A global characterization and identification of multifunctional enzymes

Abstract

Multi-functional enzymes are enzymes that perform multiple physiological functions. Characterization and identification of multi-functional enzymes are critical for communication and cooperation between different functions and pathways within a complex cellular system or between cells. In present study, we collected literature-reported 6,799 multi-functional enzymes and systematically characterized them in structural, functional, and evolutionary aspects. It was found that four physiochemical properties, that is, charge, polarizability, hydrophobicity, and solvent accessibility, are important for characterization of multi-functional enzymes. Accordingly, a combinational model of support vector machine and random forest model was constructed, based on which 6,956 potential novel multi-functional enzymes were successfully identified from the ENZYME database. Moreover, it was observed that multi-functional enzymes are non-evenly distributed in species, and that Bacteria have relatively more multi-functional enzymes than Archaebacteria and Eukaryota. Comparative analysis indicated that the multi-functional enzymes experienced a fluctuation of gene gain and loss during the evolution from S. cerevisiae to H. sapiens. Further pathway analyses indicated that a majority of multi-functional enzymes were well preserved in catalyzing several essential cellular processes, for example, metabolisms of carbohydrates, nucleotides, and amino acids. What's more, a database of known multi-functional enzymes and a server for novel multi-functional enzyme prediction were also constructed for free access at http://bioinf.xmu.edu.cn/databases/MFEs/index.htm.

Figure 1. The top 10 frequently used Pfam domain families for known MFEs.

It is noted that about 17% of SMAD-MFEs contain ArgJ. It plays key role in both N-acetylglutamate synthase and ornithine acetyltransferase activities in the cyclic version of arginine biosynthesis.

Figure 2. The evolution path of C-1-tetrahydrofolate synthase in eukaryotic representatives including M. extorquens, S. aureus, S. cerevisiae, D. melanogaster, D. rerio, X. laevis, M. musculus, H. sapiens.

It illustrated how three independent proteins (domains) fused and mutated during the evolutionary path, which resulted in the gain and loss of multiple-functionality. The THF_DHG_CYH and THF_DHG_CYH_C domains of human and mouse Mthfd1L proteins illustrated in dark block of net pattern were mutated and lost tetrahydrofolate dehydrogenase/cyclohydrolase activities.

Figure 3. The structural distribution of protein groups in the SCOP database.

It is noted that about 38.57% of MCD-MFEs, 44.83% of SMAD-MFEs, 48.84% of esterases and 42.09% of enzymes belong to alpha and beta proteins (a/b); comparatively, only 24.85% of SCOP proteins belong to a/b topology. In this analysis, 140 known MCD-MFEs, 29 known SMAD-MFEs, 69 lipases, 43 esterases, 2155 enzymes, and 38,221 proteins were included.