[Computational analysis of signal peptide-dependent secreted protein in Caenorthaditis elegans ws123].
The internet-based softwares SignalP v3.0, TargetP v1.01, big-PI predictor and TMHMM v2.0 were combined to predict the signal peptides and the signal peptide-dependent secreted proteins from the 19,855 ORFs in Caenorthaditis elegans ws123 genome. 1,990 proteins were predicted to be secreted and to contain signal peptides among 19,855 proteins, among which 1,936 have SignalPase I signal peptide (containing 41 with RR-motif signal peptide), 53 have SignalPase II signal peptide and one has SignalPase IV signal peptide. The signal peptides of 742 secreted proteins include only H-domain and C-domain, but no typical N-domain; the signal peptides of other 1,248 secreted proteins include all three domains. Although the amino acids constitution of the SignalPase I signal peptides were similar in general between Caenorthaditis elegans and prokaryote, there were apparently small differences, and the amino acid composition of Caenorthaditis elegans are more diverse and less conserved. But there are distinct differences on the amino acid composition of SignalPase II signal peptides. The signal peptides of Caenorthaditis elegans were more diverse than unicellular eukaryotic organism. The signal peptides of a few proteins were exactly the same. We used the BLAST 2 SEQUENECES aligning method to compare the homology among the secreted proteins with the same signal peptides. The alignment results indicated that the genes sharing the same signal peptide sequences were homologous to each other and were likely to have arisen from gene duplication.
Wu
Hong-Zhi
HZ
The College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China. whzsl1128@163.net
Li
Cheng-Yun
CY
Zhu
You-Yong
YY
Bi
Yu-Fen
YF
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D017173:Caenorhabditis elegans / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000502:physiology; D008969:Molecular Sequence Data; D010455:Peptides / Q000378:metabolism; D011487:Protein Conformation; D021382:Protein Sorting Signals / Q000235:genetics* / Q000502:physiology; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods; D017386:Sequence Homology, Amino Acid
D029742:Caenorhabditis elegans Proteins; D010455:Peptides; D021382:Protein Sorting Signals