Characterization of a Class A ß-Lactamase from Francisella tularensis (Ftu-1) Belonging to a Unique Subclass toward Understanding AMR.

ß-lactamase production with vast catalytic divergence in the pathogenic strain limits the antibiotic spectrum in the clinical environment. Class A carbapenemase shares significant sequence similarities, structural features, and common catalytic mechanisms although their resistance spectrum differs from class A ß-lactamase in carbapenem and monobactam hydrolysis. In other words, it limited the antibiotic treatment option against infection, causing carbapenemase-producing superbugs. Ftu-1 is a class A ß-lactamase expressed by the Francisella tularensis strain, a potent causative organism of tularemia. The chromosomally encoded class A ß-lactamase shares two conserved cysteine residues, a common characteristic of a carbapenemase, and a distinctive class in the phylogenetic tree. Complete biochemical and biophysical characterization of the enzyme was performed to understand the overall stability and environmental requirements to perform optimally. To comprehend the enzyme-drug interaction and its profile toward various chemistries of ß-lactam and ß-lactamase inhibitors, comprehensive kinetic and thermodynamic analyses were conducted using various ß-lactam drugs. The dynamic property of Ftu-1 ß-lactamase was also predicted using molecular dynamics (MD) simulation to compare its loop flexibility and ligand binding with other related class A ß-lactamases. Overall, this study fosters a comprehensive understanding of Ftu-1, proposed to be an intermediate class by characterizing its kinetic profiling, stability by biochemical and biophysical methodologies, and susceptibility profiling. This understanding would be beneficial for the design of new-generation therapeutics.

Interdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV.

Hepatitis C virus (HCV) causes hepatitis, a life-threatening disease responsible for liver cirrhosis. Urgent measures have been taken to develop therapeutics against this deadly pathogen. NS3/4A protease is an extremely important target. A series of inhibitors have been developed against this viral protease including Faldaprevir. Unfortunately, the error-prone viral RNA polymerase causes the emergence of resistance, thereby causing reduced effectiveness of those peptidomimetic inhibitors. Among the drug resistant variants, three single amino acid residues (R155, A156 and D168) are notable for their presence in clinical isolates and also their effectivity against most of the known inhibitors in clinical development. Therefore, it is crucial to understand the mechanistic role of those drug resistant variants while designing potent novel inhibitors. In this communication, we have deeply analyzed through using in silico studies to understand the molecular mechanism of alteration of inhibitor binding between wild type and its R155K, A156V and D168V variants. Principal component analysis was carried to identify the backbone fluctuations of important residues in HCV NS3/4A responsible for the inhibitor binding and maintaining drug resistance. Free energy landscape as a function of the principal components has been used to identify the stability and conformation of the key residues that regulate inhibitor binding and their impact in developing drug resistance. Our findings are consistent with the trend of experimental results. The observations are also true in case of other Faldaprevir-like peptidomimetic inhibitors. Understanding this binding mechanism would be significant for the development of novel inhibitors with less susceptibility towards drug resistance.Communicated by Ramaswamy H. Sarma.

Probiotic potential and immunomodulatory properties in Enterococcus faecium GMB24 and Enterococcus hirae SMB16 isolated from goat and sheep milk.

Probiotic attributes of lactic acid bacteria isolated from goat and sheep milk samples were analysed by culturing them on an MRS agar medium. The most potential isolates, GMB24 and SMB16, were identified by biochemical tests which had ability to tolerate different concentrations of acid and bile and phenol resistance. They were further identified as Enterococcus faecium GMB24 and Enterococcus hirae SMB16 by 16S rRNA gene sequencing approach. The probiotic potential of the isolates GMB24 and SMB16 were recorded including antimicrobial activity against pathogenic bacteria viz., Escherichia coli (MTCC118), Staphylococcus aureus (MTCC7443), Pseudomonas aeruginosa (MTCC424), Listeria monocytogens (MTCC657) and Salmonella typhimurium (MTCC733), and antibiotic susceptibility test. The isolates SMB16 and GMB24 exhibited a higher zone of inhibition against P. aeruginosa (19.00 ± 0.57 mm) and S. aureus (25.66 ± 0.88 mm), respectively. The data from these experiments were used for the principal component analysis (PCA) to assess the survivability of the isolates under different factors. The heatmap generated in this study clustered the bacterial isolates based on their phenotype properties. Further, immunomodulating activities of these probiotic bacteria were tested on neutrophil adhesion test, haemagglutinating antibody titer and delayed-type hypersensitivity. Probiotic E. faecium GMB24 and E. hirae SMB16, at 109 cells/mL doses per day, increased the neutrophil adhesion, haemagglutinating antibody titer and DTH in comparison to the untreated control group. The isolates showed negative test for haemolytic and gelatinase activities and hence were considered safe. E. faecium GMB24 and E. hirae SMB16 were shown to have high probiotic potential and immune-stimulant action.

In silico study of cox protein from P2 type enteric bacteriophages based on sequence, structure and dynamics to understand its functional integrity.

Cox protein plays a critical role in deciding the lytic-lysogenic switch of P2 enteric phages. This phenomenon makes Cox protein one of the most important candidates in developing novel phage-based therapeutics against antibacterial resistant pathogens. The principle focus concerning protein and its decision making is a DNA binding event, which helps to regulate differential promoter expression. In the current study, we have attempted to understand the sequence, structural and dynamic features associated with Cox protein and its DNA binding. Unavailability of information was a big burden in further proceedings. We have done an extensive literature search to develop a database of Cox with relevant information. That information coupled with the methods of Sequence-based phylogenetic and conservation studies, Homology Modelling, Atomic-level Docking and Molecular Dynamics (MD) Simulation (50 ns each for 10 systems, i.e. total of 500 ns) were performed in the current study. Analysis of those extensive studies has provided us the required sequence to structure to dynamics to functional understanding. Our present study would indeed be very helpful in understanding the biochemical mechanism of Cox activation as well as designing potential phage therapeutics.

Next-generation biofertilizers and novel biostimulants: documentation and validation of mechanism of endophytic plant growth-promoting rhizobacteria in tomato.

A study was conducted to determine the suitability of the endophytes as probable next-generation biofertilizers and novel biostimulants. Enterobacter turicensis RCT5 and Stenotrophomonas maltophilia RCT31 showed a zone of solubilization, of phosphate, potassium, silicate, and zinc, produced phytase. Among the three media used for phosphate solubilization, the rhizospheric medium turned out to be the best-producing results in less than 24 h, while others took a longer time to give the same results. The strains exhibited differential ability to produce organic acids in the plate assay and eight of these were profuse producers of exopolysaccharides. We were able to partially elucidate the mechanism of solubilization of insoluble salts that included organic acids and protein activity in the cell-free culture filtrates of endophytes. All the root nodule endophytes showed potential as novel biostimulants and next-generation biofertilizers as found in the germination assay of tomato, a non-host crop using different methodologies. It proved that the endophytes have different mechanism of expressions of their plant growth-promoting traits as well as can promote the growth of tomato plant irrespective of the method used.

Seed bio-priming with tri-species consortia of phosphate solubilizing rhizobacteria (PSR) and its effect on plant growth promotion.

Three potential rhizobacteria namely Burkholderia gladioli (MTCC 10216), Pseudomonas sp. (MTCC 9002) and Bacillus subtilis (MTCC 8528) procured from IMTECH, Chandigarh (India) were evaluated individually and as consortia for its phosphate (P) solubilizing ability and effect of growth of fenugreek (Trigonella foenum-graecum L.) and tomato (Lycopersicon esculentum L.). Phosphate solubilizing ability of these strains individually and as consortia was tested on Pikovskayas agar medium, Phosphate solubilizing agar medium and National Botanical Research Institute phosphate agar medium containing six different sources of insoluble inorganic phosphate such as tri-calcium phosphate (TCP), di-calcium phosphate (DCP), zinc phosphate (ZP), ferric phosphate (FP), sodium di-hydrogen phosphate (SP), and aluminum phosphate (AP), and two organic P such as calcium and sodium phytate. The maximum P solubilizing ability was recorded in consortium-4 having all three potential bacterial strains. Phosphate solubilization after 7th day of incubation was 37.9 mg/100 ml of TCP, 40.01 mg/100 ml of DCP, 15.79 mg/100 ml of FP, 43.02 mg/100 ml of SP, no solubilization of ZP and AP, 39.75 mg/100 ml of calcium phytate and 24.01mg/100 ml of sodium phytate. Seed germination and the other plant parameters such as plant height and weight significantly increased in fenugreek and tomato seeds, bio-primed with consortium-4 followed by consortium-3. After bio-priming of seeds in pot assay, the level of phosphorus in soil got increased by 54% in consortium-4 treated soil followed by consortium-3 (47%) over untreated control soil. Based on these findings, consoritium-4 could be recommended as a good bio-inoculant for fenugreek, tomato and other crops in comparison to individual strains and other consortia.

Effect of silver nanoparticles and Bacillus cereus LPR2 on the growth of Zea mays.

The effect of Plant Growth Promoting Rhizobacteria (Bacillus sp.) and silver nanoparticles on Zea mays was evaluated. The silver nanoparticles were synthesized from Tagetes erecta (Marigold) leaf and flower extracts, whereas PGPR isolated from spinach rhizosphere. The silver nanoparticles (AgNPs) were purified using ultra centrifugation and were characterized using UV-Vis spectroscopy at gradient wavelength and also by High Resolution Transmission Electron microscopy (HRTEM). The average particles size of AgNPs was recorded approximately 60 nm. Almost all potential isolates were able to produce Indole Acetic Acid (IAA), ammonia and Hydrogen cyanide (HCN), solubilized tricalcium phosphate and inhibited the growth of Macrophomina phaseolina in vitro but the isolate LPR2 was found the best among all. On the basis of 16S rRNA gene sequence, the isolate LPR2 was characterized as Bacillus cereus LPR2. The maize seeds bacterized with LPR2 and AgNPs individually showed a significant increase in germination (87.5%) followed by LPR2 + AgNPs (75%). But the maximum growth of root and shoot of maize plant was observed in seeds coated with LPR2 followed by AgNPs and a combination of both. Bacillus cereus LPR2 and silver nanoparticles enhanced the plant growth and LPR2 strongly inhibited the growth of deleterious fungal pathogen. Therefore, LPR2 and AgNPs could be utilized as bioinoculant and growth stimulator, respectively for maize.

Characterization of a plant-growth-promoting non-nodulating endophytic bacterium (Stenotrophomonas maltophilia) from the root nodules of Mucuna utilis var. capitata L. (Safed Kaunch).

Nonrhizobial root nodule endophytic bacteria are known to have beneficial effects on host plants and are also considered contaminants or opportunists. They grow either individually or as a co-occupant of the root nodules of legumes. In this study, a nonrhizobial endophytic bacterial strain was isolated from the root nodules of the medicinal legume Mucuna utilis var. capitata L.; phenotypic, genotypic, and agricultural characterization was performed using a HiMedia kit and 16S rRNA sequencing. This strain showed tremendous seedling growth potential (30%), compared with the control, as well as a strong antagonistic nature against the plant pathogenic fungus Fusarium udum when plant growth parameters were analyzed. The strain, identified by 16S rRNA as Stenotrophomonas maltophilia, showed a multitude of plant-growth-promoting attributes both direct (IAA, phosphate solubilization) and indirect (ACC deaminase, siderophore) and enhanced the growth of host plant in field trials. This is the first report of the plant-growth-promoting potential of this endophytic bacterium from the nodules of M. utilis var. capitata L.; hence, it has potential for use in various biotechnological applications in various industries.

Revisiting the plant growth-promoting rhizobacteria: lessons from the past and objectives for the future.

Plant beneficial rhizobacteria (PBR) is a group of naturally occurring rhizospheric microbes that enhance nutrient availability and induce biotic and abiotic stress tolerance through a wide array of mechanisms to enhance agricultural sustainability. Application of PBR has the potential to reduce worldwide requirement of agricultural chemicals and improve agro-ecological sustainability. The PBR exert their beneficial effects in three major ways; (1) fix atmospheric nitrogen and synthesize specific compounds to promote plant growth, (2) solubilize essential mineral nutrients in soils for plant uptake, and (3) produce antimicrobial substances and induce systemic resistance in host plants to protect them from biotic and abiotic stresses. Application of PBR as suitable inoculants appears to be a viable alternative technology to synthetic fertilizers and pesticides. Furthermore, PBR enhance nutrient and water use efficiency, influence dynamics of mineral recycling, and tolerance of plants to other environmental stresses by improving health of soils. This report provides comprehensive reviews and discusses beneficial effects of PBR on plant and soil health. Considering their multitude of functions to improve plant and soil health, we propose to call the plant growth-promoting bacteria (PGPR) as PBR.

Combined effects of rhizo-competitive rhizosphere and non-rhizosphere Bacillus in plant growth promotion and yield improvement of Eleusine coracana (Ragi).

This study emphasizes the beneficial role of rhizo-competitive Bacillus spp. isolated from rhizospheric and non-rhizospheric soil in plant growth promotion and yield improvement via nitrogen fixation and biocontrol of Sclerotium rolfsii causing foot rot disease in Eleusine coracana (Ragi). The selection of potent rhizobacteria was based on plant-growth-promoting attributes using Venn set diagram and Bonitur scale. Bacillus pumilus MSTA8 and Bacillus amyloliquefaciens MSTD26 were selected because they were effective in root colonization, rhizosphere competence, and biofilm formation using root exudates of E. coracana L. rich with carbohydrates, proteins, and amino acids. The relative chemotaxis index of the isolates expressed the invasive behavior of the rhizosphere. During pot and field trials, the consortium of the rhizobacteria in a vermiculite carrier increased the grain yield by 37.87%, with a significant harvest index of 16.45. Soil analysis after the field trial revealed soil reclamation potentials to manage soil nutrition and fertility. Both indexes ensured crop protection and production in eco-safe ways and herald commercialization of Bacillus bio-inoculant for improvement in crop production and disease management of E. coracana.

Antibacterial, antioxidant and Immuno-modulatory properties in extracts of Barleria lupulina Lindl.

BACKGROUND: Antibacterial, immunomodulatory and antioxidant properties of aerial parts of Barleria lupulina Lindl were investigated in the present communication. METHODS: The antibacterial, antioxidant and immunomodulatory properties of B. lupulina (methanol soluble leaf and stem extracts) was analyzed by minimum inhibitory concentration, total phenolic contents, DPPH radical scavenging activity, determination of toxicity, hemagglutination antibody titre, delayed type hypersensitivity and neutrophil adhesion test, respectively. RESULTS: Methanol soluble leaf extract (MLE) contains more soluble bioactive compounds inhibiting the growth of five bacterial pathogens viz., Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Salmonella typhi even at MICs of 1.25 and 2.5 mg/mL. Aqueous stem extract (ASE) was least effective while MLE was highly effective in inhibiting the growth and survival of bacterial pathogens. While testing the effect of these extracts in animal model, no mortality of albino rats was recorded by using MLE and MSE at the concentrations from 200 to 600 mg/kg of their body weight. The MLE showed significant result in agglutination reaction and induced paw edema volumes when compared with untreated group (control). Both MLE and MSE extracts significantly increased neutrophil adhesion with increase in doses of extracts. MLE was found to have more potent immune-stimulant properties than the MSE. High phenolic contents were found in MSE while lowest IC50 values were found in MLE in term of DPPH radical scavenging activity. CONCLUSIONS: Methanol soluble leaf and stem extract of Barleria lupulina contains antibacterial, antioxidants and immunomodulating phytochemical compounds that was effective for antibacterial, antioxidant and immunomodulatory properties. These may be used as synthetic drug.

In Silico Designing of an Industrially Sustainable Carbonic Anhydrase Using Molecular Dynamics Simulation.

Carbonic anhydrase (CA) is a family of metalloenzymes that has the potential to sequestrate carbon dioxide (CO2) from the environment and reduce pollution. The goal of this study is to apply protein engineering to develop a modified CA enzyme that has both higher stability and activity and hence could be used for industrial purposes. In the current study, we have developed an in silico method to understand the molecular basis behind the stability of CA. We have performed comparative molecular dynamics simulation of two homologous α-CA, one of thermophilic origin (Sulfurihydrogenibium sp.) and its mesophilic counterpart (Neisseria gonorrhoeae), for 100 ns each at 300, 350, 400, and 500 K. Comparing the trajectories of two proteins using different stability-determining factors, we have designed a highly thermostable version of mesophilic α-CA by introducing three mutations (S44R, S139E, and K168R). The designed mutant α-CA maintains conformational stability at high temperatures. This study shows the potential to develop industrially stable variants of enzymes while maintaining high activity.

Structure prediction and evolution of a halo-acid dehalogenase of Burkholderia mallei.

Environmental pollutants containing halogenated organic compounds e.g. haloacid, can cause a plethora of health problems. The structural and functional analyses of the gene responsible of their degradation are an important aspect for environmental studies and are important to human well-being. It has been shown that some haloacids are toxic and mutagenic. Microorganisms capable of degrading these haloacids can be found in the natural environment. One of these, a soil-borne Burkholderia mallei posses the ability to grow on monobromoacetate (MBA). This bacterium produces a haloacid dehalogenase that allows the cell to grow on MBA, a highly toxic and mutagenic environmental pollutant. For the structural and functional analysis, a 346 amino acid encoding protein sequence of haloacid dehalogenase is retrieve from NCBI data base. Primary and secondary structure analysis suggested that the high percentage of helices in the structure makes the protein more flexible for folding, which might increase protein interactions. The consensus protein sub-cellular localization predictions suggest that dehalogenase protein is a periplasmic protein 3D2GO server, suggesting that it is mainly employed in metabolic process followed by hydrolase activity and catalytic activity. The tertiary structure of protein was predicted by homology modeling. The result suggests that the protein is an unstable protein which is also an important characteristic of active enzyme enabling them to bind various cofactors and substrate for proper functioning. Validation of 3D structure was done using Ramachandran plot ProsA-web and RMSD score. This predicted information will help in better understanding of mechanism underlying haloacid dehalogenase encoding protein and its evolutionary relationship.

Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium.

Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (MDH). MDH is performing these functions with the help of a key protein mxaF. Unfortunately, detailed structural analysis and homology modeling of mxaF is remains undefined. Hence, the objective of this research is the characterization and three dimensional modeling of mxaF protein from three different methylotrophs by using I-TASSER server. The predicted model were further optimize and validate by Profile 3D, Errat, Verifiy3-D and PROCHECK server. Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. Active site identification revealed 11, 13 and 14 putative functional site residues in respected models. It may play a major role during protein-protein, and protein-cofactor interactions. This study can provide us an ab-initio and detail information to understand the structure, mechanism of action and regulation of mxaF protein.