Codon switching of conserved Ser residues in coagulation and fibrinolytic proteases

Abstract

Background: Unique among all amino acids, Ser is encoded by 2 sets of codons, TCN and AGY (N = any nucleotide, Y = pyrimidine), that cannot interconvert through single nucleotide substitutions. Both codons are documented at the essential residues S195 and S214 within the active site of serine proteases. However, it is not known how the codons interconverted during evolution because replacement of S195 or S214 by other amino acids typically results in loss of activity.

Objective: To characterize the prevalence of codon switching among essential and non-essential Ser residues in coagulation and fibrinolytic proteases from different vertebrate lineages.

Methods: TCN and AGY codon usage was analyzed in >550 sequences.

Results: Evolutionary pressure to preserve the codon of S195 is absolute, with no evidence of interconversion. Pressure to preserve the codon of S214 is also strong, but an AGY↔TCN interconversion is observed in factor VII-inactive and protein C from ray-finned fish. In both cases, the interconversion occurred in genes that were rapidly evolving. In contrast, codon switching at nonessential Ser residues in the kringle domains of coagulation and fibrinolytic proteases is quite common and could be identified in half of the kringles analyzed.

Conclusion: Codon interconversion of essential Ser residues of coagulation and fibrinolytic proteases only occurred in genes that were rapidly evolving and that-at least in some cases-evolved following genome duplication. Interconversion is common at nonessential Ser residues as found in kringle domains.

Keywords: blood coagulation; codons; evolution; fibrinolysis; vitamin K–dependent clotting factors.

Figure 1ABC.. AGY→TCN codon interconversion in fVII-inactive and PC from ray-finned fish.

(A) Alignment of representative fVII sequences from several species of ray-finned fish reveals the presence of D195 in fVII-inactive (fVII-i) as opposed to S195 in fVII and fVII-like. Different species of ray-finned fish express fVII-inactive with either S214, A214 or G214 as opposed to S214 that is always found in fVII and fVII-like. Alignment of representative sequences shows evidence of an AGY→TCN interconversion at position 214 in fVII (B) and PC (C). Shown are the aligned amino acids (capital letter) of a conserved sequence in the protease domain where S214 is located (colored) together with the nucleotides (small letter) that encode specific residues.

Figure 2.. Codon distribution in kringle domains.

TCN and AGY codons of the Ser residue in the CXXWXS motif following the second Cys residue in kringle domains. Codons shows refer only to the last residue (Ser or other) in the motif. Abbreviations are: ProT (prothrombin), tPA (tissue-type plasminogen activator), plgn (plasminogen), K (kringle).