Phylogenomic Study of Lipid Genes Involved in Microalgal Biofuel Production—Candidate Gene Mining and Metabolic Pathway Analyses

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dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock.

Microalgae have attracted wide attention as one of the most versatile renewable feedstocks for production of biofuel. To develop genetically engineered high lipid yielding algal strains, a thorough understanding of the lipid biosynthetic pathway and the underpinning enzymes is essential. In this work, we have systematically mined the genomes of fifteen diverse algal species belonging to Chlorophyta, Heterokontophyta, Rhodophyta, and Haptophyta, to identify and annotate the putative enzymes of lipid metabolic pathway. Consequently, we have also developed a database, dEMBF (Database of Enzymes of Microalgal Biofuel Feedstock), which catalogues the complete list of identified enzymes along with their computed annotation details including length, hydrophobicity, amino acid composition, subcellular location, gene ontology, KEGG pathway, orthologous group, Pfam domain, intron-exon organization, transmembrane topology, and secondary/tertiary structural data. Furthermore, to facilitate functional and evolutionary study of these enzymes, a collection of built-in applications for BLAST search, motif identification, sequence and phylogenetic analysis have been seamlessly integrated into the database. dEMBF is the first database that brings together all enzymes responsible for lipid synthesis from available algal genomes, and provides an integrative platform for enzyme inquiry and analysis. This database will be extremely useful for algal biofuel research. It can be accessed at http://bbprof.immt.res.in/embf

Effect of Probiotics on Host-Microbial Crosstalk: A Review on Strategies to Combat Diversified Strain of Coronavirus

The scare of the ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), does not seem to fade away, while there is a constant emergence of novel deadly variants including Alpha, Beta, Gamma, Delta and Omicron. Until now, it has claimed approximately 276,436,619 infections, and the number of deaths surpluses to 5,374,744 all over the world. While saving the life has been a priority during the ongoing SARS-CoV-2 pandemic, the post-infection healing and getting back to normalcy has been undermined. Improving general health conditions and immunity with nutritional adequacy is currently of precedence for the government as well as frontline health workers to prevent and assuage infections. Exploring the role of probiotics and prebiotics in managing the after-effects of a viral outbreak could be of great significance, considering the emergence of new variants every now and then. To enhance human immunity, the recent evidence on the connection between gut microbiota and the broad spectrum of the clinical COVID-19 disease is the reason to look at the benefits of probiotics in improving health conditions. This review aims to sketch out the prospective role of probiotics and prebiotics in improving the standard of health in common people

Comprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase:an in silico study to vitalize the development of optimum engineered strains with high lipid productivity

Microalgae as an alternative renewable resource for biofuel production have captured much significance. Nonetheless, its economic viability is a field of major concern for researchers. Unraveling the lipid catabolic pathway and gaining insights into the sequence-structural features of its primary functioning enzyme, Triacylglycerol lipase, will impart valuable information to target microalgae for augmented lipid content. In the present study, a genome-wide comparative study on putative Triacylglycerol lipase (TAGL) enzyme from algal species belonging to varied phylogenetic lineages was performed. The comprehensive sequence analysis revealed that TAGL comprises of three distinct conserved domains, such as, Patatin, Class III Lipase, and Abhydro_lipase, and also confirmed the ubiquitous presence of GXSXG motif in the sequences analyzed. In the absence of a crystal structure of algal TAGL till date, we developed the first 3D model of patatin domain of TAGL from an oleaginous microalga, Phaedactylum tricornutum, employing homology modeling, docking and molecular dynamic simulations methods. The domain-substrate complex having the low-ranking docking score revealed the binding of palmitic acid to the TAGL patatin domain surface with strong hydrogen bond interactions. The simulation results implied that the substrate-complexed patatin domain and the free enzyme adopted a more stable conformation after 40 ns. This is the first ever attempt to provide in-silico insights into the structural and dynamical insights on catalytic mechanism of the TAGL patatin domain. Subsequently, these findings aided our understanding on their structural stability, folding mechanism and protein-substrate interactions, which could be further utilized to design site-specific mutagenic experiments for engineering microalgal strains. Communicated by Ramaswamy H. Sarma</p

Screenshots of dEMBF analysis tools displaying their query pages and resulting outputs.

<p>(A) “BLAST” tool allow users to perform similarity search for protein or nucleotide sequences against NCBI, dEMBF database or against individual enzymes. A wide range of E-values are provided to control search sensitivity. BLAST results are sorted by percentage of identity, similarity, query coverage, bit score and E-value. (B) “Compare” tool to perform comparative analysis of enzyme between one or multiple algal species. Users can select various clickable annotation feature alongwith enzyme name and corresponding organisms between which comparisons is to be carried out. (C) “Motif” tool to identify conserved motifs in query sequences using the integrated MEME program. (D) “MSA” tool to align two or more protein sequences with the MUSCLE program. (E) “Phylogeny” tool to construct phylogenetic tree (Newick rooted tree or Circular tree) using PhyML and jsPhyloSVG.</p