Genome Analysis of Bacillus aryabhattai to Identify Biosynthetic Gene Clusters and In Silico Methods to Elucidate its Antimicrobial Nature

Yaraguppi, Deepak A.; Deshpande, Sanjay H.; Bagewadi, Zabin K.; Kumar, Sudeep; Muddapur, Uday M.

doi:10.1007/s10989-021-10171-6

Cited by 18 publications

(15 citation statements)

References 35 publications

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“…There was a 6.7-fold increase in production in comparison with wild iturin A, which yielded 8.86 g/L under optimized conditions (crude oil, 4.0%; yeast extract, 0.7%; NaNO3, 3.0%), as reported in our previous studies [23]. In a recent study [26], the recombinant strain HZ-PbacA showed high iturin A production owing to the replacement of the promoter PbacA in place of the promoter of the iturin A synthetase cluster.…”

Section: Expression and Purification Of His-pet-32a-iturin A Fusion P...supporting

confidence: 82%

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Gene Expression and Characterization of Iturin A Lipopeptide Biosurfactant from Bacillus aryabhattai for Enhanced Oil Recovery

Yaraguppi

Bagewadi

Mahanta

et al. 2022

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Biosurfactants are eco-friendly surface-active molecules recommended for enhanced oil recovery techniques. In the present study, a potential lipopeptide (biosurfactant) encoding the iturin A gene was synthesized from Bacillus aryabhattai. To improvise the yield of the lipopeptide for specific applications, current research tends toward engineering and expressing recombinant peptides. An iturin A gene sequence was codon-optimized, amplified with gene-specific primers, and ligated into the pET-32A expression vector to achieve high-level protein expression. The plasmid construct was transformed into an E. coli BL21 DE3 host to evaluate the expression. The highly expressed recombinant iturin A lipopeptide was purified on a nickel nitrilotriacetic acid (Ni-NTA) agarose column. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) revealed that the purity and molecular mass of iturin A was 41 kDa. The yield of recombinant iturin A was found to be 60 g/L with a 6.7-fold increase in comparison with our previously published study on the wild strain. The approach of cloning a functional fragment of partial iturin A resulted in the increased production of the lipopeptide. When motor oil was used, recombinant protein iturin A revealed a biosurfactant property with a 74 ± 1.9% emulsification index (E24). Purified recombinant protein iturin A was characterized by mass spectrometry. MALDI-TOF spectra of trypsin digestion (protein/trypsin of 50:1 and 25:1) showed desired digested mass peaks for the protein, further confirming the identity of iturin A. The iturin A structure was elucidated based on distinctive spectral bands in Raman spectra, which revealed the presence of a peptide backbone and lipid. Recombinant iturin A was employed for enhanced oil recovery through a sand-packed column that yielded 61.18 ± 0.85% additional oil. Hence, the novel approach of the high-level expression of iturin A (lipopeptide) as a promising biosurfactant employed for oil recovery from Bacillus aryabhattai is not much reported. Thus, recombinant iturin A demonstrated its promising ability for efficient oil recovery, finding specific applications in petroleum industries.

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Section: Expression and Purification Of His-pet-32a-iturin A Fusion P...supporting

confidence: 82%

“…The gene track of the lpa-14 nucleotide sequence was identified and retrieved from NCBI and showed the product obtained from the gene (nucleotide accession no. : MN006821, protein ID: QHD44466.1), and the same was confirmed from the Norine database [23,24].…”

Section: Genome Sequence Identificationsupporting

confidence: 56%

Gene Expression and Characterization of Iturin A Lipopeptide Biosurfactant from Bacillus aryabhattai for Enhanced Oil Recovery

Yaraguppi

Bagewadi

Mahanta

et al. 2022

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“…The best conformation of the protein–ligand complex was chosen based on binding energy and hydrogen bond interactions. , …”

Section: Results and Discussionmentioning

confidence: 99%

Synthesis, Structural Characterizations, and Quantum Chemical Investigations on 1-(3-Methoxy-phenyl)-3-naphthalen-1-yl-propenone

et al. 2021

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In the present study, 1-(3-methoxy-phenyl)-3-naphthalen-1-yl-propenone (MPNP) is synthesized and characterized by several experimental techniques such as Fourier transform-infrared spectroscopy (FT-IR), FT-Raman, NMR and UV–vis spectral methods. The similar techniques are also investigated by the computational method using Gaussian software. The density functional theory (DFT) method is used to obtain the optimized structure using the B3LYP/6-311++G(d,p) basis set. This optimization procedure of the molecule gives the minimum energy confirmation of the structure. The computed geometrical parameters are compared with experimental data. The experimental FT-IR and FT-Raman spectra of MPNP are obtained in the regions 4000–400 and 4000–50 cm–1 respectively. The detailed vibrational assignments of the molecule are obtained with the support of potential energy distribution. The theoretical NMR (1H and 13C) analysis is conducted by the GIAO method for its structural characterization and compared with experimental chemical shifts. The experimental UV–vis spectrum is obtained in the dimethyl sulfoxide solvent and compared with the theoretically computed spectrum by the time-dependent DFT method. In addition to these studies, other analyses such as nonlinear optical, natural bonds orbital, frontier molecular orbital, molecular electrostatic potential, and NCI have been conducted to understand the nature of the molecule. The title molecule is docked and also the drug-likeness, ADMET studies were carried out. The RBD domain bound to the ACE2 receptor during the fusion makes spike glycoprotein an elusive therapeutic target in SARS-CoV-2 infection.

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“…The system minimization was done by the implementation of OPLS_2005 force field. Once the system was prepared, the molecular dynamics production run of 50 ns was carried out with a time step of 1.2 fs and trajectory recording was done for 1000 frames [27]. RMSD (Root mean square deviation) calculation was carried out for the backbone atoms and analyzed to understand the protein-ligand interactions.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

Decipher the inhibitory potential of phytocompounds from Leptadenia reticulata on dopamine D2 receptor to enhance prolactin secretion

et al. 2022

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Dopamine is secreted by the hypothalamus, which inhibits the proliferation and effectiveness of lactotroph cells that release prolactin via dopamine D2 receptor (D2R). D2R activation inhibits lactotroph cell prolactin synthesis and regulates prolactin gene expression. Although, commercial medications are available for hypogalactia and agalactia, various plant sources significantly alleviate these problems. Leptadenia reticulata (Jivanti) is one of the important medicinal plants often consumed by nursing mothers to improve breast milk production. However, mechanism and chemical constituents involved in the inhibition of D2R by Jivanti is unclear. Therefore, in this study the phytocompounds reported from Jivanti were used for in-silico analysis to predict D2R inhibitory potential. The binding affinity value of campesterol and β-sitosterol (− 10.1 and −10.0 kcal/mol) with D2R has high revealed by molecular docking and stable interaction reveled by molecular dynamics simulation. Thus, these lead compounds could exert more D2R inhibitory activity resulting into prolactin release, which may lead to an increase in breast milk production. Although all selected compounds had fine permeation, non-toxic, and non-carcinogenic characteristics predicted by ADMET, campesterol had good solubility, absorption characteristics compared to other. Therefore, Jivanti, which is traditionally known medicinal plant, could be explored as a medication candidate to boost breast milk production.

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Genome Analysis of Bacillus aryabhattai to Identify Biosynthetic Gene Clusters and In Silico Methods to Elucidate its Antimicrobial Nature

Cited by 18 publications

References 35 publications

Gene Expression and Characterization of Iturin A Lipopeptide Biosurfactant from Bacillus aryabhattai for Enhanced Oil Recovery

Gene Expression and Characterization of Iturin A Lipopeptide Biosurfactant from Bacillus aryabhattai for Enhanced Oil Recovery

Synthesis, Structural Characterizations, and Quantum Chemical Investigations on 1-(3-Methoxy-phenyl)-3-naphthalen-1-yl-propenone

Decipher the inhibitory potential of phytocompounds from Leptadenia reticulata on dopamine D2 receptor to enhance prolactin secretion

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