Mining of Microbial Genomes for the Novel Sources of Nitrilases

Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes). This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases, Gluconacetobacter diazotrophicus, Sphingopyxis alaskensis, Saccharomonospora viridis, and Shimwellia blattae were specific for aliphatic nitriles, whereas nitrilases from Geodermatophilus obscurus, Nocardiopsis dassonvillei, Runella slithyformis, and Streptomyces albus possessed activity for aromatic nitriles. Flavobacterium indicum was specific towards potassium cyanide (KCN) which revealed the presence of nitrilase homolog, that is, cyanide dihydratase with no activity for either aliphatic, aromatic, or aryl nitriles. The present study reports the novel sources of nitrilases and cyanide dihydratase which were not reported hitherto by in silico or in vitro studies

Biotransformation of benzonitrile herbicides via the nitrile hydratase–amidase pathway in rhodococci

Abstract The aim of this work was to determine the ability of rhodococci to transform 3,5-dichloro-4-hydroxybenzonitrile (chloroxynil), 3,5-dibromo-4-hydroxybenzonitrile (bromoxynil), 3,5-diiodo-4-hydroxybenzonitrile (ioxynil) and 2,6-dichlorobenzonitrile (dichlobenil); to identify the products and determine their acute toxicities. Rhodococcus erythropolis A4 and Rhodococcus rhodochrous PA-34 converted benzonitrile herbicides into amides, but only the former strain was able to hydrolyze 2,6-dichlorobenzamide into 2,6-dichlorobenzoic acid, and produced also more of the carboxylic acids from the other herbicides compared to strain PA-34. Transformation of nitriles into amides decreased acute toxicities for chloroxynil and dichlobenil, but increased them for bromoxynil and ioxynil. The amides inhibited root growth in Lactuca sativa less than the nitriles but more than the acids. The conversion of the nitrile group may be the first step in the mineralization of benzonitrile herbicides but cannot be itself considered to be a detoxification

Detection of bacterial pathogens and antibiotic residues in chicken meat: a review

Detection of pathogenic microbes as well as antibiotic residues in food animals, especially in chicken, has become a matter of food security worldwide. The association of various pathogenic bacteria in different diseases and selective pressure induced by accumulated antibiotic residue to develop antibiotic resistance is also emerging as the threat to human health. These challenges have made the containment of pathogenic bacteria and early detection of antibiotic residue highly crucial for robust and precise detection. However, the traditional culture-based approaches are well-comprehended for identifying microbes. Nevertheless, because they are inadequate, time-consuming and laborious, these conventional methods are not predominantly used. Therefore, it has become essential to explore alternatives for the easy and robust detection of pathogenic microbes and antibiotic residue in the food source. Presently, different monitoring, as well as detection techniques like PCR-based, assay (nucleic acid)-based, enzyme-linked immunosorbent assays (ELISA)-based, aptamer-based, biosensor-based, matrix-assisted laser desorption/ionization-time of flight mass spectrometry-based and electronic nose-based methods, have been developed for detecting the presence of bacterial contaminants and antibiotic residues. The current review intends to summarize the different techniques and underline the potential of every method used for the detection of bacterial pathogens and antibiotic residue in chicken meat

Traditional foods and beverages of Himachal Pradesh

17-24Himachal Pradesh presents anthropological, cultural, environmental and topographical diversity. Its reflection is seen in the variations of architecture of houses, clothing styles, food and food habits. The variations in availability of raw materials, environmental conditions clubbed with the time tested traditional knowledge and wisdom have made the people of different regions of this hill state to formulate, develop and perpetuate the consumption of a wide range of traditional foods and beverages unique to its places since ages. Bhatooru, siddu, marchu, seera, chilra, manna, aenkadu, sepubari, patande, doo, baari, dosha, malpude, babroo, bedvin roti, madrah, tchati, churpa, sura, chhang, kinnauri, angoori, chulli, lugri, arak/ara, rak, chukh and pickles (e.g. brinjal, lingri, bidana, peach, pear, plum, tomato, bottle gourd, etc.) made from different fruits and vegetables, etc. are some popular traditional products that are unique to the tribal and rural belts of Himachal Pradesh. Some of these products, e.g. bhatooru, chilra and tchati constitute staple food in rural areas of the state while others are prepared and consumed during marriages, local festivals and special occasions, and form part of the sociocultural life of hill people. However, the production of these foods and beverages is largely limited to household level

<b>Characterization of some traditional fermented foods and beverages of Himachal Pradesh</b>

325-335Traditional fermented foods and beverages are very popular in the tribal and rural areas of Himachal Pradesh. A number of fermented foods and beverages were identified and the traditional fermentation processes were studied. Some of the popular fermented foods and beverages were analysed for their microbiological characteristics. The fermented products that are unique to the tribal and rural belts of Himachal are Bhaturu, Siddu, Chilra, Manna, Marchu, Bagpinni, Seera, Dosha, Sepubari, Sura, Chhang, Lugri, Daru, Angoori and Behmi. Besides source of nutrition, these fermented foods e.g. Bhaturu, constitute staple food in larger part of rural areas of Kullu, Kangra, Mandi and Lahaul & Spiti districts of the state while others are consumed during local festivals, marriages and special occasions. Traditional starter cultures like ‘Phab’ (dehydrated yeast formulations), ‘Treh’ (previously fermented wheat flour slurry) and ‘Malera’ (previously fermented wheat flour dough) are the inocula used in preparing fermented products. Microbiological studies revealed that species of Saccharomyces cerevisiae is a dominant microorganism in fermentation along with species of Candida, Leuconostoc and Lactobacillus. The ethanol content of some of the fermented beverages was also analysed

In vitro cyanide degradation by Serretia marcescens RL2b

ABSTRACT Detoxification of cyanide compounds using biological systems is gaining much attention due to various advantages over the traditional physical and chemical methods. In present study, a cyanide degrading bacterial strain RL2b was isolated from forest soil of Himachal Pradesh. Based on the morphology, physiological, biochemical tests and its 16S rDNA sequence, the bacterial isolate RL2b was identified as Serretia marcescens. In vitro degradation of cyanide by this organism was investigated by varying several cultural conditions viz. medium, carbon and nitrogen sources, pH and temperature. Serretia marcescens RL2b exhibited maximum cyanide degradation in medium M1 containing glycerol and tryptone as carbon and nitrogen source respectively. Cyanide degradation was maximum at pH 6.0 and 35˚C temperature. This bacterial isolate exhibited cyanide tolerance up to 16 mM and highest cyanide degradation at 12 mM in 40 h. The present study revealed that the strain Serretia marcescens RL2b has high cyanide tolerance and degradation potential at wide pH and temperature range and thus has very good potential for efficient cyanide removal from environment

Generation of mutant of Rhodococcus rhodochrous PA-34 through chemical mutagenesis for hyperproduction of nitrile hydratase

Rhodococcus rhodochrous PA-34 has been reported to produce nitrile hydratase enzyme that converts 3-cyanopyridine to nicotinamide. A mutant of R. rhodochrous PA-34 was generated through chemical mutagenesis using N-methyl-N-nitro-N-nitrosoguanidine (MNNG) that exhibited 2 times higher nitrile hydratase activity as compared to wild strain. The reaction conditions using resting cells of this mutant strain for the conversion of nicotinamide were optimized. Under the optimized reaction conditions the mutant strain exhibited maximum nitrile hydratase activity [7.8 U/mgdcm (milligram dry cell mass)] at 55 °C in 0.3 M potassium phosphate buffer (pH 5.5)

Mining of Microbial Genomes for the Novel Sources of Nitrilases

Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes). This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases, Gluconacetobacter diazotrophicus, Sphingopyxis alaskensis, Saccharomonospora viridis, and Shimwellia blattae were specific for aliphatic nitriles, whereas nitrilases from Geodermatophilus obscurus, Nocardiopsis dassonvillei, Runella slithyformis, and Streptomyces albus possessed activity for aromatic nitriles. Flavobacterium indicum was specific towards potassium cyanide (KCN) which revealed the presence of nitrilase homolog, that is, cyanide dihydratase with no activity for either aliphatic, aromatic, or aryl nitriles. The present study reports the novel sources of nitrilases and cyanide dihydratase which were not reported hitherto by in silico or in vitro studies

Mining of Microbial Genomes for the Novel Sources of Nitrilases

Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes). This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases, Gluconacetobacter diazotrophicus, Sphingopyxis alaskensis, Saccharomonospora viridis, and Shimwellia blattae were specific for aliphatic nitriles, whereas nitrilases from Geodermatophilus obscurus, Nocardiopsis dassonvillei, Runella slithyformis, and Streptomyces albus possessed activity for aromatic nitriles. Flavobacterium indicum was specific towards potassium cyanide (KCN) which revealed the presence of nitrilase homolog, that is, cyanide dihydratase with no activity for either aliphatic, aromatic, or aryl nitriles. The present study reports the novel sources of nitrilases and cyanide dihydratase which were not reported hitherto by in silico or in vitro studies