In Silico Molecular Insights on the Structure-Function Aspects of ACC Deaminase of a Non-Pathogenic Klebsiella Pneumoniae

Bacterial 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) is known to involve in breaking down the 1-aminocyclopropane-1-carboxylic acid (ACC), immediate precursor of ethylene, into a-ketobutyrate and ammonia. This is required when stress (biotic or abiotic) induced ethylene content is accelerated in plant cells resulting in reduction in plant biomass and yield. Klebsiellapneumoniae, although previously considered only as a pathogenic bacteria, there are some strains reported till date to prove it as a plant growth promoting bacteria (PGPB). ACCD activity has reported from the said strain but the present study is emphasized on its molecular proteomic structures and functions studied in silico. The present work revealed that the ACCD of K. pneumoniae is a 36.5 kDatetrameric stable protein found in intracellular condition. The phylogenetic analysis clearly depicts its similarity with several other ACCD reported from different bacterial genera. The structure-function insight would definitely help future researchers in designing wet lab as well as dry lab experiments

In Silico Structural, Functional and Phylogenetic Analyses of Corynebacterium Aspartokinase: An Enzyme of Aspartate Family of Amino Acids

Aspartokinase is the enzyme of the aspartate family of amino acid biosynthesis that catalyzes first reaction in biosynthesis of Aspartate family. This enzyme has an important role for hyper production of the Lysine or methionine or threonine by microbial fermentation. The present study was undertaken to determine the in silico analysis of the aspartokinase of Corynebacteriumglutamicum. In silicoanalysis ofAspartokinase protein of Corynebacteriumglutamicumrevealed that it is a thermostable, acidic protein having molecular weight of about 45kDa. The 3D structure and protein model with functional characters of this protein has predicted. This computational analysis might assist with useful information required during wet lab experiments

Computational based Structural, Functional and Phylogenetic Analyses Of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate (DAHP) Synthase of Corynebacterium Spp

The pathway of aromatic amino acid biosynthesis was initiated by the enzyme DAHP synthase. In this branched biosynthetic pathway phenylalanine, tyrosine and tryptophan are produced. This enzyme was repressed and inhibited by three said end product of aromatic amino acids. The importance of this enzyme is microbial fermentation of aromatic amino acid production. The present study envisaged the in silico analysis of this protein (DAHP synthase). The structural, functional and phylogenetic studies of this protein of Corynebacteriumglutamicum have been determined and it was observed that the protein of interest is a thermostable, acidic protein having molecular weight ranging in between 38.67 to 52.32 kDa

Assessment of genetic diversity using morphological and molecular markers in traditional cultivars of Mango (Mangifera indica L.)

404-413Mango (Mangifera indica L.) is an economically important tropical and subtropical fruit crop consumed worldwide. Alloploidy, nature of cross-pollination and a wide range of predominant agro-ecologies of the country have contributed large genetic diversity of mango in India. The present study assessed 16 traditional mango cultivars to get a unique insight on cultivars' diversity through deploying integration of both morphological and molecular markers. The cultivars were appraised for consecutive two years under the aegis of All India Coordinated Research Project on Fruits, Bidhan Chandra Krishi Viswavidyalaya (BCKV), Gayeshpur, West Bengal regarding observation on 26 morphological and fruit quality parameters followed by assessing diversity at molecular level through deploying 20 SSR makers. Presence of adequate genetic variability was reflected for all the tested traits. Principal Component Analysis (PCA) ascertained seven PCs towards contribution of more than 84.25% genetic diversity harbored by the tested cultivars. Out of 20 SSRs, 8 microsatellites were amplified and produced 27 putative alleles in 16 cultivars. Genetic divergence through multivariate analysis, as well as through UPGMA dendrograms, classified 16 mango cultivars into five major clusters, though, the cluster composition was different. The dendrogram affirmed that the highest similarity (88%) was observed in between Ranipasand and Gulab Khas. Sharing of common gene pool coupled with exertion of similar selection pressure during domestication as well as selection of cultivars in this region exhibited similar tradition

Growth promoting properties of Mycobacterium and Bacillus on rice plants under induced drought

Management of drought stress through application of plant growth promoting rhizobacteria (PGPR) is now considered as an effective strategy in the present scenario of altered environmental conditions of the world. The aims and objectives of the present investigation was isolation, characterization and identification of some potential microbial resources (PGPR) from drought-affected upland rice fields of South Bengal followed by experimentation on the effect of isolated PGPR on drought induced rice seedlings. Selected isolates were isolated from rice field rhizospheric soils and tested for their PGPR activity, through phosphate solubilization, nitrogen fixation, IAA production and ACC deaminase activity. Then, the selected isolates were identified through 16S rDNA sequencing and phylogenetic analysis. Among the screened isolates two (isolate 1 and isolate 6) showing plant growth promoting traits, was applied on studied germplasm (IR64) to find out the influence of the applied organisms on rice growth and development under induced drought. Both organisms showed a positive influence (through increase in germination percentage, root growth, shoot growth, fresh weight and dry weight) on the studied rice growth and development under induced drought. Isolate 1 and 6 identified as species of Mycobacterium sp and Bacillus sp respectively through molecular taxonomy. Hence, these two isolates are expected to alleviate drought stress in the rice field for their nature of plant growth promotion under drought stress

Structural heterogeneity assessment among the isoforms of fungal 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase: a comparative in silico perspective

Highlights • First comprehensive in silico annotation of fungal ACC deaminases (fACCD). • Colletotrichum, Fusarium, and Trichoderma are predominant to possess fACCD. • fACCD are 16.18–82.47 kDa proteins with optimal pH between 4.76 and 10.06. • Majority are thermostable with higher aliphatic indices and instability indices < 40. • fACCD are found as homo-dimer except ACCNK13, a homo-tetramer. Graphical Abstrac

Assessment of genetic diversity using morphological and molecular markers in traditional cultivars of Mango (Mangifera indica L.)

Mango (Mangifera indica L.) is an economically important tropical and subtropical fruit crop consumed worldwide. Alloploidy, nature of cross-pollination and a wide range of predominant agro-ecologies have contributed large genetic diversity of mango in India. In the present study attempt has been made with 16 traditional mango cultivars to get phenomenal insight on genetic variability and cultivars' diversity through deploying morphological and molecular markers. The cultivars were tested for consecutive two years under the aegis of All India Coordinated Research Project on Fruits, Bidhan Chandra Krishi Viswavidyalaya (BCKV), Gayeshpur, West Bengal regarding observation on 26 morphological and fruit quality parameters followed by assessing diversity at molecular level through deploying 20 SSR makers. Result showed that adequate genetic variability was existed among the tested genotypes with predominance of additive gene action regarding inheritance of most of the characters. Principal Component Analysis detected seven PCs towards contribution of more than 84.25% genetic diversity harboured by the tested genotypes. Out of 20 SSRs, 8 microsatellites were amplified and produced 27 putative alleles in 16 cultivars. Genetic Divergence through multivariate analysis, as well as through UPGMA dendrograms classified 16 mango cultivars in to five major clusters. The dendrogram revealed that Ranipasand and Gulab Khas were the most similar cultivars with 88 % similarity. Sharing of common gene pool as well as exertion of similar selection pressure during domestication as well as selection of cultivars in this region exhibited similar tradition

Studies on genetic variability and identification of sequence variations among cultivars and landraces of rice (Oryza sativa L.) for apparent amylose and amylopectin contents

Starch is the main component of cereals like rice. It is mainly composed of amylose and amylopectin. Apparent amylose content (AAC) in rice grain controlled by granule bound starch synthase enzyme (GBSS) is the key factor determining cooking and processing quality. The present study has been attempted to decipher the genetic variability among 36 cultivars of rice for agro-morphological parameters along with AAC and amylopectin content, to determine the extent of association among yield and its contributing characters and to detect the sequence variations among the cultivars having differential AAC. Results revealed the presence of adequate genetic variability among the tested rice cultivars for yield attributing traits, as well as their AAC and amylopectin content. Most of the yield attributing traits was under control of additive genes. Genetic diversity study of the tested rice cultivars grouped them into four clusters. The nucleotide sequence and derived amino acid sequence variations among the region spanning between the intron 7 and exon 10 of GBSSI allele from the rice cultivars differing in AAC detected the presence of several SNPs, deletions and insertions within the tested exon and intron regions. Presence of methionine (M) or isoleucine (I) at 308 aa position and presence of phenylalanine (F) at 425 or 434 aa position of GBSSI protein across the tested rice cultivars can be exploited in marker-assisted breeding programme for developing high yielding rice cultivars with proper grain quality as per consumer’s preference

An in silico structural, functional and phylogenetic analysis with three dimensional protein modeling of alkaline phosphatase enzyme of Pseudomonas aeruginosa

Phosphorus is a primary macronutrient required for normal plant health, metabolism and survival. It is present in soil in compound insoluble form for which plant cannot uptake it directly from the soil. Some phosphate solubilizing bacteria possess some important enzymes for phosphate solubilization as well as mineralization. Alkaline (or basic) phosphatase (EC 3.1.3.1) is a type of zinc containing dimeric hydrolase enzyme responsible for removing the phosphate groups from various kinds of molecules including nucleotides, proteins, and alkaloids. Unlike acid phosphatases alkaline phosphatases are most effective in an alkaline environment. Alkaline phosphatases (ALPs) are of immense importance in various agricultural industries including dairy industries for testing successful pasteurization process. In this present study, Pseudomonas aeruginosa phosphatase was selected for a detailed computational investigation to exploit its physicochemical characteristics, structural properties including 3D model, model quality analysis, phylogenetic assessment and functional analysis using a number of available standard bioinformatics tools. The protein having average molecular weight about 51 kDa, was found thermostable and alkaline in nature belonging to metalloenzyme superfamily. Specifically, the thermostable behavior of the protein is suitable for the dairy industry. Moreover, this theoretical overview will help researchers to get an idea about the predicted protein structure and it may also help to design genetically engineered phosphate solubilizing bacteria by designing specific primers