Comparative analysis of structural and functional aspects of phytoene synthase from Meiothermus taiwanensis strain RP

Abstract

Purpose: The aim of this study is the in silico characterization of the structure and function of the phytoene synthase (PSY) of a red carotenoid producing thermophile Meiothermus taiwanensis strain RP with a comparative approach. Methods: PSYs from M. taiwanensis strain RP and other groups of thermophilic, mesophilic and psychrophilic bacteria, plants, protozoa, and algae were analyzed by ExPASy ProtParam, NCBI Conserved Domain Search, SOPMA, PSIPRED, Robetta server, ProQ, and QMEAN, with the superposition of 3-D structures in PyMOL.Results: RP PSY shows the highest (97.5 %) similarity with M. ruber and the lowest with the psychrophile Gelidibacter algens (36.7 %). The amino acid sequence of RP PSY is one of the shortest, with 275 residues. The instability index of RP PSY is much lower compared with plant sequences. Alanine, arginine, glycine, and leucine residues are the highest in Meiothermus sp., and they have a high amount of alpha-helix. Most of the 32 active site residues are conserved in all the sequences. However, some residues are more prone to substitutions in other PSYs except M. ruber. The three-dimensional structures of M. taiwanensis strain RP, Gelidibacter algens, Thermus thermophiles, Meiothermus ruber, and Brassica napus PSYs were homology modeled, validated, and submitted to Protein Model Databank. The superposition of the 3-D structures shows that their active site region structure is identical.Conclusion: RP PSY is one of the most stable PSYs and knowledge of its individual properties, similarities, and dissimilarities with other PSYs may be useful for genetic engineering and purification of the protein for improved carotenoid production.

Phytoene Synthase: The Key Rate-Limiting Enzyme of Carotenoid Biosynthesis in Plants

“…PSY also has a specific galactolipid and membrane association requirement for its catalytic activity ( Schledz et al, 1996 ; Welsch et al, 2000 ). In general, plant PSY proteins are unstable ( Mukherjee and Mukhopadhyay, 2020 ). This is especially true in photosynthetically active tissues, where PSY protein amounts are extremely low and subjected to a relatively high protein turnover rate.…”

“…The active site of PSY enzymes is comprised of six conserved motifs, i.e., substrate binding pocket, catalytic residues, active lid-residues, two aspartate-rich regions, and substrate Mg 2+ binding site (GGPP is usually complexed with Mg 2+ ) ( Figure 1 ). Most residues of the active site are identical and conserved even with the bacterial and fungal orthologs ( Mukherjee and Mukhopadhyay, 2020 ). The three-dimensional structure modeling shows an identical structure of the active site region of PSY enzymes from evolutionarily distant lineages, despite that their global structure vary ( Cao et al, 2019 ; Mukherjee and Mukhopadhyay, 2020 ).…”

“…Most residues of the active site are identical and conserved even with the bacterial and fungal orthologs ( Mukherjee and Mukhopadhyay, 2020 ). The three-dimensional structure modeling shows an identical structure of the active site region of PSY enzymes from evolutionarily distant lineages, despite that their global structure vary ( Cao et al, 2019 ; Mukherjee and Mukhopadhyay, 2020 ).…”