Physico-chemical properties reflect the functional and structural characteristics of a protein. The comparative study of the physicochemical properties is important to know role of a protein in exploring its molecular evolution. A number of online and offline tools are available for calculating the physico-chemical properties of a single protein sequence. However, a tool is not available for a comparative study with graphical visualization of Multi-FASTA sequences. Hence, we describe the development and utility of MFPPI V.1.0 (a web interface developed in JAVA platform) to input each FASTA sequence from Multi-FASTA file into the ProtParam web server for the calculation of physico-chemical properties. MFPPI V.1.0 calculates different physico-chemical properties for a given set of proteins in a single run and saves the data in the MSExcel sheet. Furthermore, it provides a graphical representation of protein physico-chemical properties for analysis and visualization of data in a user-friendly manner. Therefore, the output from the analysis helps to understand compositional changes and functional relationship in evolution among organisms. We have demonstrated the utility of MFPPI V.1.0 using 17 mtATP6 protein sequences from different mammalian species. It is available for free at http://insilicogenomics.in/mfpcalc/mfppi.html.

Lipoxygenase-1 (LOX-1) protein provides defense against pests and pathogens and its presence have been positively correlated with plant resistance against pathogens. Linoleate is a known substrate of lipoxygenase and it induces necrosis leading to the accumulation of isoflavonoid phytoalexins in plant leaves. Therefore, it is of interest to study the structural features of LOX-1 from Finger millet. However, the structure ofLOX-1 from Finger millet is not yet known. A homology model of LOX-1 from Finger millet is described. Domain architecture study suggested the presence of two domains namely PLAT (Phospho Lipid Acyl Transferase) and lipoxygenase. Molecular docking models of linoleate with lipoxygenase from finger millet, rice and sorghum are reported. The features of docked models showed that finger millet have higher pathogen resistance in comparison to other cereal crops. This data is useful for the molecular cloning of fulllength LOX-1 gene for validating its role in improving plant defense against pathogen infection and for various other biological processes.

Finger millet is being recognized as a potential future crop due to their nutrient contents and antioxidative properties, which are much higher compared to the other minor millets for providing health benefits. The synthesis of these nutritional components is governed by the expression of several gene(s). Therefore, it is necessary to characterize these genes for understanding the molecular mechanisms behind de novo synthesis of nutrient components. Apart from this, these important compounds could also serve as candidate genes for imparting stress tolerance in other crop plants also. In the present study, effort has been made to identify genes involved in Ascorbate-Glutathione cycle (Halliwell-Asada Pathway) and related pathway genes for elucidating its role in antioxidative potential mechanism through transcriptome data analysis. APX, DHAR, MDHAR, GR, and SOD have been identified as the key genes of the pathway in two genotypes GP-1 (low Ca 2+) and GP-45 (high Ca 2+) of finger millet with reference to rice as a model system, besides, 30 putatively expressed genes/proteins were also investigated. Furthermore, the sequences of identified genes were analyzed systematically; gene ontology (GO) annotation and enrichment analysis of assembled unitranscripts were also performed using Blast2GO. As a result, 49 GO terms, 5 Enzyme Commission (EC) numbers, and 2 KEGG pathway maps were generated. GO results revealed that these genes are mainly involved in two biological processes (BP), viz., oxidation-reduction process (GO:0055114) and cellular oxidant detoxification (GO:0098869), and showed oxidoreductase activity (GO:0016491). KEGG analysis showed that APX, DHAR, MDHAR, and GR are directly connected to biosynthetic pathways of secondary metabolites, mainly polyphenolic compounds (flavonoid, tannin, and lignin) involved in glutathione metabolism (KEGG:00480) and ascorbate and aldarate metabolism (KEGG:00053). While SOD, is indirectly connected and also has significant medicinal attributes and antioxidant properties. Moreover, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were also calculated for expression analysis and found that the FPKM values of genes present in GP-1 are higher than that of GP-45. Thus, GP-1 genotype was found to have higher stress regulated gene expression in comparison to GP-45. Taken together, the present transcriptome-based investigation unlocks new avenues for systematic functional analysis of novel ROS scavenging candidate genes that could be effectively applied for improvising human health and nutrition.

Antioxidants play a key role in maintaining cell activity in plants and animals by scavenging reactive oxygen species. Hence, it is very important to understand genes associated with antioxidant activity for improving the varieties. In this study, we compared structural and functional aspects of antioxidant genes viz., APX, DHAR, MDHAR, GR, and SOD of two contrasting genotypes viz. GP-1 (low Ca 2+ ) and GP-45 (high Ca 2+ ) of finger millet with other cereal crops such as rice, sorghum, and foxtail millet. The structural analysis shows that all genes are conserved and shares almost the same domains such as ascorbate peroxidase, glutathione dehydrogenase, glutathione reductase, Fe, and Cu-Zn superoxide dismutase domains which play a significant role in antioxidant activity and drought tolerance. These genes were mainly localized in chloroplast and cytoplasm which prove that both are the major ROS-scavenging sites. Furthermore, several putative cis-acting regulatory elements such as AuxRE, DRE, GARE, G-box, GATA-box, MBS, MYBR, and W-box are also studied and found that these genes are involved in defense mechanisms which allow responses against drought stress. Antioxidant activity of these genes was compared using expression analysis in terms of FPKM values and found that the genes of low Ca 2+ genotype are highly expressed compared to the genes of high Ca 2+ genotype and the genes of rice, sorghum, and foxtail millet. These results revealed that a low Ca 2+ genotype of finger millet has higher antioxidant activity in comparison to high Ca 2+ genotype and other cereal crops. Based on the results, we hypothesize that these candidate genes could be a target to develop highly antioxidative potential and drought tolerant genotypes of other cereal crops through appropriate breeding approaches.