Biomineralization Potential of Bacillus subtilis,Rummeliibacillus Stabekisii and Staphylococcus Epidermidis Strains In Vitro Isolated from Speleothems,Khasi Hill Caves,Meghalaya, India

Microorganisms were isolated and identified from speleothems at Khasi hill caves, Meghalaya. The aim was to understand their biomineralization potential. Analyses of the speleothems from Krem Soitan, Krem Mawpun, and Krem Lawbah using scanning electron microscope (SEM) showed evidences for microbe–mineral interactions. SEM showed microbial reticulate and beaded filaments, cells, fiber calcites, and clusters of coccoid-like structures. A total of 113 bacterial strains were isolated and identified by a combination of conventional and molecular based tools. 105 strains that were sequenced belonged to the genus: Bacillus, Rummeliibacillus, Staphylococcus, and Brevibacterium. The BLASTn sequence search of 16S rRNA sequences with the National Centre for Biotechnology Information database to establish the identity of the strains yielded similarity scores of ≥99% with the respective organisms. The strains were identified as Bacillus simplex, Bacillus gaemokensis, Bacillus subtilis, Bacillus thuringiensis, Bacillus albus, Bacillus cereus, Bacillus anthracis, Bacillus weihenstephanensis, Rummeliibacillus stabekisii, Bacillus wiedmannii, Staphylococcus epidermidis, Rummeliibacillus pycnus, Kurthia zopfii, and Brevibacterium frigoritolerans. These strains were tested for biomineralization on B-4 medium. Five strains (B. subtilis, R. stabekisii, Staphylococcus epiderdimis, B. cereus, and B. wiedmannii) had the capability to precipitate biominerals in vitro. B. subtilis, R. stabekisii, and S. epidermidis precipitated 0.24, 0.36, and 0.35 g/L of biominerals at 22°C at the end of the four week experiment period. These strains increased the pH of the medium from 7 to 8.95. The precipitated biominerals were imaged using an ultra-high resolution field emission SEM. X-ray diffraction of the biomineral precipitated by R. stabekisii showed that it was composed of vaterite and jungite. Whereas S. epidermidis showed that it was composed of calcite, vaterite, and jungite. B. subtilis produced small, circular calcite crystals. This is the first comprehensive report on the possible evidences about the role of R. stabekisii and S. epidermidis in calcite precipitation isolated from speleothems in the Indian caves. These results allow us to postulate that the identified strains have biomineralization potential. Further evidences of the coexistence of exopolysaccharides, whisker fiber calcites, microbial filaments, and coccoid-like forms point to biogenic inputs in the cave mineral formations.     

Isolation and characterization of a reducing polyketide synthase gene from the lichen-forming fungus Usnea longissima

The reducing polyketide synthases found in filamentous fungi are involved in the biosynthesis of many drugs and toxins. Lichens produce bioactive polyketides, but the roles of reducing polyketide synthases in lichens remain to be clearly elucidated. In this study, a reducing polyketide synthase gene (U1PKS3) was isolated and characterized from a cultured mycobiont of Usnea longissima. Complete sequence information regarding U1PKS3 (6,519 bp) was obtained by screening a fosmid genomic library. A U1PKS3 sequence analysis suggested that it contains features of a reducing fungal type I polyketide synthase with β-ketoacyl synthase (KS), acyltransferase (AT), dehydratase (DH), enoyl reductase (ER), ketoacyl reducatse (KR), and acyl carrier protein (ACP) domains. This domain structure was similar to the structure of ccRadsl, which is known to be involved in resorcylic acid lactone biosynthesis in Chaetomium chiversii. The results of phylogenetic analysis located U1PKS3 in the clade of reducing polyketide synthases. RT-PCR analysis results demonstrated that UIPKS3 had six intervening introns and that UIPKS3 expression was upregulated by glucose, sorbitol, inositol, and mannitol.     

Investigation on the role of p53 codon 72 polymorphism and interactions with tobacco, betel quid, and alcohol in susceptibility to cancers in a high-risk population from North East India

The association of TP53 codon 72 polymorphism with cancer susceptibility remains uncertain and varies with ethnicity. Northeast India represents a geographically, culturally, and ethnically isolated population. The area reports high rate of tobacco usage in a variety of ways of consumption, compared with the rest of Indian population. A total of 411 cancer patients (161 lung, 134 gastric, and 116 oral) and 282 normal controls from the ethnic population were analyzed for p53 codon 72 polymorphism by polymerase chain reaction-restriction fragment length polymorphism. No significant difference in genotypic distribution of p53 between cases and controls was observed. Results suggested betel quid chewing as a major risk factor for all the three cancers (odds ratio [OR]=3.54, confidence interval [CI]=2.01-6.25, p<0.001; OR=1.74, CI=1.04-2.92, p=0.03; and OR=1.85, CI=1.02-3.33, p=0.04 for lung, gastric, and oral cancers, respectively). Tobacco smoking was associated with risk of lung and oral cancers (OR=1.88, CI=1.11-3.19, p=0.01 and OR=1.68, CI=1.00-2.81, p=0.04). Interactions between p53 genotypes and risk factors were analyzed to look for gene-environment interactions. Interaction of smoking and p53 genotype was significant only for oral cancer. Interactions of betel quid with p53 genotypes in lung cancer showed significant increase for all the three genotypes, indicating a major role of betel quid (OR=5.90, CI=1.67-20.81, p=0.006; OR=5.44, CI=1.67-17.75, p=0.005; and OR=5.84, CI=1.70-19.97, p=0.005 for Arg/Arg, Arg/Pro, and Pro/Pro, respectively). In conclusion, high incidence of these cancers in northeast India might be an outcome of risk habits; further, tissue- and carcinogen-specific risk modification by p53 gene is probable.     

Novel Route for Agmatine Catabolism in Aspergillus niger Involves 4-Guanidinobutyrase

Agmatine, a significant polyamine in bacteria and plants, mostly arises from the decarboxylation of arginine. The functional importance of agmatine in fungi is poorly understood. The metabolism of agmatine and related guanidinium group-containing compounds in Aspergillus niger was explored through growth, metabolite, and enzyme studies. The fungus was able to metabolize and grow on l-arginine, agmatine, or 4-guanidinobutyrate as the sole nitrogen source. Whereas arginase defined the only route for arginine catabolism, biochemical and bioinformatics approaches suggested the absence of arginine decarboxylase in A. niger. Efficient utilization by the parent strain and also by its arginase knockout implied an arginase-independent catabolic route for agmatine. Urea and 4-guanidinobutyrate were detected in the spent medium during growth on agmatine. The agmatine-grown A. niger mycelia contained significant levels of amine oxidase, 4-guanidinobutyraldehyde dehydrogenase, 4-guanidinobutyrase (GBase), and succinic semialdehyde dehydrogenase, but no agmatinase activity was detected. Taken together, the results support a novel route for agmatine utilization in A. niger. The catabolism of agmatine by way of 4-guanidinobutyrate to 4-aminobutyrate into the Krebs cycle is the first report of such a pathway in any organism. A. niger GBase peptide fragments were identified by tandem mass spectrometry analysis. The corresponding open reading frame from the A. niger NCIM 565 genome was located and cloned. Subsequent expression of GBase in both Escherichia coli and A. niger along with its disruption in A. niger functionally defined the GBase locus (gbu) in the A. niger genome.     

Acetoxy drug: protein transacetylase of buffalo liver-characterization and mass spectrometry of the acetylated protein product

The purification and characterization of the buffalo liver microsomal transacetylase (TAase) catalyzing the transfer of acetyl groups from a model acetoxy drug: 7,8-diacetoxy-4-methylcoumarin (DAMC) to GST3-3 has been described here. The enzyme was routinely assayed using DAMC and cytosolic GST as the substrates and was partially purified from microsomes of the buffalo liver. The enzyme was found to have approximate molecular of weight 65 kDa. The action of TAase and DAMC on liver cytosolic GST resulted in the formation of monoacetoxymonohydroxy-4-methylcoumarin (MAMHC) and 7,8-dihydroxy-4-methylcoumarin (DHMC), although the former was the major metabolite. The buffalo liver microsomal TAase exhibited hyperbolic kinetics and yielded K(m) (1667 microM) and V(max) (192 units) when the concentration of DAMC was varied keeping the concentration of GST constant. After having characterized the nature of the substrates and a product of the TAase-catalyzed reaction, we set out to identify the acetylated protein which is another product of the reaction. GST3-3 was used as a model protein substrate for the action of TAase using DAMC as the acetyl donor. The subunit of control and modified GST3-3 were separated by SDS-polyacrylamide gel electrophoresis (PAGE) and digested with trypsin. The tryptic peptides were extracted from the gel pieces and analyzed by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOFMS). The data search for calibrated and labeled mass peaks of peptides was performed on the Matrix Science Server using the search engine Mascot. The peptide maps so obtained covered 97% of the GST3-3 sequence. On comparison of MALDI peptide maps of modified and control GST, seven new peaks were recognized corresponding to the potentially acetylated peptides in peptide map. The mass value of each of them was 42 Da higher than the theoretical mass of a non-modified GST3-3 tryptic peptide, strongly suggesting acetylation. By examining the fragmentation patterns and by comparing experimental and predicted values for MS/MS daughter ions, the identity of the seven acetylated GST tryptic peptides could be confirmed by the application of LC/MS/MS. In the modified GST, N-terminal proline and six lysines (Lys(51), Lys(82), Lys(123), Lsy(181), Lys(191) and Lys(210)) were found to be acetylated. The structure of acetylated GST revealed that the lysines that underwent acetylation were peripheral in positions.     

Cultivable Bacterial Diversity of Alkaline Lonar Lake, India

Aerobic, alkaliphilic bacteria were isolated and characterized from water and sediment samples collected in the winter season, January 2002 from alkaline Lonar lake, India, having pH 10.5. The total number of microorganisms in the sediment and water samples was found to be 10²–10⁶ cfu g⁻¹ and 10²–10⁴ cfu ml⁻¹, respectively. One hundred and ninety-six strains were isolated using different enrichment media. To study the bacterial diversity of Lonar lake and to select the bacterial strains for further characterization, screening was done on the basis of pH and salt tolerance of the isolates. Sixty-four isolates were subjected to phenotypic, biochemical characterization and 16S rRNA sequencing. Out of 64, 31 bacterial isolates were selected on the basis of their enzyme profile and further subjected to phylogenetic analysis. Phylogenetic analysis indicated that most of the Lonar lake isolates were related to the phylum Firmicutes, containing Low G+C, Gram-positive bacteria, with different genera: Bacillus, Paenibacillus, Alkalibacillus, Exiguobacterium, Planococcus, Enterococcus and Vagococcus. Seven strains constituted a Gram-negative bacterial group, with different genera: Halomonas, Stenotrophomonas and Providencia affiliated to γ-Proteobacteria, Alcaligenes to β-Proteobacteria and Paracoccus to α-Proteobacteria. Only five isolates were High G+C, Gram-positive bacteria associated with phylum Actinobacteria, with various genera: Cellulosimicrobium, Dietzia, Arthrobacter and Micrococcus. Despite the alkaline pH of the Lonar lake, most of the strains were alkalitolerant and only two strains were obligate alkaliphilic. Most of the isolates produced biotechnologically important enzymes at alkaline pH, while only two isolates (ARI 351 and ARI 341) showed the presence of polyhydroxyalkcanoate (PHA) and exopolysaccharide (EPS), respectively.     

Novel synthesis of 2'-O-methylguanosine

An efficient and chemoselective synthesis of 2'-O-methylguanosine (6) has been accomplished in high yield without protection of the guanine base. The salient feature of the synthesis of 6 lies in the application of methylene-bis-(diisopropylsilyl chloride), (MDPSCl(2), 2) as a new 3',5'-O-protecting group for nucleosides. Use of CH(3)Cl as a weak electrophile and NaHMDS as a mild base was crucial to the success of the 2'-O-methylation of 3',5'-O-protected guanosine.     

Metabolic fate of glutamate and evaluation of flux through the 4-aminobutyrate (GABA) shunt in Aspergillus niger

Accumulation of GABA and a concurrent block in the Krebs cycle suggest a functional GABA bypass in the acidogenic Aspergillus niger. Apart from the demonstration of enzyme machinery required, a direct measurement of flux through this glutamate decarboxylation loop was attempted. The distribution of carbon from glucose and glutamate was studied using A. niger mycelia grown on different media. The uptake and incorporation of (14)C label into organic acids and amino acids was followed by paper chromatography. Flow of label from glucose into citrate, glutamate and GABA increased in cells harvested at later stages of acidogenic growth. Very little citrate was derived from glutamate while ten times more label reached GABA from labeled glutamate. Radioactivity from L-[U-(14)C]glutamate and not from L-[1-(14)C]glutamate was recovered in GABA. This demonstrated that alpha-decarboxylation of L-glutamate was the source of GABA. Unless grown on GABA, A. niger mycelia did not take up externally supplied GABA. A direct measure of GABA shunt flux was thus not feasible. Therefore a combination of metabolite balance technique and the kinetic approach was applied to evaluate flux from glutamate to succinate in normal and acidogenic A. niger. The flux relative to TCA cycle was estimated by using uptake rate for radiolabeled glutamate, rate of accumulation of certain metabolites and the reactions of GABA metabolism. The analysis indicated that GABA shunt is operative in A. niger and its operation is enhanced during acidogenic growth of the fungus. This is the first report of an estimation of the flux through GABA shunt in a fungus.     

Energetic Pathway Sampling in a Protein Interaction Domain

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