Amino acid patterns within short consensus repeats define conserved duplicons shared by genes of the RCA complex.
Complement control proteins (CCPs) contain repeated protein domains, short consensus repeats (SCRs), which must be relevant to diverse functions such as complement activation, coagulation, viral binding, fetal implantation, and self-nonself recognition. Although SCRs share some discontinuous and imperfect motifs, there are many variable positions and indels making classification in subfamilies extremely difficult. Using domain-by-domain phylogenetic analysis, we have found that most domains can be classified into only 11 subfamilies, designated a, b, c, d, e, f, g, h, i, j, or k and identified by critical residues. Each particular CCP is characterized by the order of representatives of the subfamilies. Human complement receptor 1 (CR1) has ajefbkd repeated four times and followed by ch. The classification crosses CCPs and indicates that a particular CCP is a function of the mix of SCRs. The aje set is a feature of several CCPs including human CR1 and DAF and murine Crry and appears to be associated with the success or failure of implantation inter alia. This approach facilitates genomic analysis of available sequences and suggests a framework for the evolution of CCPs. Units of duplication range from single SCRs, to septamers such as efbkdaj, to extensive segments such as MCP-CR1L. Imperfections of duplication with subsequent deletion have contributed to diversification.
Centre for Molecular Immunology and Instrumentation, University of Western Australia, Nedlands, 6907 Western Australia. cmii@cyllene.uwa.edu.au.
Craig A
CA
McLure
Roger L
RL
Dawkins
Joseph F
JF
Williamson
Richard A
RA
Davies
Jemma
J
Berry
Longman-Jacobsen
LJ
Natalie
Rebecca
R
Laird
Silvana
S
Gaudieri
D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D003167:Complement Activation / Q000235:genetics; D003165:Complement System Proteins / Q000235:genetics*; D016384:Consensus Sequence / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D023281:Genomics / Q000379:methods; D006801:Humans; D051379:Mice / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011323:Primates / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D003165:Complement System Proteins