Displaying publications 1 - 20 of 223 in total

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  1. Cross-linked enzyme aggregates of polyethylene terephthalate hydrolyse (PETase) from Ideonella sakaiensis for the improvement of plastic degradation
    Lee YL, Jaafar NR, Ling JG, Huyop F, Abu Bakar FD, Rahman RA, et al.
    Int J Biol Macromol, 2024 Apr;263(Pt 1):130284.
    PMID: 38382786 DOI: 10.1016/j.ijbiomac.2024.130284
    Polyethylene terephthalate (PET) is one of the most produced plastics globally and its accumulation in the environment causes harm to the ecosystem. Polyethylene terephthalate hydrolyse (PETase) is an enzyme that can degrade PET into its monomers. However, free PETase lacks operational stabilities and is not reusable. In this study, development of cross-linked enzyme aggregate (CLEA) of PETase using amylopectin (Amy) as cross-linker was introduced to solve the limitations of free PETase. PETase-Amy-CLEA exhibited activity recovery of 81.9 % at its best immobilization condition. Furthermore, PETase-Amy-CLEA exhibited 1.37-, 2.75-, 2.28- and 1.36-fold higher half-lives than free PETase at 50 °C, 45 °C, 40 °C and 35 °C respectively. Moreover, PETase-Amy-CLEA showed broader pH stability from pH 5 to 10 and could be reused up to 5 cycles. PETase-Amy-CLEA retained >70 % of initial activity after 40 days of storage at 4 °C. In addition, lower Km of PETase-Amy-CLEA indicated better substrate affinity than free enzyme. PETase-Amy-CLEA corroded PET better and products yielded was 66.7 % higher than free PETase after 32 h of treatment. Hence, the enhanced operational stabilities, storage stability, reusability and plastic degradation ability are believed to make PETase-Amy-CLEA a promising biocatalyst in plastic degradation.
    Matched MeSH terms: Hydrolases/metabolism
  2. Application of different feeding strategies in fed batch culture for pullulanase production using sago starch
    R S, M S M, E M S, K O NA, A A S, K K
    Carbohydr Polym, 2014 Feb 15;102:962-9.
    PMID: 24507370 DOI: 10.1016/j.carbpol.2013.10.031
    The production of pullulanase by Bacillus flavothermus KWF-1 in batch and fed batch culture were compared using 2L bioreactor. In batch culture, 0.0803 U/mL of pullulanase activity with specific activity of 0.0213 U/mg was produced by controlling the agitation speed and temperature at 200 rpm and 50 °C, respectively. Fed batch production was studied by feeding the culture with different sago starch concentrations in various feeding modes for enhanced pullulanase production. Exponential feeding mode at dilution rate of 0.01/h was the preeminent strategy for enhanced pullulanase production of 0.1710 U/mL with specific activity of 0.066 U/mg. It had shown an increment of pullulanase production and specific activity by 2.1 and 3.1-fold, respectively when compared to batch culture. Increment of pullulanase activity in exponential feeding mode improved hydrolyzation of sago starch into maltotriose and panose by 4.5 and 2.5-fold respectively compared to batch system.
    Matched MeSH terms: Glycoside Hydrolases/biosynthesis*
  3. Strategy in manipulating transglycosylation activity of glycosyl hydrolase for oligosaccharide production
    Abdul Manas NH, Md Illias R, Mahadi NM
    Crit Rev Biotechnol, 2018 Mar;38(2):272-293.
    PMID: 28683572 DOI: 10.1080/07388551.2017.1339664
    BACKGROUND: The increasing market demand for oligosaccharides has intensified the need for efficient biocatalysts. Glycosyl hydrolases (GHs) are still gaining popularity as biocatalyst for oligosaccharides synthesis owing to its simple reaction and high selectivity.

    PURPOSE: Over the years, research has advanced mainly directing to one goal; to reduce hydrolysis activity of GHs for increased transglycosylation activity in achieving high production of oligosaccharides.

    DESIGN AND METHODS: This review concisely presents the strategies to increase transglycosylation activity of GHs for oligosaccharides synthesis, focusing on controlling the reaction equilibrium, and protein engineering. Various modifications of the subsites of GHs have been demonstrated to significantly modulate the hydrolysis and transglycosylation activity of the enzymes. The clear insight of the roles of each amino acid in these sites provides a platform for designing an enzyme that could synthesize a specific oligosaccharide product.

    CONCLUSIONS: The key strategies presented here are important for future improvement of GHs as a biocatalyst for oligosaccharide synthesis.

    Matched MeSH terms: Hydrolases/chemistry*
  4. Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria
    Oyewusi HA, Wahab RA, Huyop F
    Mol Biol Rep, 2021 Mar;48(3):2687-2701.
    PMID: 33650078 DOI: 10.1007/s11033-021-06239-7
    An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.
    Matched MeSH terms: Hydrolases/biosynthesis*; Hydrolases/genetics; Hydrolases/metabolism; Hydrolases/chemistry
  5. In silico analysis of a putative dehalogenase from the genome of halophilic bacterium Halomonas smyrnensis AAD6T
    Oyewusi HA, Akinyede KA, Abdul Wahab R, Huyop F
    J Biomol Struct Dyn, 2023 Jan;41(1):319-335.
    PMID: 34854349 DOI: 10.1080/07391102.2021.2006085
    Microbial-assisted removal of natural or synthetic pollutants is the prevailing green, low-cost technology to treat polluted environments. However, the challenge with enzyme-assisted bioremediation is the laborious nature of dehalogenase-producing microorganisms' bioprospecting. This bottleneck could be circumvented by in-silico analysis of certain microorganisms' whole-genome sequences to predict their protein functions and enzyme versatility for improved biotechnological applications. Herein, this study performed structural analysis on a dehalogenase (DehHsAAD6) from the genome of Halomonas smyrnensis AAD6 by molecular docking and molecular dynamic (MD) simulations. Other bioinformatics tools were also employed to identify substrate preference (haloacids and haloacetates) of the DehHsAAD6. The DehHsAAD6 preferentially degraded haloacids and haloacetates (-3.2-4.8 kcal/mol) and which formed three hydrogen bonds with Tyr12, Lys46, and Asp182. MD simulations data revealed the higher stability of DehHsAAD6-haloacid- (RMSD 0.22-0.3 nm) and DehHsAAD6-haloacetates (RMSF 0.05-0.14 nm) complexes, with the DehHsAAD6-L-2CP complex being the most stable. The detail of molecular docking calculations ranked complexes with the lowest binding free energies as: DehHsAAD6-L-2CP complex (-4.8 kcal/mol) = DehHsAAD6-MCA (-4.8 kcal/mol) < DehHsAAD6-TCA (-4.5 kcal/mol) < DehHsAAD6-2,3-DCP (-4.1 kcal/mol) < DehHsAAD6-D-2CP (-3.9 kcal/mol) < DehHsAAD6-2,2-DCP (-3.5 kcal/mol) < DehHsAAD6-3CP (-3.2 kcal/mol). In a nutshell, the study findings offer valuable perceptions into the elucidation of possible reaction mechanisms of dehalogenases for extended substrate specificity and higher catalytic activity.Communicated by Ramaswamy H. Sarma.
    Matched MeSH terms: Hydrolases/genetics; Hydrolases/chemistry
  6. Fulltext Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil
    Goh KM, Chan KG, Yaakop AS, Chan CS, Ee R, Tan WS, et al.
    Genome Announc, 2015;3(3).
    PMID: 25999554 DOI: 10.1128/genomeA.00512-15
    Jeotgalibacillus soli, a bacterium capable of degrading N-acyl homoserine lactone, was isolated from a soil sample in Portugal. J. soli constitutes the only Jeotgalibacillus species isolated from a non-marine source. Here, the draft genome, several interesting glycosyl hydrolases, and its putative N-acyl homoserine lactonases are presented.
    Matched MeSH terms: Carboxylic Ester Hydrolases; Hydrolases
  7. Fulltext Evaluation of Aqueous Biphasic Electrophoresis System Based on Halide-Free Ionic Liquids for Direct Recovery of Keratinase
    Kee PE, Yim HS, Kondo A, Lan JC, Ng HS
    Mar Drugs, 2021 Aug 17;19(8).
    PMID: 34436302 DOI: 10.3390/md19080463
    Aqueous biphasic electrophoresis system (ABES) incorporates electric fields into the biphasic system to separate the target biomolecules from crude feedstock. Ionic liquid (IL) is regarded as an excellent candidate as the phase-forming components for ABES because of the great electrical conductivity, which can promote the electromigration of biomolecules in ABES, and thereby enhances the separation efficiency of the target biomolecules from crude feedstock. The application of electric fields to the conventional biphasic system expedites the phase settling time of the biphasic system, which eases the subsequent scaling-up steps and reduces the overall processing time of the recovery process. Alkyl sulphate-based IL is a green and economical halide-free surfactant when compared to the other halide-containing IL. The feasibility of halide-free IL-based ABES to recover Kytococcus sedentarius TWHK01 keratinase was studied. Optimum partition coefficient (Ke = 7.53 ± 0.35) and yield (YT = 80.36% ± 0.71) were recorded with IL-ABES comprised of 15.0% (w/w) [EMIM][ESO4], 20.0% (w/w) sodium carbonate and 15% (w/w) crude feedstock. Selectivity (S) of 5.75 ± 0.27 was obtained with the IL-ABES operated at operation time of 5 min with 10 V voltage supplied. Halide-free IL is proven to be a potential phase-forming component of IL-ABES for large-scale recovery of keratinase.
    Matched MeSH terms: Peptide Hydrolases/chemistry*
  8. Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey
    Wahhab BH, Oyewusi HA, Wahab RA, Mohammad Hood MH, Abdul Hamid AA, Al-Nimer MS, et al.
    J Biomol Struct Dyn, 2024;42(3):1429-1442.
    PMID: 37038649 DOI: 10.1080/07391102.2023.2199870
    This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of -2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of -4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (-21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.Communicated by Ramaswamy H. Sarma.
    Matched MeSH terms: Hydrolases*
  9. Expression and biochemical characterization of a novel thermostable alkaline β-1,3-1,4-glucanase (lichenase) from an alkaliphilic Bacillus lehensis G1
    Mat Yajit NL, Fazlin Hashim NH, Illias RM, Abdul Murad AM
    Protein Expr Purif, 2024 Jul;219:106486.
    PMID: 38642864 DOI: 10.1016/j.pep.2024.106486
    New thermostable β-1,3-1,4-glucanase (lichenase) designated as Blg29 was expressed and purified from a locally isolated alkaliphilic bacteria Bacillus lehensis G1. The genome sequence of B. lehensis predicted an open reading frame of Blg29 with a deduced of 249 amino acids and a molecular weight of 28.99 kDa. The gene encoding for Blg29 was successfully amplified via PCR and subsequently expressed as a recombinant protein using the E. coli expression system. Recombinant Blg29 was produced as a soluble form and further purified via immobilized metal ion affinity chromatography (IMAC). Based on biochemical characterization, recombinant Blg29 showed optimal activity at pH9 and temperature 60 °C respectively. This enzyme was stable for more than 2 h, incubated at 50 °C, and could withstand ∼50 % of its activity at 70 °C for an hour and a half. No significant effect on Blg29 was observed when incubated with metal ions except for a small increase with ion Ca2+. Blg29 showed high substrate activity towards lichenan where Vm, Km, Kcat, and kcat/Km values were 2040.82 μmolmin‾1mg‾1, 4.69 mg/mL, and 986.39 s‾1 and 210.32 mLs‾1mg‾1 respectively. The high thermostability and activity make this enzyme useable for a broad prospect in industry applications.
    Matched MeSH terms: Glycoside Hydrolases/biosynthesis; Glycoside Hydrolases/genetics; Glycoside Hydrolases/isolation & purification; Glycoside Hydrolases/metabolism; Glycoside Hydrolases/chemistry
  10. Crystal structure of a neoagarobiose-producing GH16 family β-agarase from Persicobacter sp. CCB-QB2
    Teh AH, Fazli NH, Furusawa G
    Appl Microbiol Biotechnol, 2020 Jan;104(2):633-641.
    PMID: 31784792 DOI: 10.1007/s00253-019-10237-y
    PdAgaC from the marine bacterium Persicobacter sp. CCB-QB2 is a β-agarase belonging to the glycoside hydrolase family 16 (GH16). It is one of only a handful of endo-acting GH16 β-agarases able to degrade agar completely to produce neoagarobiose (NA2). The crystal structure of PdAgaC's catalytic domain, which has one of the highest Vmax value at 2.9 × 103 U/mg, was determined in order to understand its unique mechanism. The catalytic domain is made up of a typical β-jelly roll fold with two additional insertions, and a well-conserved but wider substrate-binding cleft with some minor changes. Among the unique differences, two unconserved residues, Asn226 and Arg286, may potentially contribute additional hydrogen bonds to subsites -1 and +2, respectively, while a third, His185 from one of the additional insertions, may further contribute another bond to subsite +2. These additional hydrogen bonds may probably have enhanced PdAgaC's affinity for short agaro-oligosaccharides such as neoagarotetraose (NA4), rendering it capable of binding NA4 strongly enough for rapid degradation into NA2.
    Matched MeSH terms: Glycoside Hydrolases/metabolism; Glycoside Hydrolases/chemistry*
  11. Effects of single and co-immobilization on the product specificity of type I pullulanase from Anoxybacillus sp. SK3-4
    Kahar UM, Chan KG, Sani MH, Mohd Noh NI, Goh KM
    Int J Biol Macromol, 2017 Nov;104(Pt A):322-332.
    PMID: 28610926 DOI: 10.1016/j.ijbiomac.2017.06.054
    Type I pullulanase from Anoxybacillus sp. SK3-4 (PulASK) is an unusual debranching enzyme that specifically hydrolyzes starch α-1,6 linkages at long branches producing oligosaccharides (≥G8), but is nonreactive against short branches; thus, incapable of producing reducing sugars (G1-G7). We report on the effects of both single and co-immobilization of PulASK on product specificity. PulASK was purified and immobilized through covalent attachment to three epoxides (ReliZyme EP403/M, Immobead IB-150P, and Immobead IB-150A) and an amino-epoxide (ReliZyme HFA403/M) activated supports. Following immobilization, all PulASK derivatives were active on both short and long branches in starch producing reducing sugars (predominantly maltotriose) and oligosaccharides (≥G8), respectively, a feature that is absent in the free enzyme. This study also demonstrated that co-immobilization of PulASK and α-amylase from Anoxybacillus sp. SK3-4 (TASKA) on ReliZyme HFA403/M significantly changed the product specificity compared to the free enzymes alone or individually immobilized enzymes. In conclusion, individual or co-immobilization caused changes in the product specificity, presumably due to changes in the enzyme binding pocket caused by the influence of carrier surface properties (hydrophobic or hydrophilic) and the lengths of the spacer arms.
    Matched MeSH terms: Glycoside Hydrolases/metabolism*; Glycoside Hydrolases/chemistry*
  12. Fulltext Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola
    Looi HK, Toh YF, Yew SM, Na SL, Tan YC, Chong PS, et al.
    PeerJ, 2017;5:e2841.
    PMID: 28149676 DOI: 10.7717/peerj.2841
    Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008). The isolation of UM 591 from a patient's contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases. The assembly size of UM 591 genome is 41.8 Mbp, and a total of 13,531 (≥99 bp) genes have been predicted. UM 591 is enriched with genes that encode for glycoside hydrolases, carbohydrate esterases, auxiliary activity enzymes and cell wall degrading enzymes. Virulent genes comprising of CAZymes, peptidases, and hypervirulence-associated cutinases were found to be present in the fungal genome. Comparative analysis result shows that UM 591 possesses higher number of carbohydrate esterases family 10 (CE10) CAZymes compared to other species of fungi in this study, and these enzymes hydrolyses wide range of carbohydrate and non-carbohydrate substrates. Putative melanin, siderophore, ent-kaurene, and lycopene biosynthesis gene clusters are predicted, and these gene clusters denote that UM 591 are capable of protecting itself from the UV and chemical stresses, allowing it to adapt to different environment. Putative sterigmatocystin, HC-toxin, cercosporin, and gliotoxin biosynthesis gene cluster are predicted. This finding have highlighted the necrotrophic and invasive nature of UM 591.
    Matched MeSH terms: Carboxylic Ester Hydrolases; Glycoside Hydrolases; Peptide Hydrolases
  13. A comparative study of cobra (Naja) venom enzymes
    Tan NH, Tan CS
    Comp. Biochem. Physiol., B, 1988;90(4):745-50.
    PMID: 2854766
    1. The L-amino acid oxidase, hyaluronidase, alkaline phosphomonoesterase, protease, phosphodiesterase, acetylcholinesterase, phospholipase A and 5'-nucleotidase activities of 47 samples of venoms from all the six species of cobra (Naja), including five subspecies of Naja naja, were examined. 2. The results demonstrated interspecific differences in the venom contents of phospholipase A, acetylcholinesterase, hyaluronidase and phosphodiesterase. These differences in venom enzyme contents can be used for the differentiation of species of the genus Naja. 3. Thus, our results revealed a correlation between the enzyme composition of venom and the taxonomic status of the snake at the species level for the genus Naja.
    Matched MeSH terms: Peptide Hydrolases/analysis; Phosphoric Diester Hydrolases/analysis; Phosphoric Monoester Hydrolases/analysis
  14. Fulltext Biotechnological Aspects and Perspective of Microbial Keratinase Production
    Gopinath SC, Anbu P, Lakshmipriya T, Tang TH, Chen Y, Hashim U, et al.
    Biomed Res Int, 2015;2015:140726.
    PMID: 26180780 DOI: 10.1155/2015/140726
    Keratinases are proteolytic enzymes predominantly active when keratin substrates are available that attack disulfide bridges in the keratin to convert them from complex to simplified forms. Keratinases are essential in preparation of animal nutrients, protein supplements, leather manufacture, textile processing, detergent formulation, feather meal processing for feed and fertilizer, the pharmaceutical and biomedical industries, and waste management. Accordingly, it is necessary to develop a method for continuous production of keratinase from reliable sources that can be easily managed. Microbial keratinase is less expensive than conventionally produced keratinase and can be obtained from fungi, bacteria, and actinomycetes. In this overview, the expansion of information about microbial keratinases and important considerations in keratinase production are discussed.
    Matched MeSH terms: Peptide Hydrolases/chemistry*
  15. A comparative study of the biological activities of venoms from snakes of the genus Agkistrodon (moccasins and copperheads)
    Tan NH, Ponnudurai G
    Comp. Biochem. Physiol., B, 1990;95(3):577-82.
    PMID: 2158874
    1. The hemorrhagic, procoagulant, anticoagulant, phosphodiesterase, alkaline phosphomonoesterase, 5'-nucleotidase, hyaluronidase, arginine ester hydrolase, phospholipase A, L-amino acid oxidase and protease activities of 31 samples of venom from three species of Agkistrodon (A. bilineatus, A. contortrix and A. piscivorus) and 10 venom samples from five other related species belonging to the same tribe of Agkistrodontini were examined. 2. The results indicate that interspecific differences in certain biological activities of the Agkistrodon venoms are more marked than individual variations of the activities, and that these differences can be used for differentiation of the species. Particularly useful for this purpose are the phosphodiesterase, arginine ester hydrolase and anticoagulant activities of the venoms. 3. Venoms of the subspecies of A. contortrix and A. piscivorus do not differ significantly in their biological activities.
    Matched MeSH terms: Carboxylic Ester Hydrolases/metabolism; Peptide Hydrolases/metabolism; Phosphoric Diester Hydrolases/metabolism; Phosphoric Monoester Hydrolases/metabolism
  16. EPOXID HYDROLASE SINGLE GENE POLYMORPHISM (RS1051740) AND SEVERITY OF CHRONIC OBSTRUCTIVE DISEASE
    Antonova I, Gridnyev O, Galchinskaya V
    Wiad Lek, 2022;75(11 pt 2):2779-2784.
    PMID: 36591768 DOI: 10.36740/WLek202211211
    OBJECTIVE: The aim: The aim of the present study was to establish a link between polymorphic variants of the microsomal epoxide hydrolase gene and the severity of COPD in patients with COPD and coronary heart disease.

    PATIENTS AND METHODS: Materials and methods: The study included 128 patients with COPD and IHD, who were divided into two groups: group 1 included 72 patients with in¬frequent exacerbations of COPD (0-1 per year) and group 2 included 56 patients with frequent exacerbations of COPD (exacerbation of COPD ≥2 per year). The control groups consisted of 15 smokers without COPD and IHD, 11 practically healthy non-smokers and 11 patients with IHD who do not smoke. All patients underwent DNA isolation and purification, followed by determination of the Tyr113His polymorphism of the EPHX1 microsomal epoxide hydrolase gene (rs1051740).

    RESULTS: Results: There was a significant association of the carriage of the CC genotype of the EPHX1 gene in patients with COPD and IHD (RO = 21.326 [95.0% CI 4.217-107.846], p <0.001) with a more severe course of COPD compared with the TT genotype of the EPHX1 gene.

    CONCLUSION: Conclusions: Patients with COPD and coronary heart disease who were carriers of a homozygous variant СС of the EPHX1 gene have a reliable association with a more severe course of COPD with frequent exacerbations (higher class according to GOLD classification and more severe symptoms of COPD according to the СAT questionnaire).

    Matched MeSH terms: Hydrolases/genetics
  17. Response of soil microbial glycoside hydrolase family 6 cellulolytic population to lignocellulosic biochar reveals biochar stability toward microbial degradation
    Halmi MFA, Simarani K
    J Environ Qual, 2024;53(4):546-551.
    PMID: 38840421 DOI: 10.1002/jeq2.20588
    Biochar produced from lignocellulosic biomass offers an opportunity to recycle waste into a valuable soil amendment. The application of biochar has been proposed to mitigate climate change by sequestering carbon in the soil. However, the field impact of biochar treatment on the cellulolytic microbial populations involved in the earlier steps of cellulose degradation is poorly understood. A field trial spanning three consecutive crop cycles of Zea mays was conducted in a degraded tropical Ultisol of Peninsular Malaysia. The soil was amended with two contrasting biochar made from oil palm kernel shells (pyrolyzed at 400°C) and rice husks (gasified at 800°C) with or without fertilizer supplementation. Soil samples were taken at each harvesting stage and analyzed for total organic carbon, labile active organic carbon, total cellulase, and β-glucosidase. Microbial glycoside hydrolase family 6 (GH6) cellulase genes and transcripts, involved in the early steps of cellulose degradation, were quantified from the extracted soil deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), respectively. Total organic carbon, labile active organic carbon, and β-glucosidase activity were significantly increased, while no effect on total cellulase activity was found. Both biochars stimulated the total population (DNA-derived) abundance of soil microorganisms harboring the GH6 cellulase genes. The biochar amendment did not affect the active population (RNA-derived) of the GH6 cellulolytic community, showing no significant changes in transcript expression. This indirectly corroborates the role of biochar as a potential carbon sequester in the soil.
    Matched MeSH terms: Glycoside Hydrolases/metabolism
  18. Cloning, expression and characterization of a novel cold‑adapted GDSL family esterase from Photobacterium sp. strain J15
    Shakiba MH, Ali MS, Rahman RN, Salleh AB, Leow TC
    Extremophiles, 2016 Jan;20(1):44-55.
    PMID: 26475626 DOI: 10.1007/s00792-015-0796-4
    The gene encoding for a novel cold-adapted enzyme from family II of bacterial classification (GDSL family) was cloned from the genomic DNA of Photobacterium sp. strain J15 in an Escherichia coli system, yielding a recombinant 36 kDa J15 GDSL esterase which was purified in two steps with a final yield and purification of 38.6 and 15.3 respectively. Characterization of the biochemical properties showed the J15 GDSL esterase had maximum activity at 20 °C and pH 8.0, was stable at 10 °C for 3 h and retained 50 % of its activity after a 6 h incubation at 10 °C. The enzyme was activated by Tween-20, -60 and Triton-X100 and inhibited by 1 mM Sodium dodecyl sulphate (SDS), while β-mercaptoethanol and Dithiothreitol (DTT) enhanced activity by 4.3 and 5.4 fold respectively. These results showed the J15 GDSL esterase was a novel cold-adapted enzyme from family II of lipolytic enzymes. A structural model constructed using autotransporter EstA from Pseudomonas aeruginosa as a template revealed the presence of a typical catalytic triad consisting of a serine, aspartate, and histidine which was verified with site directed mutagenesis on active serine.
    Matched MeSH terms: Carboxylic Ester Hydrolases/genetics; Carboxylic Ester Hydrolases/metabolism*; Carboxylic Ester Hydrolases/chemistry
  19. Fulltext An S188V mutation alters substrate specificity of non-stereospecific α-haloalkanoic acid dehalogenase E (DehE)
    Hamid AA, Hamid TH, Wahab RA, Omar MS, Huyop F
    PLoS One, 2015;10(3):e0121687.
    PMID: 25816329 DOI: 10.1371/journal.pone.0121687
    The non-stereospecific α-haloalkanoic acid dehalogenase E (DehE) degrades many halogenated compounds but is ineffective against β-halogenated compounds such as 3-chloropropionic acid (3CP). Using molecular dynamics (MD) simulations and site-directed mutagenesis we show here that introducing the mutation S188V into DehE improves substrate specificity towards 3CP. MD simulations showed that residues W34, F37, and S188 of DehE were crucial for substrate binding. DehE showed strong binding ability for D-2-chloropropionic acid (D-2CP) and L-2-chloropropionic acid (L-2CP) but less affinity for 3CP. This reduced affinity was attributed to weak hydrogen bonding between 3CP and residue S188, as the carboxylate of 3CP forms rapidly interconverting hydrogen bonds with the backbone amide and side chain hydroxyl group of S188. By replacing S188 with a valine residue, we reduced the inter-molecular distance and stabilised bonding of the carboxylate of 3CP to hydrogens of the substrate-binding residues. Therefore, the S188V can act on 3CP, although its affinity is less strong than for D-2CP and L-2CP as assessed by Km. This successful alteration of DehE substrate specificity may promote the application of protein engineering strategies to other dehalogenases, thereby generating valuable tools for future bioremediation technologies.
    Matched MeSH terms: Hydrolases/genetics*; Hydrolases/metabolism; Hydrolases/chemistry*
  20. Fulltext Draft Genome Sequence of Lysinibacillus sp. Strain A1, Isolated from Malaysian Tropical Soil
    Chan KG, Chen JW, Chang CY, Yin WF, Chan XY
    Genome Announc, 2015;3(2).
    PMID: 25814592 DOI: 10.1128/genomeA.00095-15
    In this work, we describe the genome of Lysinibacillus sp. strain A1, which was isolated from tropical soil. Analysis of its genome sequence shows the presence of a gene encoding for a putative peptidase responsible for nitrogen compounds.
    Matched MeSH terms: Peptide Hydrolases
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