ancestor.