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Bint-e-Zahira S, Khalid AN, Yousaf N, Iqbal M, Anwar T, Qureshi H, Salmen SH, Ansari MJ. Exploring Trichoderma Species in Industrial Wastewater: Morphological and Molecular Insights from Isolates. Life (Basel) 2024; 14:750. [PMID: 38929733 PMCID: PMC11204433 DOI: 10.3390/life14060750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The genus Trichoderma holds economic significance due to its widespread distribution and diverse applications, including biological control, enzyme production, and various biotechnological uses. The accurate identification of Trichoderma species is crucial given their close association with human activities. Despite previous efforts in classification, a comprehensive analysis combining morphological and molecular approaches is necessary. This study focuses on the isolation of four Trichoderma species from industrial wastewater in Pakistan, expanding on the known diversity in the region; isolation involved collecting samples from industrial wastewater effluents at specific sites in Punjab, Pakistan. Trichoderma strains were cultured and purified on solid media, with subsequent biomass production for bisorptional activity. Morphological characterization included colony features and microscopic examinations. DNA extraction, polymerase chain reaction (PCR), and sequencing of the internal transcribed spacer (ITS) region were conducted for molecular analysis. Phylogenetic analysis was performed using the Maximum Likelihood Algorithm. The study identified three Trichoderma species, viz. T. citrinoviride, T. erinaceum, and T. longibrachiatum. Each species was characterized morphologically and supported by molecular-phylogenetic analysis. Illustrations of microscopic features and a phylogenetic tree based on the ITS-nrDNA region were recorded. T. citrinoviride and T. longibrachiatum, isolated from steel mill and tanneries wastewater, respectively, were differentiated based on morphological characteristics such as phialides and conidia. The combination of morphological and molecular techniques enhances the accuracy of species identification. The study highlights the significance of Trichoderma in industrial wastewater environments and underscores the need for continued research in this area. Future research should focus on exploring the ecological roles and potential applications of the newly identified Trichoderma species. Additionally, further investigations into the biotechnological potential of these species, including enzyme production and bioremediation capabilities, would contribute to their practical applications.
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Affiliation(s)
| | | | - Nousheen Yousaf
- Department of Botany, Government College University, Lahore 54000, Pakistan
| | - Muhammad Iqbal
- Department of Botany, University of Chakwal, Chakwal 48800, Pakistan
| | - Tauseef Anwar
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Huma Qureshi
- Department of Botany, University of Chakwal, Chakwal 48800, Pakistan
| | - Saleh H. Salmen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad, Mahatma Jyotiba Phule Rohilkhand University Bareilly, Bareilly 244001, India;
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Chin SY, Shahruddin S, Chua GK, Samsudin NA, Mudalip SKA, Ghazali NFS, Jemaat Z, Salleh SF, Said FM, Nadir N, Ismail NL, Ng SH. Toward Sustainable Production of Sugar-Based Alkyl Polyglycoside Surfactant─A Comprehensive Review on Synthesis Route and Downstream Processing. Ind Eng Chem Res 2023. [DOI: 10.1021/acs.iecr.2c04039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Affiliation(s)
- Sim Yee Chin
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang, 26300 Gambang, Kuantan, Pahang Darul Makmur Malaysia
| | - Sara Shahruddin
- PETRONAS Research Sdn. Bhd., Lot 3288 and 3289, Off Jalan Ayer Itam, Kawasan Institusi Bangi, 43000 Kajang, Selangor Darul Ehsan Malaysia
| | - Gek Kee Chua
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang, 26300 Gambang, Kuantan, Pahang Darul Makmur Malaysia
| | - Nur Amalina Samsudin
- PETRONAS Research Sdn. Bhd., Lot 3288 and 3289, Off Jalan Ayer Itam, Kawasan Institusi Bangi, 43000 Kajang, Selangor Darul Ehsan Malaysia
| | - Siti Kholijah Abdul Mudalip
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang, 26300 Gambang, Kuantan, Pahang Darul Makmur Malaysia
| | - Noor Fadhila Syahida Ghazali
- PETRONAS Research Sdn. Bhd., Lot 3288 and 3289, Off Jalan Ayer Itam, Kawasan Institusi Bangi, 43000 Kajang, Selangor Darul Ehsan Malaysia
| | - Zulkifly Jemaat
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang, 26300 Gambang, Kuantan, Pahang Darul Makmur Malaysia
| | - Siti Fatihah Salleh
- PETRONAS Research Sdn. Bhd., Lot 3288 and 3289, Off Jalan Ayer Itam, Kawasan Institusi Bangi, 43000 Kajang, Selangor Darul Ehsan Malaysia
| | - Farhan Mohd Said
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang, 26300 Gambang, Kuantan, Pahang Darul Makmur Malaysia
| | - Najiah Nadir
- PETRONAS Research Sdn. Bhd., Lot 3288 and 3289, Off Jalan Ayer Itam, Kawasan Institusi Bangi, 43000 Kajang, Selangor Darul Ehsan Malaysia
| | - Nur Liyana Ismail
- PETRONAS Research Sdn. Bhd., Lot 3288 and 3289, Off Jalan Ayer Itam, Kawasan Institusi Bangi, 43000 Kajang, Selangor Darul Ehsan Malaysia
| | - Su Han Ng
- PETRONAS Research Sdn. Bhd., Lot 3288 and 3289, Off Jalan Ayer Itam, Kawasan Institusi Bangi, 43000 Kajang, Selangor Darul Ehsan Malaysia
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Eneyskaya EV, Bobrov KS, Kashina MV, Borisova AS, Kulminskaya AA. A novel acid-tolerant β-xylanase from Scytalidium candidum 3C for the synthesis of o-nitrophenyl xylooligosaccharides. J Basic Microbiol 2020; 60:971-982. [PMID: 33103248 DOI: 10.1002/jobm.202000303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/31/2020] [Accepted: 09/15/2020] [Indexed: 11/06/2022]
Abstract
Endo-β-xylanases are hemicellulases involved in the conversion of xylans in plant biomass. Here, we report a novel acidophilic β-xylanase (ScXynA) with high transglycosylation abilities that was isolated from the filamentous fungus Scytalidium candidum 3C. ScXynA was identified as a glycoside hydrolase family 10 (GH10) dimeric protein, with a molecular weight of 38 ± 5 kDa per subunit. The enzyme catalyzed the hydrolysis of different xylans under acidic conditions and was stable in the pH range 2.6-4.5. The kinetic parameters of ScXynA were determined in hydrolysis reactions with p-nitrophenyl-β-d-cellobioside (pNP-β-Cel) and p-nitrophenyl-β-d-xylobioside (pNP-β-Xyl2 ), and kcat /Km was found to be 0.43 ± 0.02 (s·mM)-1 and 57 ± 3 (s·mM)-1 , respectively. In the catalysis of the transglycosylation o-nitrophenyl-β-d-xylobioside (oNP-β-Xyl2 ) acted both as a donor and an acceptor, resulting in the efficient production of o-nitrophenyl xylooligosaccharides, with a degree of polymerization of 3-10 and o-nitrophenyl-β-d-xylotetraose (oNP-β-Xyl4 ) as the major product (18.5% yield). The modeled ScXynA structure showed a favorable position for ligand entry and o-nitrophenyl group accommodation in the relatively open -3 subsite, while the cleavage site was covered with an extended loop. These structural features provide favorable conditions for transglycosylation with oNP-β-Xyl2 . The acidophilic properties and high transglycosylation activity make ScXynA a suitable choice for various biotechnological applications, including the synthesis of valuable xylooligosaccharides.
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Affiliation(s)
- Elena V Eneyskaya
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center, Kurchatov Institute, Gatchina, Leningrad Region, Russia.,Kurchatov Genome Center - PNPI, Gatchina, Leningrad Region, Russia
| | - Kirill S Bobrov
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center, Kurchatov Institute, Gatchina, Leningrad Region, Russia.,Kurchatov Genome Center - PNPI, Gatchina, Leningrad Region, Russia
| | - Maria V Kashina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Anna S Borisova
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center, Kurchatov Institute, Gatchina, Leningrad Region, Russia.,VTT Technical Research Center of Finland Ltd., Otaniemi, Finland
| | - Anna A Kulminskaya
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center, Kurchatov Institute, Gatchina, Leningrad Region, Russia.,Kurchatov Genome Center - PNPI, Gatchina, Leningrad Region, Russia
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An endoxylanase rapidly hydrolyzes xylan into major product xylobiose via transglycosylation of xylose to xylotriose or xylotetraose. Carbohydr Polym 2020; 237:116121. [PMID: 32241400 DOI: 10.1016/j.carbpol.2020.116121] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Here, we proposed an effective strategy to enhance a novel endoxylanase (Taxy11) activity and elucidated an efficient catalysis mechanism to produce xylooligosaccharides (XOSs). Codon optimization and recruitment of natural propeptide in Pichia pastoris resulted in achievement of Taxy11 activity to 1405.65 ± 51.24 U/mL. Analysis of action mode reveals that Taxy11 requires at least three xylose (xylotriose) residues for hydrolysis to yield xylobiose. Results of site-directed mutagenesis indicate that residues Glu119, Glu210, and Asp53 of Taxy11 are key catalytic sites, while Asp203 plays an auxiliary role. The novel mechanism whereby Taxy11 catalyzes conversion of xylan or XOSs into major product xylobiose involves transglycosylation of xylose to xylotriose or xylotetraose as substrate, to form xylotetraose or xylopentaose intermediate, respectively. Taxy11 displayed highly hydrolytic activity toward corncob xylan, producing 50.44 % of xylobiose within 0.5 h. This work provides a cost-effective and sustainable way to produce value-added biomolecules XOSs (xylobiose-enriched) from agricultural waste.
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Exploring the aglycone subsite of a GH11 xylanase for the synthesis of xylosides by transglycosylation reactions. J Biotechnol 2018; 272-273:56-63. [PMID: 29501471 DOI: 10.1016/j.jbiotec.2018.02.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/18/2018] [Accepted: 02/27/2018] [Indexed: 11/22/2022]
Abstract
Xylanases Tx-xyn10 and Tx-xyn11 were compared for their transxylosylation abilities in the presence of various acceptors. Tx-xyn10 exhibited a broad specificity for various acceptors, whereas xylanase Tx-xyn11 catalysed transxylosylation reactions only in presence of polyphenolic acceptors. A modelling approach was developed to study the molecular bottlenecks into the active site of the enzyme that could be responsible for this restricted specificity. The glycosyl-enzyme intermediate of Tx-xyn11 was modelled, and a rotamer of the Y78 residue was integrated. In silico mutations of some residues from the (+1) and (+2) subsites were tested for the deglycosylation step in the presence of non-polyphenolic acceptors. The results indicated that the mutant W126A was able to use aliphatic alcohols and benzyl alcohol as acceptors for transxylosylation. Experimental validation was tested by mutating the xylanase Tx-xyn11 at position W126 into alanine. The specific activity and catalytic efficiency of the W126A mutant during the hydrolysis of xylans decreased by 2-fold and 4-fold, respectively, compared to wild-type xylanase. Among tested acceptors, transxylosylation catalysed by mutant W126A was improved with benzyl alcohol leading to a 2-fold higher concentration of benzyl xylobioside, as predicted by in silico mutation. This improved transxylosylation in the presence of benzyl alcohol leading to higher synthesis of benzyl xylobioside could likely be explained by lowest steric hindrance in the aglycone subsite of the mutated xylanase. No secondary hydrolysis of benzyl xylobioside occurred for both wild-type and mutant xylanases. Finally, our results demonstrated that the modelling approach was limited and that accounting for protein dynamics can lead to improved models.
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Otsuka Y, Sato T. Saccharide Primers Comprising Xylosyl-Serine Primed Phosphorylated Oligosaccharides Act as Intermediates in Glycosaminoglycan Biosynthesis. ACS OMEGA 2017; 2:3110-3122. [PMID: 30023684 PMCID: PMC6044892 DOI: 10.1021/acsomega.7b00073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 05/29/2023]
Abstract
β-Xylosides have been used as an artificial initiator of glycosaminoglycan (GAG) biosynthesis to investigate its mechanism and to obtain these oligosaccharides. In GAG biosynthesis, phosphorylation on the xylose residue is a crucial step. However, little attention has been paid to phosphorylated oligosaccharides obtained from β-xylosides. In a previous study, we demonstrated that a novel β-xyloside, N-lauryl-O-β-xyloyranosyl-serinamide (Xyl-Ser-C12), had excellent GAG-type oligosaccharide priming ability, whereas phosphorylated oligosaccharides were not found in the primed oligosaccharides. This study examines the potential of Xyl-Ser-C12 and three of its derivatives for use as a probe to investigate the GAG biosynthesis mechanism. Glycosylated products were obtained by incubation of the β-xylosides in normal human dermal fibroblast cells and compared by liquid chromatography-electrospray ionization-mass spectrometry. By the optimized method to detect phosphorylated products, Xyl-Ser-C12 was demonstrated to prime not only GAG-type oligosaccharides but also a variety of xylose-phosphorylated products. Among the synthesized β-xylosides, those consisting of xylosyl-serine primed large amounts of phosphorylated and GAG-type oligosaccharides, whereas the others primed sialyloligosaccharides mainly. The majority of the phosphorylated products were considered to be GAG intermediates, which are less observed in nature. To our best knowledge, this is the first report showing that the amino acid residues around the Xyl attachment position strongly affect the phosphorylation efficiency and GAG chain-priming ability of β-xylosides. This study leads to the possibility of the use of β-xyloside as a probe to observe the Xyl phosphorylation process during GAG biosynthesis and investigate comparative glycosaminoglycomics between different cells.
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Affiliation(s)
- Yuya Otsuka
- Central Research
Laboratories, Seikagaku Corporation, 1253, Tateno 3-chome, Higashiyamato-shi, Tokyo 207-0021, Japan
- Department
of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohokuku, Yokohama, Kanagawa 223-8522, Japan
| | - Toshinori Sato
- Department
of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohokuku, Yokohama, Kanagawa 223-8522, Japan
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Brusa C, Muzard M, Rémond C, Plantier-Royon R. β-Xylopyranosides: synthesis and applications. RSC Adv 2015. [DOI: 10.1039/c5ra14023d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In recent years, β-xylopyranosides have attracted interest due to the development of biomass-derived molecules. This review focuses on general routes for the preparation of β-xylopyranosides by chemical and enzymatic pathways and their main uses.
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Affiliation(s)
- Charlotte Brusa
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims (ICMR)
- CNRS UMR 7312
- UFR Sciences Exactes et Naturelles
- F-51687 Reims Cedex 2
| | - Murielle Muzard
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims (ICMR)
- CNRS UMR 7312
- UFR Sciences Exactes et Naturelles
- F-51687 Reims Cedex 2
| | - Caroline Rémond
- Université de Reims Champagne-Ardenne
- UMR 614
- Fractionnement des AgroRessources et Environnement
- France
- INRA
| | - Richard Plantier-Royon
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims (ICMR)
- CNRS UMR 7312
- UFR Sciences Exactes et Naturelles
- F-51687 Reims Cedex 2
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Arab-Jaziri F, Bissaro B, Tellier C, Dion M, Fauré R, O’Donohue MJ. Enhancing the chemoenzymatic synthesis of arabinosylated xylo-oligosaccharides by GH51 α-l-arabinofuranosidase. Carbohydr Res 2015; 401:64-72. [DOI: 10.1016/j.carres.2014.10.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 02/04/2023]
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Brusa C, Ochs M, Rémond C, Muzard M, Plantier-Royon R. Chemoenzymatic synthesis of “click” xylosides and xylobiosides from lignocellulosic biomass. RSC Adv 2014. [DOI: 10.1039/c3ra46173d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Veličković D, Dimitrijević A, Bihelović F, Bezbradica D, Knežević-Jugović Z, Milosavić N. Novel glycoside of vanillyl alcohol, 4-hydroxy-3-methoxybenzyl-α-d-glucopyranoside: study of enzymatic synthesis, in vitro digestion and antioxidant activity. Bioprocess Biosyst Eng 2012; 35:1107-15. [DOI: 10.1007/s00449-012-0695-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/22/2012] [Indexed: 10/14/2022]
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A response surface methodological study on prediction of glucosylation yields of thiamin using immobilized β-glucosidase. Process Biochem 2009. [DOI: 10.1016/j.procbio.2008.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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