Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches

• Published in: PloS one 2012-06, Vol.7 (6), p.e38864
• Main Authors: Edwards, Nathan C, Hing, Zachary A, Perry, Avital, Blaisdell, Adam, Kopelman, David B, Fathke, Robert, Plum, William, Newell, Jordan, Allen, Courtni E, S, Geetha, Shapiro, Aaron, Okunji, Chinyere, Kosti, Idit, Shomron, Noam, Grigoryan, Vahan, Przytycka, Teresa M, Sauna, Zuben E, Salari, Raheleh, Mandel-Gutfreund, Yael, Komar, Anton A, Kimchi-Sarfaty, Chava
• Format: Article
• Language: English
• Subjects: Acids; ADAM Proteins - chemistry; ADAM Proteins - genetics; ADAM Proteins - metabolism; ADAMTS13 Protein; Amino Acid Substitution - genetics; Amino acids; Analysis; Bias; Bioinformatics; Biology; Biotechnology; Codon - genetics; Codons; Computational Biology - methods; Conservation; Conserved Sequence - genetics; Food; Gene expression; Gene Expression Regulation, Enzymologic; Genes; Genomes; HEK293 Cells; Hematology; Humans; Hypotheses; Laboratories; Medical research; Medicine; Messenger RNA; mRNA stability; Mutant Proteins - chemistry; Mutant Proteins - genetics; Mutant Proteins - metabolism; National libraries; Protein expression; Protein structure; Protein Structure, Secondary; Proteins; Proteolysis; RNA Stability - genetics; RNA, Messenger - chemistry; RNA, Messenger - genetics; RNA, Messenger - metabolism; Species Specificity; Studies; Trypsin - metabolism; Variation; Vectors (Biology); Von Willebrand factor
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0038864

Synonymous variations, which are defined as codon substitutions that do not change the encoded amino acid, were previously thought to have no effect on the properties of the synthesized protein(s). However, mounting evidence shows that these "silent" variations can have a significant impact on protein expression and function and should no longer be considered "silent". Here, the effects of six synonymous and six non-synonymous variations, previously found in the gene of ADAMTS13, the von Willebrand Factor (VWF) cleaving hemostatic protease, have been investigated using a variety of approaches. The ADAMTS13 mRNA and protein expression levels, as well as the conformation and activity of the variants have been compared to that of wild-type ADAMTS13. Interestingly, not only the non-synonymous variants but also the synonymous variants have been found to change the protein expression levels, conformation and function. Bioinformatic analysis of ADAMTS13 mRNA structure, amino acid conservation and codon usage allowed us to establish correlations between mRNA stability, RSCU, and intracellular protein expression. This study demonstrates that variants and more specifically, synonymous variants can have a substantial and definite effect on ADAMTS13 function and that bioinformatic analysis may allow development of predictive tools to identify variants that will have significant effects on the encoded protein.