In-silico study of fatty acid biosynthesis pathway enzymes in microalga Scenedesmus

Abstract

Scenedesmus quadricauda is an important, rapidly growing, freshwater microalga explored as a source of alternative fuel because of its significantly high lipid content. However, the molecular basis of fatty acid biosynthesis is scarcely elucidated not only in S. quadricauda but also in Scenedesmus as a whole. This study aims to understand the 3D model structure of enzymes involved in fatty acid synthesis, and their catalytic sites compared to other Scenedesmus species. The first genome sequence S. quadricauda was carried initially in our isolate LWG002611 (GenBank ID NNCB00000000). However, till date, no study has been carried out on the 3D modelling and identifying the catalytic sites of fatty acid biosynthesis pathway enzymes. Mining the genome sequence of our isolated S. quadricauda LWG002611 as well as other Scenedesmus sequences taken from PhycoCosm and NCBI, we identified sequences of the crucial enzymes involved in fatty acid biosynthesis pathways such as acetyl-CoA carboxylase (ACC), malonyl-CoA:ACP transacylase (MAT) and fatty-acyl thioesterases (FAT) for comparative study on homology, catalytic sites, domains, and protein 3D models. Detailed comparative analyses of these identified enzymes were carried out using various bioinformatics tools. Which demonstrated highly significant sequence similarity with homologs of bacteria as well as with homologs of lower groups of eukaryotes suggesting an evolutionary linkage with them. The molecular modeling and 3D structures of the chloroplastic enzymes by AlphaFold Multimer revealed the overall structural orientation and well-conserved catalytic residues. On the other hand, biotin protein ligase and cytosolic acetyl-CoA carboxylase isoforms presented some significant differences with respect to the previously reported protein models. The conserved domain suggests the preservation of the fatty acid biosynthesis pathway in Scenedesmaceae family. However, some contrasting results, unique sequences and binding sites of some enzymes in S. quadricauda may have a significant role in higher lipid accumulation than the other species. Our analysis describes some specific features in S. quadricauda fatty acid synthesis enzymes that could open up the scope of further analysis of these enzymes.