Metaproteomic Discovery and Characterization of a Novel Lipolytic Enzyme From an Indian Hot Spring.

Lipolytic enzymes are produced by animals, plants and microorganisms. With their chemo-, regio-, and enantio-specific characteristics, lipolytic enzymes are important biocatalysts useful in several industrial applications. They are widely used in the processing of fats and oils, detergents, food processing, paper and cosmetics production. In this work, we used a new functional metaproteomics approach to screen sediment samples of the Indian Bakreshwar hot spring for novel thermo- and solvent-stable lipolytic enzymes. We were able to identify an enzyme showing favorable characteristics. DS-007 showed high hydrolytic activity with substrates with shorter chain length (C10, significantly less hydrolytic activity was observed. A preference for short chain acyl groups is characteristic for esterases, suggesting that DS-007 is an esterase. Consistent with the high temperature at its site of isolation, DS-007 showed a temperature optimum at 55°C and retained 80% activity even after prolonged exposure to temperatures as high as 60°C. The enzyme showed optimum activity at pH 9.5, with more than 50% of its optimum activity between pH 8.0 and pH 9.5. DS-007 also exhibited tolerance toward organic solvents at a concentration of 1% (v/v). One percent of methanol increased the activity of DS-007 by 40% in comparison to the optimum conditions without solvent. In the presence of 10% methanol, DMSO or isopropanol DS-007 still showed around 50% activity. This data indicates that DS-007 is a temperature- and solvent-stable thermophilic enzyme with reasonable activity even at lower temperatures as well as a catalyst that can be used at a broad range of pH values with an optimum in the alkaline range, showing the adaptation to the habitat's temperature and alkaline pH.

Plant Growth-Promoting Traits of a Thermophilic Strain of the Klebsiella Group with its Effect on Rice Plant Growth.

In agriculture, instead of synthetic fertilizers, natural bio-inoculants can be used to increase growth and yield of crops. For this purpose, we report a thermophilic bacteria Klebsiella sp. strain PMnew, isolated from Paniphala hot spring. The strain was characterized and assessed for plant growth-promoting traits. Oryza sativa L. var Swarna (rice) seeds were inoculated with the strain to study the bacterization effect on vegetative and reproductive growth of rice plants. The results indicate that PMnew produces organic acids to solubilize phosphate (550.16 ± 0.04 µg/ml), fixes nitrogen, produces indole compounds, siderophore, and ACC deaminase, and shows heavy metal resistance to chromium, cobalt, arsenic, cadmium, and mercury. It also possesses the ability to utilize several monomeric and polymeric sugars as sole carbon source including starch, agar, xylan, gelatin, and pectin, and can grow under both nutrient-rich and deficient conditions. Inoculated rice plants grew twice the length of control plants and surpassed the total grain mass yield of control plants by almost 18 times. Thus, this study brings forth a broad spectrum and easy to cultivate bio-inoculant, which can be used to increase rice production.

CdS quantum dots embedded in PVP: Inorganic phosphate ion sensing in real sample and its antimicrobial activity.

Polyvinyl-pyrrolidone capped spherical cadmium sulphide quantum dots (CdS-PVP QDs), 2-6 nm in size, were developed as a selective turn-on fluorescence nanosensor for monohydrogen phosphate ion (HPO42-) in aqueous medium. Fluorescence intensity of CdS-PVP QDs significantly increased with addition of HPO42- ions, whereas the other common inorganic ions had very little effect on the fluorescence intensity. The proposed sensor may be efficiently used for the detection of HPO42- ions at a low level of concentration up to 213 nM in real urine sample. Cell imaging study indicates that the CdS-PVP QDs are cell permeable and can detect the intracellular distribution of HPO42- ions under fluorescence microscope. The CdS-PVP QDs showed considerable activity against Staphylococcus aureus also.

Antioxidant properties of the carotenoid extracts of three Deinococcus­Thermus phylum bacteria, Meiothermus sp. strains RP and TP and Thermus sp. strain YY from Paniphala hot spring, India

BACKGROUND:The purpose of the study was to extract carotenoids from thermophilic bacteria which show efficient antioxidant and protein oxidation inhibition properties, characterize and identify those isolates, extract the carotenoids in different solvents, quantify the carotenoids and perform concentration-dependent and solvent-dependent quantitative assays validated and analysed by appropriate statistical tests. METHODS: Three pigment-forming thermophilic strains were isolated from water sample of Paniphala hot spring, India, and tentatively identified by 16S ribosomal DNA (rDNA) homology. Different concentrations of the carotenoid extracts (100, 80, 40 and 20µg) in three solvents, methanol, DMSO and water, were used to determine the antioxidant activity through five methods: the DPPH (1,1-diphenyl-2-picrylhydrazyl) assay, the ABTS (2,2-azino-bis (3-ethylbenz-thiazoline-6-sulfonic acid)) assay, the hydrogen peroxide assay, TOC (total antioxidant capacity) assay and inhibition of protein oxidation assay. Statistical analysis of mean, standard deviation, ANOVA and Pearson correlationcoefficient was performed in Microsoft Excel statistical package.Results:The isolates were tentatively identified as Meiothermussp. strain RP, Meiothermussp. strain TP and Thermusstrain YY.Meiothermussp. formed red coloured pigment, where as Thermussp. formed yellow coloured pigment. Allof the extracts showed positive results in DPPH assay, ABTS assay and hydrogen peroxide radical scavenging assaywith best results obtained when the extracts were dissolved in water. Total antioxidant capacity assay was also highin all the extracts. Protein oxidation inhibition activity was only seen in extracts of strain YY. One-way ANOVA(analysis of variance) clearly showed that choice of solvent influenced the antioxidant capacity of all of the extracts. CONCLUSIONS: Newer and efficient antioxidative compounds are constantly being searched for, and the carotenoid extracts of RP, TP and YY have been shown to catalyze various types of antioxidative reactions, including proteinoxidation inhibition by YY. Thus, all these extracts have huge potential to be industrially and pharmaceutically useful.

Genome Sequence of the Multiple-Protease-Producing Strain Geobacillus thermoleovorans N7, a Thermophilic Bacterium Isolated from Paniphala Hot Spring, West Bengal, India.

Here, we present the draft genome sequence of Geobacillus thermoleovorans strain N7 (MCC 3175), isolated from Paniphala Hot Spring, West Bengal, India, which contains genes that encode several industrially and medically important thermostable enzymes like neutral protease, xylose isomerase, rhamnogalacturonan acetylesterase, nitrate and nitrite reductase, l-asparaginase, glutaminase, and RNase P.

Genome Sequence of the Arsenic-Resistant Haladaptatus sp. Strain R4 Isolated from Ramnagar, West Bengal, India.

Here, we present the draft genome of Haladaptatus sp. strain R4, a halophilic archaea that produces an orange-pink pigment and is capable of growing in a wide salinity range. The genome assembly shows genes for arsenic resistance, siderophore production, trehalose and glycine betaine biosynthesis, uptake and transporters of sodium, potassium, and chloride ions.

Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India.

Here we report the draft genome sequence of Meiothermus taiwanensis strain RP (MCC 2966), isolated from the Paniphala hot spring of India, which contains genes encoding for enzymes of the methyl erythritol 4-phosphate (MEP) pathway of isoprenoid biosynthesis and carotenoid backbone synthesis.

Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria.

Exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 pH) mid-temperature (55-85°C) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. To gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of Gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media with 50 µg ml(-1) vancomycin. Surprisingly, this Gram-positive-specific antibiotic eliminated the entire culturable-diversity of chemoorganotrophic and sulfur-chemolithotrophic bacteria present in the tested hot water inocula. Moreover, it also killed all the Gram-negative hot-spring isolates that were obtained in vancomycin-free media. Concurrent literature search for the description of Gram-negative thermophilic bacteria revealed that at least 16 of them were reportedly vancomycin-susceptible. While these data suggested that vancomycin-susceptibility could be a global trait of thermophilic bacteria (irrespective of their taxonomy, biogeography and Gram-character), MALDI Mass Spectroscopy of the peptidoglycans of a few Gram-negative thermophilic bacteria revealed that tandem alanines were present in the fourth and fifth positions of their muropeptide precursors (MPPs). Subsequent phylogenetic analyses revealed a close affinity between the D-alanine-D-alanine ligases (Ddl) of taxonomically-diverse Gram-negative thermophiles and the thermostable Ddl protein of Thermotoga maritima, which is well-known for its high specificity for alanine over other amino acids. The Ddl tree further illustrated a divergence between the homologs of Gram-negative thermophiles and mesophiles, which broadly coincided with vancomycin-susceptibility and vancomycin-resistance respectively. It was thus hypothesized that thermophilic Ddls have been evolutionarily selected to favor a D-ala-D-ala bonding. However, preference for D-ala-D-ala-terminated MPPs does not singlehandedly guarantee vancomycin susceptibility of thermophilic bacteria as the large and relatively-hydrophilic vancomycin molecule has to cross the outer membrane before it can inhibit peptidoglycan biosynthesis. Literature shows that many mesophilic Gram-negative bacteria also have D-ala-D-ala-terminated MPPs, but they still remain resistant to vancomycin due to the relative impermeability of their membranes. But the global vancomycin-susceptibility phenotype of thermophilic bacteria itself testifies that the drug crosses the membrane in all these cases. As a corollary, it seems quite likely that the outer membranes of thermophilic bacteria have some yet-unknown characteristic feature(s) that invariably ensures the entry of vancomycin.

Exploring 1,4-dihydroxyanthraquinone as long-range emissive ratiometric fluorescent probe for signaling Zn(2+)/PO4(3-): Ensemble utilization for live cell imaging.

Fluorescent 1,4-dihydroxyanthraquinone 1 was found to demonstrate its ratiometric signaling property upon interaction with divalent zinc (Zn(2+)). While the probe itself exhibited fluorescence emission in the yellow region (λem=544 nm and 567 nm), binding with Zn(2+) induced strong emission in the orange region (λem=600 nm) which was mainly due to a combination of CHEF and ICT mechanism. The probe was found to be highly sensitive toward the detection of zinc and the limit of detection (LOD) was calculated to be 9×10(-7) M. The possibility of using this probe for real-time analysis was strongly supported by the striking stability of fluorescence signal for more than five days with similar fluorescence intensity as observed during instant signaling. The present probe works within physiological pH range and is devoid of any interference caused by the same group elements such as Cd(2+)/Hg(2+). The probe possesses excellent excitation/emission wavelength profile and can penetrate cell membrane to image low concentration of zing inside living system. The in situ formed zinc-probe ensemble was further explored as ratiometric sensing platform for detecting another bio-relevant analyte phosphate anion through a zinc-displacement approach.

Highly photostable zinc selective molecular marker bearing flexible pivotal unit: opto-fluorescence enhancement effect and imaging applications in living systems.

Novel molecular probes for imaging zinc in biological systems are gaining interest as they help in understanding the role of zinc in regulating various bio-events. In this regard, a new C2-symmetric molecular system has been developed and successfully applied as light-up material for signaling divalent zinc with green emission. The fluorescence enhancement was highly zinc specific and this newly developed probe bears a submicromolar detection capability. While probe and the ensemble -Zn(2+) exhibited remarkably high photostability, light-triggered fluorescence enhancement was observed in the case of -Zn(2+). The nature of the -Zn(2+) complex and the associated spectral shift are further supported by theoretical calculations. As the present probe absorbs in the visible region and emits in the green, it was preferred as a potential material for imaging zinc in biological systems including animal and plant cells such as pollen grains and fish egg cells. Such fluorescence imaging of zinc revealed the efficacy of the probe in detection and localization of zinc in various biological systems.

Functional molecular lumino-materials to probe serum albumins: solid phase selective staining through noncovalent fluorescent labeling.

Selective staining of human serum albumin protein in gel electrophoresis over wide range of other protein(s) is extremely important because it contains more than 60% volume of serum fluid in human body. Given the nonexistence of suitable dye materials for selective staining of serum albumins in gel electrophoresis, we report a new class of easy synthesizable and low molecular weight staining agents based on 3-amino-N-alkyl-carbazole scaffold for selective staining of serum albumins in solid phase. A detailed structure-efficiency relationship (SER) study enabled us to develop two such potent functional molecular probes which stain both human and bovine serum albumin selectively in gel electrophoresis in the presence of other proteins and enzymes. The present gel staining process was found to be very simple and less time-consuming as compared to the conventional coomassie blue staining which in turn makes these probes a new class of serum albumin-specific staining materials in proteome research. Moreover, these molecular lumino-materials can detect serum albumins at subnanomolar level in the presence of broad spectrum of other proteins/enzymes in aqueous buffer (99.9% water, pH = 7.3) keeping the protein secondary structure intact. Our experimental and the docking simulation results show that these probes bind preferentially at 'binding site I' of both the serum proteins.

Triazole-based Zn²âº-specific molecular marker for fluorescence bioimaging.

Fluorescence bioimaging potential, both in vitro and in vivo, of a yellow emissive triazole-based molecular marker has been investigated and demonstrated. Three different kinds of cells, viz Bacillus thuringiensis, Candida albicans, and Techoma stans pollen grains were used to investigate the intracellular zinc imaging potential of 1 (in vitro studies). Fluorescence imaging of translocation of zinc through the stem of small herb, Peperomia pellucida, having transparent stem proved in vivo bioimaging capability of 1. This approach will enable in screening cell permeability and biostability of a newly developed probe. Similarly, the current method for detection and localization of zinc in Gram seed sprouts could be an easy and potential alternative of the existing analytical methods to investigate the efficiency of various strategies applied for increasing zinc-content in cereal crops. The probe-zinc ensemble has efficiently been applied for detecting phosphate-based biomolecules.

Turn-on trivalent cation selective chemodosimetric probe to image native cellular iron pools.

A new turn-on cell permeable chemodosimetric probe has been developed and its application in the selective detection of trivalent cations (Fe(3+)/Cr(3+)/Al(3+)) at a sub-nanomolar level has been demonstrated. The selectivity of over a broad spectrum of mono- and divalent metal ions was established using fluorescence spectroscopy. Moreover, the changes in the absorption spectra of in the presence of trivalent cations enabled the most bio-relevant metal ion Fe(3+) over Cr(3+)/Al(3+) to be distinguished. The probe was found to be successful in the fluorescence imaging of native cellular iron pools. The fluorescence imaging of the native iron pools of banana pith further supported the high sensitivity of towards Fe(3+) present in living systems. To the best of our knowledge, this is the first example of a turn-on chemodosimetric probe to image native cellular Fe(3+) pools.

Cysteamine-based cell-permeable Zn(2+)-specific molecular bioimaging materials: from animal to plant cells.

Structure-interaction/fluorescence relationship studies led to the development of a small chemical library of Zn(2+)-specific cysteamine-based molecular probes. The probe L5 with higher excitation/emission wavelengths, which absorbs in the visible region and emits in the green, was chosen as a model imaging material for biological studies. After successful imaging of intracellular zinc in four different kinds of cells including living organisms, plant, and animal cells, in vivo imaging potential of L5 was evaluated using plant systems. In vivo imaging of translocation of zinc through the stem of a small herb with a transparent stem, Peperomia pellucida, confirmed the stability of L5 inside biological systems and the suitability of L5 for real-time analysis. Similarly, fluorescence imaging of zinc in gram sprouts revealed the efficacy of the probe in the detection and localization of zinc in cereal crops. This imaging technique will help in knowing the efficiency of various techniques used for zinc enrichment of cereal crops. Computational analyses were carried out to better understand the structure, the formation of probe-Zn(2+) complexes, and the emission properties of these complexes.