Sequence-related human proteins cluster by degree of evolutionary conservation.
Gene duplication followed by adaptive evolution is thought to be a central mechanism for the emergence of novel genes. To illuminate the contribution of duplicated protein-coding sequences to the complexity of the human genome, we study the connectivity of pairwise sequence-related human proteins and construct a network (N) of linked protein sequences with shared similarities. We find that (i) the connectivity distribution P (k) for k sequence-related proteins decays as a power law P (k) approximately k(-gamma) with gamma approximately 1.2 , (ii) the top rank of N consists of a single large cluster of proteins ( approximately 70%) , while bottom ranks consist of multiple isolated clusters, and (iii) structural characteristics of N show both a high degree of clustering and an intermediate connectivity ("small-world" features). We gain further insight into structural properties of N by studying the relationship between the connectivity distribution and the phylogenetic conservation of proteins in bacteria, plants, invertebrates, and vertebrates. We find that (iv) the proportion of sequence-related proteins increases with increasing extent of evolutionary conservation. Our results support that small-world network properties constitute a footprint of an evolutionary mechanism and extend the traditional interpretation of protein families.
Mrowka
Ralf
R
Systems Biology Group, Department of Physiology, Charité Universitätsmedizin Berlin, Tucholskystrasse 2, 10117 Berlin, Germany. ralf.mrowka@charite.de
Patzak
Andreas
A
Herzel
Hanspeter
H
Holste
Dirk
D
D002874:Chromosome Mapping / Q000379:methods*; D016000:Cluster Analysis; D017124:Conserved Sequence; D019143:Evolution, Molecular; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D011506:Proteins