Abstract
PurposeThe 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.MethodsPSYs 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.ResultsRP 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.ConclusionRP 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.
Highlights
Carotenoids are a subfamily of isoprenoids with an extensive conjugated double bond system, acting as chromophores
There is a marked difference in the molecular weight and instability index of RP phytoene synthase (PSY) and plant-origin PSYs, which lie at two extremities of the graph with the forming having one of the smallest values and the latter having the highest value
There is a significant difference in the percentages of some amino acid residues between the psychrophilic G. algens PSY and the thermophilic M. taiwanensis
Summary
Carotenoids are a subfamily of isoprenoids with an extensive conjugated double bond system, acting as chromophores. They are red, yellow, or orange colored and are found in plants, fungi, bacteria, protozoa, algae, and archaea. Mukherjee and Mukhopadhyay Annals of Microbiology (2020) 70:15 et al 2014). This enzyme is so important that when suppressed it leads to a decreased production of carotenoids (Kato et al 2017). Most of the previous studies on phytoene synthases have focused on plant origin enzymes; studies on phytoene synthases of bacterial origin are few (Iwata-Reuyl et al 2003). We need to focus more on bacterial origin PSYs, especially thermostable ones
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