Functional attributes of bioactive peptides of bovine milk origin and application of in silico approaches for peptide prediction and functional annotations.

Bovine milk peptides are the protein fragments with diverse bioactive properties having antioxidant, anticarcinogenic, other therapeutic and nutraceutical potentials. These peptides are formed in milk by enzymatic hydrolysis, gastrointestinal digestion and fermentation processes. They have significant health impact with high potency and low toxicity making them a suitable natural alternative for preventing and managing diseases. Antibiotic resistance has increased the quest for better peptide candidates with antimicrobial effects. This article presents a comprehensive review on well documented antimicrobial, immunological, opioid, and anti-hypertensive activities of bovine milk peptides. It also covers the usage of computational biology tools and databases for prediction and analysis of the food-derived bioactive peptides. In silico analysis of amino acid sequences of Bos taurus milk proteins have been predicted to generate peptides with dipeptidyl peptidase IV inhibitory and ACE inhibitory properties, making them favorable candidates for developing blood sugar lowering drugs and anti-hypertensives. In addition to the prediction of new bioactive peptides, application of bioinformatics tools to predict novel functions of already known peptides is also discussed. Overall, this review focuses on the reported as well as predicted biologically active peptide of casein and whey proteins of bovine milk that can be utilized to develop therapeutic agents.

Genome-Wide Identification of Aquaporin Genes in Adzuki Bean (Vigna angularis) and Expression Analysis under Drought Stress.

The adzuki bean Vigna angularis (Wild.) is an important leguminous crop cultivated mainly for food purposes in Asian countries; it represents a source of carbohydrates, digestible proteins, minerals, and vitamins. Aquaporins (AQPs) are crucial membrane proteins involved in the transmembrane diffusion of water and small solutes in all living organisms, including plants. In this study, we used the whole genome sequence of the adzuki bean for in silico analysis to comprehensively identify 40 Vigna angularis aquaporin (VaAQP) genes and reveal how these plants react to drought stress. VaAQPs were compared with AQPs from other closely-related leguminous plants, and the results showed that mustard (Brassica rapa) (59), barrel medic (Medicago truncatula) (46), soybean (Glycine max) (66), and common bean (Phaseolus vulgaris L.) (41) had more AQP genes. Phylogenetic analysis revealed that forty VaAQPs belong to five subfamilies, with the VaPIPs (fifteen) subfamily the largest, followed by the VaNIPs (ten), VaTIPs (ten), VaSIPs (three), and VaXIPs (two) subfamilies. Furthermore, all AQP subcellular locations were found at the plasma membrane, and intron-exon analysis revealed a relationship between the intron number and gene expression, duplication, evolution, and diversity. Among the six motifs identified, motifs one, two, five, and six were prevalent in VaTIP, VaNIP, VaPIP, and VaXIP, while motifs one, three, and four were not observed in VaPIP1-3 and VaPIP1-4. Under drought stress, two of the VaAQPs (VaPIP2-1 and VaPIP2-5) showed significantly higher expression in the root tissue while the other two genes (VaPIP1-1 and VaPIP1-7) displayed variable expression in leaf tissue. This finding revealed that the selected VaAQPs might have unique molecular functions linked with the uptake of water under drought stress or in the exertion of osmoregulation to transport particular substrates rather than water to protect plants from drought. This study presents the first thorough investigation of VaAQPs in adzuki beans, and it reveals the transport mechanisms and related physiological processes that may be utilized for the development of drought-tolerant adzuki bean cultivars.

Heavy metal stress in rice: Uptake, transport, signaling, and tolerance mechanisms.

Heavy metal contamination of agricultural fields has become a global concern as it causes a direct impact on human health. Rice is the major food crop for almost half of the world population and is grown under diverse environmental conditions, including heavy metal-contaminated soil. In recent years, the impact of heavy metal contamination on rice yield and grain quality has been shown through multiple approaches. In this review article, different aspects of heavy metal stress, that is uptake, transport, signaling and tolerance mechanisms, are comprehensively discussed with special emphasis on rice. For uptake, some of the transporters have specificity to one or two metal ions, whereas many other transporters are able to transport many different ions. After uptake, the intercellular signaling is mediated through different signaling pathways involving the regulation of various hormones, alteration of calcium levels, and the activation of mitogen-activated protein kinases. Heavy metal stress signals from various intermediate molecules activate various transcription factors, which triggers the expression of various antioxidant enzymes. Activated antioxidant enzymes then scavenge various reactive oxygen species, which eventually leads to stress tolerance in plants. Non-enzymatic antioxidants, such as ascorbate, metalloids, and even metal-binding peptides (metallothionein and phytochelatin) can also help to reduce metal toxicity in plants. Genetic engineering has been successfully used in rice and many other crops to increase metal tolerance and reduce heavy metals accumulation. A comprehensive understanding of uptake, transport, signaling, and tolerance mechanisms will help to grow rice plants in agricultural fields with less heavy metal accumulation in grains.

Unveiling silicon-mediated cadmium tolerance mechanisms in mungbean (Vigna radiata (L.) Wilczek): Integrative insights from gene expression, antioxidant responses, and metabolomics.

Cadmium (Cd), one of the most phytotoxic heavy metals, is a major contributor to yield losses in several crops. Silicon (Si) is recognized for its vital role in mitigating Cd toxicity, however, the specific mechanisms governing this mitigation process are still not fully understood. In the present study, the effect of Si supplementation on mungbean (Vigna radiata (L.) Wilczek) plants grown under Cd stress was investigated to unveil the intricate pathways defining Si derived stress tolerance. Non-invasive leaf imaging technique revealed improved growth, biomass, and photosynthetic efficiency in Si supplemented mungbean plants under Cd stress. Further, physiological and biochemical analysis revealed Si mediated increase in activity of glutathione reductase (GR), ascorbate peroxidase (APX), and catalase (CAT) enzymes involved in reactive oxygen species (ROS) metabolism leading to mitigation of cellular damage and oxidative stress. Untargeted metabolomic analysis using liquid chromatography coupled with mass spectrometry (LC-MS/MS) provided insights into Si mediated changes in metabolites and their respective pathways under Cd stress. Alteration in five different metabolic pathways with major changes in flavanols and flavonoids biosynthesis pathway which is essential for controlling plants antioxidant defense system and oxidative stress management were observed. The information reported here about the effects of Si on photosynthetic efficiency, antioxidant responses, and metabolic changes will be helpful in understanding the Si-mediated resistance to Cd stress in plants.

Biotechnology and urban agriculture: A partnership for the future sustainability.

The global population is growing rapidly, and with it, the demand for food. In the coming decades, more and more people will be living in urban areas, where land for traditional agriculture is scarce. Urban agriculture can help to meet this growing demand for food in a sustainable way. Urban agriculture is the practice of growing food in urban areas. It can be done on rooftops, balconies, vacant lots, and even in alleyways. Urban agriculture can produce a variety of crops, including fruits, vegetables, and herbs. It can also help to improve air quality, reduce stormwater runoff, and create jobs. Biotechnology can be used to improve the efficiency and sustainability of urban agriculture. Biotechnological tools can be used to develop crops that are resistant to pests and diseases, that are more tolerant of drought and heat, and that have higher yields. Biotechnology can also be used to improve the nutritional value of crops. This review article discusses the need for and importance of urban agriculture, biotechnology, and genome editing in meeting the growing demand for food in urban areas. It also discusses the potential of biotechnology to improve the sustainability of urban agriculture.

Microbial remediation and plant-microbe interaction under arsenic pollution.

Arsenic contamination in aquatic and terrestrial ecosystem is a serious environmental issue. Both natural and anthropogenic processes can introduce it into the environment. The speciation of the As determine the level of its toxicity. Among the four oxidation states of As (-3, 0, +3, and + 5), As(III) and As(V) are the common species found in the environment, As(III) being the more toxic with adverse impact on the plants and animals including human health. Therefore, it is very necessary to remediate arsenic from the polluted water and soil. Different physicochemical as well as biological strategies can be used for the amelioration of arsenic polluted soil. Among the microbial approaches, oxidation of arsenite, methylation of arsenic, biosorption, bioprecipitation and bioaccumulation are the promising transformation activities in arsenic remediation. The purpose of this review is to discuss the significance of the microorganisms in As toxicity amelioration in soil, factors affecting the microbial remediation, interaction of the plants with As resistant bacteria, and the effect of microorganisms on plant arsenic tolerance mechanism. In addition, the exploration of genetic engineering of the bacteria has a huge importance in bioremediation strategies, as the engineered microbes are more potent in terms of remediation activity along with quick adaptively in As polluted sites.

Genomic Insights into Omega-3 Polyunsaturated Fatty Acid Producing Shewanella sp. N2AIL from Fish Gut.

The genus Shewanella is widely distributed in niches ranging from an aquatic environment to spoiled fish and is loaded with various ecologically and commercially important metabolites. Bacterial species under this genus find application in bioelectricity generation and bioremediation due to their capability to use pollutants as the terminal electron acceptor and could produce health-beneficial omega-3 fatty acids, particularly eicosapentaenoic acid (EPA). Here, the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gastrointestinal tract of Tilapia fish, is reported. The genome size of the strain was 4.8 Mb with a GC content of 46.3% containing 4385 protein-coding genes. Taxonogenomic analysis assigned this strain to the genus Shewanella on the basis of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), phylogenetically most closely related with S. baltica NCTC 10735T. The comparative genome analysis with the type strain of S. baltica revealed 693 unique genes in the strain N2AIL, highlighting the variation at the strain level. The genes associated with stress adaptation, secondary metabolite production, antibiotic resistance, and metal reduction were identified in the genome suggesting the potential of the bacterium to be explored as an industrially important strain. PUFA synthase gene cluster of size ~20.5 kb comprising all the essential domains for EPA biosynthesis arranged in five ORFs was also identified in the strain N2AIL. The study provides genomic insights into the diverse genes of Shewanella sp. N2AIL, which is particularly involved in adaptation strategies and prospecting secondary metabolite potential, specifically the biosynthesis of omega-3 polyunsaturated fatty acids.

Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium Enterobacter sp. LR6.

Silicon (Si) is gaining widespread attention due to its prophylactic activity to protect plants under stress conditions. Despite Si's abundance in the earth's crust, most soils do not have enough soluble Si for plants to absorb. In the present study, a silicate-solubilizing bacterium, Enterobacter sp. LR6, was isolated from the rhizospheric soil of rice and subsequently characterized through whole-genome sequencing. The size of the LR6 genome is 5.2 Mb with a GC content of 54.9% and 5182 protein-coding genes. In taxogenomic terms, it is similar to E. hormaechei subsp. xiangfangensis based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). LR6 genomic data provided insight into potential genes involved in stress response, secondary metabolite production, and growth promotion. The LR6 genome contains two aquaporins, of which the aquaglyceroporin (GlpF) is responsible for the uptake of metalloids including arsenic (As) and antimony (Sb). The yeast survivability assay confirmed the metalloid transport activity of GlpF. As a biofertilizer, LR6 isolate has a great deal of tolerance to high temperatures (45 °C), salinity (7%), and acidic environments (pH 9). Most importantly, the present study provides an understanding of plant-growth-promoting activity of the silicate-solubilizing bacterium, its adaptation to various stresses, and its uptake of different metalloids including As, Ge, and Si.

Exploration of silicate solubilizing bacteria for sustainable agriculture and silicon biogeochemical cycle.

Silicon (Si), a quasi-essential element for plants, is abundant in the soil typically as insoluble silicate forms. However, plants can uptake Si only in the soluble form of monosilicic acid. Production of monosilicic acid by rock-weathering mostly depends on temperature, pH, redox-potential, water-content, and microbial activities. In the present review, approaches involved in the efficient exploration of silicate solubilizing bacteria (SSB), its potential applications, and available technological advances are discussed. Present understanding of Si uptake, deposition, and subsequent benefits to plants has also been discussed. In agricultural soils, pH is found to be one of the most critical factors deciding silicate solubilization and the formation of different Si compounds. Numerous studies have predicted the role of Indole-3-Acetic Acid (IAA) and organic acids produced by SSB in silicate solubilization. In this regard, approaches for the isolation and characterization of SSB, quantification of IAA, and subsequent Si solubilization mechanisms are addressed. Phylogenetic evaluation of previously reported SSB showed a highly diverse origin which provides an opportunity to study different mechanisms involved in Si solubilization. Soil biochemistry in concern of silicon availability, microbial activity and silicon mediated changes in plant physiology are addressed. In addition, SSB's role in Si-biogeochemical cycling is summarized. The information presented here will be helpful to explore the potential of SSB more efficiently to promote sustainable agriculture.

Genome assembly of Chryseobacterium sp. strain IHBB 10212 from glacier top-surface soil in the Indian trans-Himalayas with potential for hydrolytic enzymes.

The cold-active esterases are gaining importance due to their catalytic activities finding applications in chemical industry, food processes and detergent industry as additives, and organic synthesis of unstable compounds as catalysts. In the present study, the complete genome sequence of 4,843,645 bp with an average 34.08% G + C content and 4260 protein-coding genes are reported for the low temperature-active esterase-producing novel strain of Chrysobacterium isolated from the top-surface soil of a glacier in the cold deserts of the Indian trans-Himalayas. The genome contained two plasmids of 16,553 and 11,450 bp with 40.54 and 40.37% G + C contents, respectively. Several genes encoding the hydrolysis of ester linkages of triglycerides into fatty acids and glycerol were predicted in the genome. The annotation also predicted the genes encoding proteases, lipases, amylases, ß-glucosidases, endoglucanases and xylanases involved in biotechnological processes. The complete genome sequence of Chryseobacterium sp. strain IHBB 10212 and two plasmids have been deposited vide accession numbers CP015199, CP015200 and CP015201 at DDBJ/EMBL/GenBank.

Complete genome sequence of a low-temperature active and alkaline-stable endoglucanase-producing Paenibacillus sp. strain IHB B 3084 from the Indian Trans-Himalayas.

A genome of 5.88Mb with 46.83% G+C content is reported for an endoglucanase-producing bacterium Paenibacillus sp. strain IHB B 3084 isolated from the cold environments of the Indian Trans-Himalayas. The psychrotrophic bacterium produces low-temperature active and alkaline-stable endoglucanases of industrial importance. The genomic data has provided insight into genomic basis of cellulase production and survival of the bacterium in the cold environments.

Cloning and expression of low temperature active endoglucanase EG5C from Paenibacillus sp. IHB B 3084.

The endoglucanase gene designated as EG5C encoding cold active endoglucanase produced by Paenibacillus sp. IHB B 3084 was cloned and expressed in Escherichia coli BL21(DE3). The gene consisting of 1719bp open reading frame encoded a protein of 573 amino acids with a predicted molecular weight of 63.5kDa. The presence of N-terminal catalytic domain of the glycosyl hydrolase family 5 (GH5) and C-terminal carbohydrate binding X2 domain suggested the modular nature of the enzyme. The native signal peptide of EG5C was capable of efficiently secreting the enzyme with near equal activities in the cytoplasmic and extracellular fractions. The recombinant enzyme purified 9.46 fold to homogeneity with 22.33% yield gave 7.758IU/mg specific activity. The enzyme was stable over the broad pH range of 4-12 with more than 50% residual activity. The optimal activity was at 40°C with 70% relative activity at 5°C. The low temperature activity despite the shorter linker region suggested a novel cold adaptation mechanism by the enzyme. The enzyme displayed higher activity on carboxymethylcellulose than avicel which is useful in maintaining the tensile strength of fiber. The efficient secretion and low temperature activity offer prospect for large-scale production and industrial application of the endoglucanase.

Draft Genome Sequence of a Cellulase-Producing Psychrotrophic Paenibacillus Strain, IHB B 3415, Isolated from the Cold Environment of the Western Himalayas, India.

Paenibacillus sp. strain IHB B 3415 is a cellulase-producing psychrotrophic bacterium isolated from a soil sample from the cold deserts of Himachal Pradesh, India. Here, we report an 8.44-Mb assembly of its genome sequence with a G+C content of 50.77%. The data presented here will provide insights into the mechanisms of cellulose degradation at low temperature.

A rapid and easy method for the detection of microbial cellulases on agar plates using gram's iodine.

Screening for cellulase-producing microorganisms is routinely done on carboxymethylcellulose (CMC) plates. The culture plates are flooded either with 1% hexadecyltrimethyl ammonium bromide or with 0.1% Congo red followed by 1 M NaCl. In both cases, it takes a minimum of 30 to 40 minutes to obtain the zone of hydrolysis after flooding, and the hydrolyzed area is not sharply discernible. An improved method is reported herein for the detection of extracellular cellulase production by microorganisms by way of plate assay. In this method, CMC plates were flooded with Gram's iodine instead of the reagents just mentioned. Gram's iodine formed a bluish-black complex with cellulose but not with hydrolyzed cellulose, giving a sharp and distinct zone around the cellulase-producing microbial colonies within 3 to 5 minutes. The new method is rapid and efficient; therefore, it can be easily performed for screening large numbers of microbial cultures of both bacteria and fungi. This is the first report on the use of Gram's iodine for the detection of cellulase production by microorganisms using plate assay.