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Biological and molecular approaches of the degradation or decolorization potential of the hypersaline Lake Tuz Bacillus megaterium H2 isolate

Oyewusi HA, Adedamola Akinyede K, Wahab RA, Susanti E, Syed Yaacob SN, Huyop F

J Biomol Struct Dyn, 2023 Jul 16.
PMID: 37455463 DOI: 10.1080/07391102.2023.2234040

The presence of synthetic dyes in water bodies and soil is one of the major issues affecting the global ecology, possibly impacting societal well-being adversely due to the colorants' recalcitrance and toxicity. Herein, the study spectrophotometrically monitored the ability of the Bacillus megaterium H2 azoreductase (AzrBmH2) to degrade four synthetic dyes, reactive blue 4, remazol brilliant red, thymol blue, and methyl red, followed by in-silico assessment using GROMACS. We found that the bacterium degraded as much as 60% of all four synthetic dyes at various tested concentrations. The genome analysis revealed five different azoreductase genes, which were then modeled into the AzrBmH21, AzrBmH22/3, and AzrBmH24/5 templates. The AzrBmH2-substrate complexes showed binding energies with all the dyes of between -10.6 to -6.9 kcal/mol and formed 4-6 hydrogen bonds with the predicted catalytic binding residues (His10, Glu 14, Ser 58, Met 99, Val 107, His 183, Asn184 and Gln 191). In contrast, the lowest binding energies were observed for the AzrBmH21-substrates (-10.6 to -7.9). Molecular dynamic simulations revealed that the AzrBmH21-substrate complexes were more stable (RMSD 0.2-0.25 nm, RMSF 0.05 - 0.3 nm) and implied strong bonding with the dyes. The Molecular Mechanics Poisson-Boltzmann Surface Area results also mirrored this outcome, showing the lowest azoreductase-dye binding energy in the order of AzrBmH21-RB4 (-78.18 ± 8.92 kcal/mol), AzrBmH21-RBR (-67.51 ± 7.74 kcal/mol), AzrBmH21-TB (-46.62 ± 5.23 kcal/mol) and AzrBmH21-MR (-40.78 ± 7.87 kcal/mol). In short, the study demonstrated the ability of the B. megaterium H2 to efficiently decolorize the above-said synthetic dyes, conveying the bacterium's promising use for large-scale dye remediation.Communicated by Ramaswamy H. Sarma.
Co-production of cellulose and lignin by Taguchi-optimized one-pot deep eutectic solvent-assisted ball milling pretreatment of raw oil palm leaves

Teo HL, Abdul Wahab R, Zainal-Abidin MH, Mark-Lee WF, Susanti E

Int J Biol Macromol, 2024 Nov;280(Pt 2):135787.
PMID: 39304051 DOI: 10.1016/j.ijbiomac.2024.135787

This study explores an eco-friendly delignification technique for raw oil palm leaves (OPL), highlighting the optimized conditions of choline chloride-lactic acid deep eutectic solvent (DES)-mediated ball milling pretreatment to maximize the co-production yields of highly crystalline cellulose and lignin. Our five-level-four-factor Taguchi design identified the optimal reaction settings for cellulose production (85.83 % yield, 47.28 % crystallinity) as 90-minute milling, 1500 rpm, mill-ball size ratio of 30:10, ball-to-sample mass ratio of 20:1, DES-to-sample mass ratio of 3:1. Conversely, the maximal lignin extraction yield (35.23 %) occurred optimally at 120-minute milling, 600 rpm, mill-ball size ratio of 25:5, ball-to-sample mass ratio of 20:1 and DES-to-sample mass ratio of 9:1. Statistical results showed that milling frequency (p-value ≤ 0.0001) was highly significant in improving cellulose crystallinity and yield, while DES-to-sample mass ratio (p-value ≤ 0.0001) was the most impacting on lignin yield. The thermogravimetric method affirmed the elevated cellulose thermal stability, corroborating the enhanced cellulose content (40.14 % to 73.67 %) alongside elevated crystallinity and crystallite size (3.31 to 4.72 nm) shown by X-ray diffractograms. The increased surface roughness seen in micrographs mirrored the above-said post-treatment changes. In short, our optimized one-pot dual-action pretreatment effectively delignified the raw OPL to produce cellulose-rich material with enhanced crystallinity and lignin solidity.
Taguchi-assisted multi-response improved simultaneous nanocellulose and sugar production from microcrystalline cellulose derived from raw oil palm leaves

Teo HL, Wahab RA, Mark-Lee WF, Zainal-Abidin MH, Huyop F, Susanti E

Int J Biol Macromol, 2024 Aug 25.
PMID: 39209591 DOI: 10.1016/j.ijbiomac.2024.134983

Enzymatic treatment on lignocellulosic biomass has become a trend in preparing nanocellulose (NC), but the process must be optimized to guarantee high production yield and crystallinity. This study offers insights into an innovative protocol using cultivated fungal cellulase and xylanase to improve NC production from raw oil palm leaves (OPL) using five-factor-four-level Taguchi orthogonal design for optimizing parameters, namely substrate and enzyme loading, surfactant concentration, incubation temperature and time. Statistical results revealed the best condition for producing NC (66.06 % crystallinity, 43.59 % yield) required 10 % (w/v) substrate, 1 % (v/v) enzyme, 1.4 % (w/v) Tween-80, with 72-h incubation at 30 °C. Likewise, the highest sugar yield (47.07 %) was obtained using 2.5 % (w/v) substrate, 2.0 % (v/v) enzyme, 2.0 % (w/v) Tween-80, with 72-h incubation at 60 °C. The auxiliary enzymes used in this study, i.e., xylanase, produced higher crystallinity NC, showing widths between 8 and 12 nm and lengths >1 μm and sugars at 47.07 % yield. Thus, our findings proved that optimizing the single-step enzymatic hydrolysis of raw OPL could satisfactorily produce relatively crystalline NC and sugar yield for further transformation into bio-nanocomposites and biofuels. This study presented a simple, innovative protocol for NC synthesis showing characteristics comparable to the traditionally-prepared NC, which is vital for material's commercialization.
In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET)

Khairul Anuar NFS, Abdul Wahab R, Huyop F, Normi YM, Oyewusi HA, Susanti E

J Biomol Struct Dyn, 2024 Nov 28.
PMID: 39609936 DOI: 10.1080/07391102.2024.2431655

Polyethylene terephthalate (PET) pollution is an emerging environmental hazard because of its recalcitrance to degradation. This study proposes an in silico mutagenesis of LipKV1 from Acinetobacter haemolyticus for improved lipase-PET interaction, using the PET-degrading Thermobifida cutinase (TfCut2) as the structural benchmark. Results revealed that lid deletion on LipKV1 (LipKV1_LE) facilitated the entry of PET into the active site. The mutation of several predicted amino acids into alanine expanded the LipKV1 active site for better PET binding. Docking results indicated that the LipKV1_LE mutants, Var9 (-6.2 kcal/mol), Var18 (-6.0 kcal/mol), and Var181 (-6.0 kcal/mol), produced higher binding affinities with PET than the wild-type LipKV1 (-2.5 kcal/mol) and TfCut2 (-4.6 kcal/mol), attesting that the selected mutation sites played prominent role in altering the abilities of LipKV1_LE mutants to bind to PET. Our molecular dynamics (MD) simulation results corroborated the variant-PET complexes' improved binding, mirrored by their improved conformations (RMSD ∼0.35 nm). The RMSF results also showed acceptable fluctuation limits of the LipKV1_PET mutant complexes (RMSF < 0.5 nm). Rg data of the complexes showed that they are conformationally stable, with a maximum of three H-bonds in their interaction with PET. SASA results showed that the mutations did not profoundly alter the hydrophobicity of the amino acid residues. MM-PBSA calculations on the LipKV1_PET mutant complexes estimated binding free energies between -28.29 kcal/mol to -23.25 kcal/mol, comparable to the molecular docking data. Thus, the MD data conveyed the practicality of the above-said site mutations in rationally designing the LipKV1 active site for better PET degradation.
Fulltext The Cortisol Levels, Histology, and Fine Structure of Various Tissues of Fish Gambusia affinis (Baird and Girard, 1853) after Exposure to Lead

Adam MA, Soegianto A, Risjani Y, Payus CM, Yoga RGP, Sadi NH, et al.

Scientifica (Cairo), 2023;2023:6649258.
PMID: 38046196 DOI: 10.1155/2023/6649258

BACKGROUND: Aquatic organisms demonstrate a high vulnerability to mortality when exposed to Pb, even at low concentrations. The objective of this investigation is to ascertain the histopathological alterations and cortisol concentrations in diverse tissues of Gambusia affinis, with a specific focus on the eggs and larvae, following exposure to varying concentrations of PbCl2.
METHODS: Adult specimens of G. affinis measuring 5-6 cm in length were obtained from a commercial fish breeding facility. A total of 8 fish with a 1 : 1 ratio of 4 pairs of broodstock were placed in an 8-liter aquarium. Following the adaptation phase, the broodstock underwent a spawning process that lasted for a duration of 7 days. Throughout the spawning process, assessments were conducted on the progression of the abdominal growth of the broodstock. Eggs ready to hatch and Gambusia larvae were taken and exposed to 0.1 mg/L PbCl2, 1 mg/L PbCl2, and control (without PbCl2) for 24 hours, with three replications. At the end of the experiment, histopathological analysis was conducted using the hematoxylin Ehrlich-eosin staining method and scanning electron microscopic (SEM) observation. The levels of Pb in gills were determined by employing atomic absorption spectrophotometer. The cortisol concentration in organ samples of fish was determined through the utilization of a cortisol ELISA Kit.
RESULTS: The findings of this investigation demonstrated an important bioaccumulation occurrence of Pb within the gills of Gambusia fish that were specifically subjected to 0.1 and 1 mg/L PbCl2. The histological structures of eggs and larvae that were subjected to PbCl2 exhibited impairment in comparison to the control group. The present study observed a significant elevation in cortisol levels among fish specimens that were subjected to PbCl2 exposure.
CONCLUSIONS: The findings of this investigation suggest that the occurrence of Pb is linked to a rise in cortisol concentrations in various organs of G. affinis larvae. Furthermore, the research indicates that the exposure to Pb has a notable impact on the histological alterations in the eggs and larvae of Gambusia fish, implying that they are undergoing stress as a result of the Pb exposure.