Genome-wide identification, characterization, and expression analysis of MIPS family genes in legume species.

BACKGROUND: Evolutionarily conserved in plants, the enzyme D-myo-inositol-3-phosphate synthase (MIPS; EC 5.5.1.4) regulates the initial, rate-limiting reaction in the phytic acid biosynthetic pathway. They are reported to be transcriptional regulators involved in various physiological functions in the plants, growth, and biotic/abiotic stress responses. Even though the genomes of most legumes are fully sequenced and available, an all-inclusive study of the MIPS family members in legumes is still ongoing. RESULTS: We found 24 MIPS genes in ten legumes: Arachis hypogea, Cicer arietinum, Cajanus cajan, Glycine max, Lablab purpureus, Medicago truncatula, Pisum sativum, Phaseolus vulgaris, Trifolium pratense and Vigna unguiculata. The total number of MIPS genes found in each species ranged from two to three. The MIPS genes were classified into five clades based on their evolutionary relationships with Arabidopsis genes. The structural patterns of intron/exon and the protein motifs that were conserved in each gene were highly group-specific. In legumes, MIPS genes were inconsistently distributed across their genomes. A comparison of genomes and gene sequences showed that this family was subjected to purifying selection and the gene expansion in MIPS family in legumes was mainly caused by segmental duplication. Through quantitative PCR, expression patterns of MIPS in response to various abiotic stresses, in the vegetative tissues of various legumes were studied. Expression pattern shows that MIPS genes control the development and differentiation of various organs, and have significant responses to salinity and drought stress. CONCLUSION: The MIPS genes in the genomes of legumes have been identified, characterized and their expression was analysed. The findings pave way for understanding their molecular functions and evolution, and lead to identify the putative MIPS genes associated with different cell and tissue development.

Genome wide identification and characterization of MATE family genes in mangrove plants.

Multidrug and Toxic Compound Extrusion (MATE) proteins are essential transporters that extrude metabolites and participate in plant development and cellular detoxification. MATE transporters, which play crucial roles in the survival of mangrove plants under highly challenged environments, by specialized salt extrusion mechanisms, are mined from their genomes and reported here for the first time. Through homology search and domain prediction in the genome assemblies of Avicennia marina, Bruguiera sexangula, Ceriops zippeliana, Kandelia obovata, Rhizophora apiculata and Ceriops tagal, 74, 68, 66, 66, 63 and 64 MATE proteins, respectively were identified. The phylogenetic analysis divided the identified proteins into five major clusters and following the clustering pattern of the functionally characterized proteins, functions of the transporters in each cluster were predicted. Amino acid sequences, exon-intron structure, motif details and subcellular localization pattern for all the 401 proteins are described. The custom designed repeat masking libraries generated for each of these genomes, which will be of extensive use for the researchers worldwide, are also provided in this paper. This is the first study on the MATE genes in mangroves and the results provide comprehensive information on the molecular mechanisms enabling the survival of mangroves under hostile conditions.

Novel MicroRNAs and their Functional Targets from Phytophthora infestans and Phytophthora cinnamomi.

Background: Even though miRNAs play vital roles in developmental biology by regulating the translation of mRNAs, they are poorly studied in oomycetes, especially in the plant pathogen Phytophthora. Objective: The study aimed to predict and identify the putative miRNAs and their targets in Phytophthora infestans and Phytophthora cinnamomi. Methods: The homology-based comparative method was used to identify the unique miRNA sequences in P. infestans and P. cinnamomi with 148,689 EST and TSA sequences of these species. Secondary structure prediction of sRNAs for the 76 resultant sequences has been performed with the MFOLD tool, and their targets were predicted using psRNATarget. Results: Novel miRNAs, miR-8210 and miR-4968, were predicted from P. infestans and P. cinnamomi, respectively, along with their structural features. The newly identified miRNAs were identified to play important roles in gene regulation, with few of their target genes predicted as transcription factors, tumor suppressor genes, stress-responsive genes, DNA repair genes, etc. Conclusion: The miRNAs and their targets identified have opened new interference and editing targets for the development of Phytophthora resistant crop varieties.

Evolutionary history of the neuropeptide S receptor/neuropeptide S system.

The neuropeptide S receptor (NPSR) belongs to the G protein-coupled receptor (GPCR) superfamily and is activated by the neuropeptide S (NPS). Although recently discovered, the vertebrate NPSR-NPS system has been established as an important signaling system in the central nervous system and is involved in physiological processes such as locomotor activity, wakefulness, asthma pathogenesis, anxiety and food intake. The availability of a large number of genome sequences from multiple bilaterian lineages has provided an opportunity to establish the evolutionary history of the system. This review describes the origin and the molecular evolution of the NPSR-NPS system using data derived primarily from comparative genomic analyses. These analyses indicate that the NPSR-NPS system and the vasopressin-like receptor-vasopressin/oxytocin peptide (VPR-VP/OT) system originated from a single system in an ancestral bilaterian. Multiple duplications of this ancestral system gave rise to the bilaterian VPR-VP/OT system and to the protostomian cardioacceleratory peptide receptor-cardioacceleratory peptide (CCAPR-CCAP) system and to the NPSR-NPS system in the deuterostomes. Gene structure features of the receptors were consistent with the orthology annotations derived from phylogenetic analyses. The orthology of the peptide precursors closely paralleled that of the receptors suggesting an ancient coevolution of the receptor-peptide pair. An important challenge for the coevolution hypothesis will be to establish the molecular and structural basis of the divergence between orthologous receptor-ligand pairs in this system.

Genome-wide mining and characterization of MATE transporters in Coriandrum sativum L.

Multidrug and Toxic Compound Extrusion (MATE) proteins are responsible for the transport of a wide range of metabolites out of plant cells. This helps to protect the cells from toxins and other harmful compounds. MATE proteins also play a role in plant development, by regulating the transport of hormones and other signalling molecules. They transport a wide variety of substances, including organic acids, plant hormones, flavonoids, alkaloids, terpenes and other secondary metabolites. MATE proteins are thought to play similar roles in Coriander, in addition to stress responses. The MATE genes in the coriander genome have been identified and characterized. Detailed genome homology search and domain identification analysis have identified 91 MATE proteins in the genome assembly of coriander. A phylogenetic analysis of the identified proteins divided them into five major clades. The functions of the transporters in each cluster were predicted based on the clustering pattern of the functionally characterized proteins. The amino acid sequences, exon-intron structures and motif details of all the 91 proteins are identified and described. This is the first work on the MATE transporters in coriander and the results deliver clues for the molecular mechanisms behind the stress responses and secondary metabolite transport in coriander.

Early vertebrate origin of melanocortin 2 receptor accessory proteins (MRAPs).

The melanocortin 2 receptor (MC2R) accessory proteins, MRAP, along with its homolog, MRAP2, are two among a growing number of G protein-coupled receptor accessory proteins that have been identified in recent years. These proteins interact directly with MC2R and are essential for trafficking of this receptor from the endoplasmic reticulum to the cell surface, where it mediates the effects of ACTH. lthough earlier studies have identified MRAP and MRAP2 subtypes in distant species, an overall evolutionary analysis of these families is still missing. Here, we performed a comprehensive evolutionary analysis of the MRAP and MRAP2 homologs based on whole genome sequences. We systematically mined and analyzed the genomes of metazoans to identify these genes. Overall, we identified 70 sequences of MRAP and MRAP2 from 44 species belonging to several vertebrate lineages, including at least 40 new sequences previously not reported in the literature. Herein, we provide evidence that MRAP2 is likely to be the ancestor of the MRAP family because MRAP2-like protein, but not MRAP, was identified in Petromyzon marinus (sea lamprey), which belong to an ancient basal vertebrate lineage. Later in vertebrate evolution, MRAP2 duplicated and gave rise to MRAP in an event before the emergence of actinopterygii (ray-finned fishes). However, we observed losses of MRAP in sarcopterygii (lobe-finned fish), amphibians and reptiles while both subtypes are present in chicken and most mammals studied. Synteny analysis showed a conserved synteny within same lineages and an inversion of gene order between lineages. An evolutionary rate shift analysis indicated that these genes were under high purifying selection. Overall, this study provides a comprehensive analysis of the evolution and gene repertoire of MRAP and MRAP2.

Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potential.

BACKGROUND: Gongronella butleri is a fungus with many industrial applications including the composting of solid biowaste. Kerala Agricultural University, India, has developed a microbial consortium of which GbKAU strain of G. butleri is a major component. Even with great industrial significance, genome of this fungus is not published, and the genes and pathways contributing to the applications are not understood. This study had the objective to demonstrate the solid biowaste decomposing capability of the strain, to sequence and annotate the genome, and to reveal the genes and pathways contributing to its biodegradation potential. RESULTS: Strain GbKAU of G. butleri isolated and purified from the organic compost was found to produce higher levels of laccase and amylase, compared to Bacillus subtilis which is being widely used in biosolid waste management. Both were shown to be equally efficient in the in vivo composting capabilities. Whole genome sequencing has given ~11 million paired-end good quality reads. De novo assembly using dual-fold approach has yielded 44,639 scaffolds with draft genome size of 29.8 Mb. A total of 11,428 genes were predicted and classified into 359 groups involved in diverse pathways, of which 14 belonged to the enzymes involved in the degradation of macromolecules. Seven previously sequenced strains of the fungus were assembled and annotated. A direct comparison showed that the number of genes present in those strains was comparable to our strain, while all the important biodegrading genes were conserved across the genomes. Gene Ontology analysis had classified the genes according to their molecular function, biological process, and cellular component. A total of 104,718 SSRs were mined and classified to mono- to hexa-nucleotide repeats. The variant analysis in comparison with the closely related genus Cunninghamella has revealed 1156 variants. CONCLUSIONS: Apart from demonstrating the biodegradation capabilities of the GbKAU strain of G. butleri, the genome of this industrially important fungus was sequenced, de novo assembled, and annotated. GO analysis has classified the genes based on their functions, and the genes involved in biodegradation were revealed. Biodegradation potential, genome features in comparison with other strains, and the functions of the identified genes are discussed.

Draft genome of Meyerozyma guilliermondii strain vka1: a yeast strain with composting potential.

BACKGROUND: Meyerozyma guilliermondii is a yeast which could be isolated from a variety of environments. The vka1 strain isolated and purified from the organic compost was found to have composting potential. To better understand the genes assisting the composting potential in this yeast, whole genome sequencing and sequence annotation were performed. RESULTS: The genome of M. guilliermondii vka1 strain was sequenced using a hybrid approach, on Illumina Hiseq-2500 platform at 100× coverage followed by Nanopore platform at 20× coverage. The de novo assembly using dual-fold approach had given draft genome of 10.8 Mb size. The genome was found to contain 5385 genes. The annotation of the genes was performed, and the enzymes identified to have roles in the degradation of macromolecules are discussed in relation to its composting potential. Annotation of the genome assembly of the related strains had revealed the unique biodegradation related genes in this strain. Phylogenetic analysis using the rDNA region has confirmed the position of this strain in the Ascomycota family. Raw reads are made public, and the genome wide proteome profile is presented to facilitate further studies on this organism. CONCLUSIONS: Meyerozyma guilliermondii vka1 strain was sequenced through hybrid approach and the reads were de novo assembled. Draft genome size and the number of genes in the strain were assessed and discussed in relation to the related strains. Scientific insights into the composting potential of this strain are also presented in relation to the unique genes identified in this strain.

EGFR gene regulation in colorectal cancer cells by garlic phytocompounds with special emphasis on S-Allyl-L-Cysteine Sulfoxide.

Colorectal cancer is one among the most common cancers in the world and a major cause of cancer related deaths. Similar to other cancers, colorectal carcinogenesis is often associated with over expression of genes related to cell growth and proliferation, especially Epidermal Growth Factor Receptor (EGFR). There is an increasing attention towards the plant derived compounds in prevention of colorectal carcinogenesis by downregulating EGFR. Among plants, garlic (Allium sativum L.) is emerging with anticancer properties by virtue of its organosulfur compounds. The present study was aimed to analyze the interaction ability of garlic compounds in the active region of EGFR gene by in silico molecular docking studies and in vitro validation. This was conducted using the Discovery studio software version 4.0. Among the tested compounds, s-allyl-l-cysteine-sulfoxide (SACS)/alliin showed higher affinity towards EGFR. Furthermore, wet lab analysis using cell viability test and EGFR expression analysis in colorectal cancer cells confirmed its efficacy as a potent anticancer agent.

Coconut phytocompounds inhibits polyol pathway enzymes: Implication in prevention of microvascular diabetic complications.

Coconut oil (CO), the primary choice of cooking purposes in the south Asian countries, is rich in medium chain saturated fatty acids, especially lauric acid (50-52%). The oil has high medicinal use in Ayurvedic system and known to contain polyphenolic antioxidants. Studies have reported that CO improves insulin sensitivity and shows hypoglycemic effect. However, there is no information regarding its effect on chronic diabetic complications including retinopathy and nephropathy is available. The secondary diabetic complications are mediated by the activation of polyol pathway, where aldose reductase (AR) plays crucial role. In this study, in silico analysis has been used to screen the effect of CO as well as its constituents, MCFAs and phenolic compounds, for targeting the molecules in polyol pathway. The study revealed that lauric acid (LA) interacts with AR and DPP-IV of polyol pathway and inhibits the activity of these enzymes. Validation studies using animal models confirmed the inhibition of AR and SDH in wistar rats. Further, the LA dose dependently reduced the expression of AR in HCT-15 cells. Together, the study suggests the possible role of CO, particularly LA in reducing secondary diabetic complications.

Plant Phenolics Ferulic Acid and P-Coumaric Acid Inhibit Colorectal Cancer Cell Proliferation through EGFR Down-Regulation.

BACKGROUND: Colorectal cancer (CRC) or bowel cancer is one of the most important cancer diseases, needing serious attention. The cell surface receptor gene human epidermal growth factor receptor (EGFR) may have an important role in provoking CRC. In this pharmaceutical era, it is always attempted to identify plant-based drugs for cancer, which will have less side effects for human body, unlike the chemically synthesized marketed drugs having serious side effects. So, in this study the authors tried to assess the activity of two important plant compounds, ferulic acid (FA) and p-coumaric acid (pCA), on CRC. MATERIALS AND METHODS: FA and pCA were tested for their cytotoxic effects on the human CRC cell line HCT 15 and also checked for the level of gene expression of EGFR by real time PCR analysis. Positive results were confirmed by in silico molecular docking studies using Discovery Studio (DS) 4.0. The drug parallel features of the same compounds were also assessed in silico. RESULTS: Cytotoxicity experiments revealed that both the compounds were efficient in killing CRC cells on a controlled concentration basis. In addition, EGFR expression was down-regulated in the presence of the compounds. Docking studies unveiled that both the compounds were able to inhibit EGFR at its active site. Pharmacokinetic analysis of these compounds opened up their drug like behaviour. CONCLUSIONS: The findings of this study emphasize the importance of plant compounds for targeting diseases like CRC.

Molecular docking studies of phytochemicals from Phyllanthus niruri against Hepatitis B DNA Polymerase.

Hepatitis B virus (HBV) infection is the leading cause for liver disorders and can lead to hepatocellular carcinoma, cirrhosis and liver damage which in turn can cause death of patients. HBV DNA Polymerase is essential for HBV replication in the host and hence is used as one of the most potent pharmacological target for the inhibition of HBV. Chronic hepatitis B is currently treated with nucleotide analogues that suppress viral reverse transcriptase activity and most of them are reported to have viral resistance. Therefore, it is of interest to model HBV DNA polymerase to dock known phytochemicals. The present study focuses on homology modeling and molecular docking analysis of phytocompounds from the traditional antidote Phyllanthus niruri and other nucleoside analogues against HBV DNA Polymerase using the software Discovery studio 4.0. 3D structure of HBV DNA Polymerase was predicted based on previously reported alignment. Docking studies revealed that a few phytochemicals from Phyllanthus niruri had good interactions with HBV DNA Polymerase. These compounds had acceptable binding properties for further in vitro validation. Thus the study puts forth experimental validation for traditional antidote and these phytocompounds could be further promoted as potential lead molecule.