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Akpinar Z, Karaoglu H. Characterization of a highly thermostable recombinant xylanase from Anoxybacillus ayderensis. Protein Expr Purif 2024; 219:106478. [PMID: 38570105 DOI: 10.1016/j.pep.2024.106478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/05/2024]
Abstract
Xylanases are the main enzymes to hydrolyze xylan, the major hemicellulose found in lignocellulose. Xylanases also have a wide range of industrial applications. Therefore, the discovery of new xylanases has the potential to enhance efficiency and sustainability in many industries. Here, we report a xylanase with thermophilic character and superior biochemical properties for industrial use. The new xylanase is discovered in Anoxybacillus ayderensis as an intracellular xylanase (AAyXYN329) and recombinantly produced. While AAyXYN329 shows significant activity over a wide pH and temperature range, optimum activity conditions were determined as pH 6.5 and 65 °C. The half-life of the enzyme was calculated as 72 h at 65 °C. The enzyme did not lose activity between pH 6.0-9.0 at +4 °C for 75 days. Km, kcat and kcat/Km values of AAyXYN329 were calculated as 4.09824 ± 0.2245 μg/μL, 96.75 1/sec, and 23.61/L/g.s -1, respectively. In conclusion, the xylanase of A. ayderensis has an excellent potential to be utilized in many industrial processes.
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Affiliation(s)
- Zuleyha Akpinar
- Department of Basic Sciences, Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, 53100, Rize, Turkey.
| | - Hakan Karaoglu
- Department of Basic Sciences, Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, 53100, Rize, Turkey.
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Shrestha P, Karmacharya J, Han SR, Lee JH, Oh TJ. Elucidation of bacterial trehalose-degrading trehalase and trehalose phosphorylase: physiological significance and its potential applications. Glycobiology 2024; 34:cwad084. [PMID: 37847605 DOI: 10.1093/glycob/cwad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023] Open
Abstract
Bacteria possess diverse metabolic and genetic processes, resulting in the inability of certain bacteria to degrade trehalose. However, some bacteria do have the capability to degrade trehalose, utilizing it as a carbon source, and for defense against environmental stress. Trehalose, a disaccharide, serves as a carbon source for many bacteria, including some that are vital for pathogens. The degradation of trehalose is carried out by enzymes like trehalase (EC 3.2.1.28) and trehalose phosphorylase (EC 2.4.1.64/2.4.1.231), which are classified under the glycoside hydrolase families GH37, GH15, and GH65. Numerous studies and reports have explored the physiological functions, recombinant expression, enzymatic characteristics, and potential applications of these enzymes. However, further research is still being conducted to understand their roles in bacteria. This review aims to provide a comprehensive summary of the current understanding of trehalose degradation pathways in various bacteria, focusing on three key areas: (i) identifying different trehalose-degrading enzymes in Gram-positive and Gram-negative bacteria, (ii) elucidating the mechanisms employed by trehalose-degrading enzymes belonging to the glycoside hydrolases GH37, GH15, and GH65, and (iii) discussing the potential applications of these enzymes in different sectors. Notably, this review emphasizes the bacterial trehalose-degrading enzymes, specifically trehalases (GH37, GH15, and GH65) and trehalose phosphorylases (GH65), in both Gram-positive and Gram-negative bacteria, an aspect that has not been highlighted before.
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Affiliation(s)
- Prasansah Shrestha
- Department of Life Sciences and Biochemical Engineering, Graduate School, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do, 31460, South Korea
| | - Jayram Karmacharya
- Department of Life Sciences and Biochemical Engineering, Graduate School, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do, 31460, South Korea
| | - So-Ra Han
- Department of Life Sciences and Biochemical Engineering, Graduate School, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do, 31460, South Korea
- Genome-based Bio-IT Convergence Institute, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon Asan-si, Chungcheongnam-do, 31460, South Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Materials, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea
| | - Tae-Jin Oh
- Department of Life Sciences and Biochemical Engineering, Graduate School, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do, 31460, South Korea
- Genome-based Bio-IT Convergence Institute, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon Asan-si, Chungcheongnam-do, 31460, South Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221beon-gil, Tangjeong-myeon, Asan-si, Chungcheongnam-do 31460, South Korea
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3
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Zhang Y, Jiang C, Li Y, Sun J, Chen Z, Zhang Q, Sun G. Screening, identification, and mechanism analysis of starch-degrading bacteria during curing process in tobacco leaf. Front Bioeng Biotechnol 2024; 12:1332113. [PMID: 38567082 PMCID: PMC10985783 DOI: 10.3389/fbioe.2024.1332113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/07/2024] [Indexed: 04/04/2024] Open
Abstract
Tobacco, a vital economic crop, had its quality post-curing significantly influenced by starch content. Nonetheless, the existing process parameters during curing were inadequate to satisfy the starch degradation requirements. Microorganisms exhibit inherent advantages in starch degradation, offering significant potential in the tobacco curing process. Our study concentrated on the microbial populations on the surface of tobacco leaves and in the rhizosphere soil. A strain capable of starch degradation, designated as BS3, was successfully isolated and identified as Bacillus subtilis by phylogenetic tree analysis based on 16SrDNA sequence. The application of BS3 on tobacco significantly enhanced enzyme activity and accelerated starch degradation during the curing process. Furthermore, analyses of the metagenome, transcriptome, and metabolome indicated that the BS3 strain facilitated starch degradation by regulating surface microbiota composition and affecting genes related to starch hydrolyzed protein and key metabolites in tobacco leaves. This study offered new strategies for efficiently improving the quality of tobacco leaves.
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Affiliation(s)
- Yan Zhang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Chuandong Jiang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yangyang Li
- Hunan Tobacco Research Institute, Changsha, China
| | - Jingguo Sun
- Hubei Provincial Tobacco Research Institute, Wuhan, China
| | - Zhenguo Chen
- Hubei Provincial Tobacco Research Institute, Wuhan, China
| | - Qiang Zhang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Guangwei Sun
- Hubei Provincial Tobacco Research Institute, Wuhan, China
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4
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Jafari S, Ryde U, Irani M. QM/MM study of the catalytic reaction of aphid myrosinase. Int J Biol Macromol 2024; 262:130089. [PMID: 38360236 DOI: 10.1016/j.ijbiomac.2024.130089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/07/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122 must be protonated on NE2, and Glu-167 must be protonated on OE2. Our model reproduces the anomeric retaining characteristic of myrosinase and indicates that the deglycosylation reaction is the rate-determining step of the reaction. Based on the calculations, we propose a reaction mechanism for aphid myrosinase-mediated hydrolysis of glucosinolates with an overall barrier of 15.2 kcal/mol. According to the results, removing a proton from Arg-312 or altering it to valine or methionine increases glycosylation barriers but decreases the deglycosylation barrier.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, Sanandaj, Iran.
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5
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Yaşar Yildiz S. Exploring the Hot Springs of Golan: A Source of Thermophilic Bacteria and Enzymes with Industrial Promise. Curr Microbiol 2024; 81:101. [PMID: 38376803 DOI: 10.1007/s00284-024-03617-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/14/2024] [Indexed: 02/21/2024]
Abstract
In recent years, there has been a surge in research on extremophiles due to their remarkable ability to survive in harsh environments. Extremophile thermophilic bacteria provide thermostable enzymes for biotechnology and industry. Thermophilic bacteria live in extreme environments like hot springs at 45-80 °C. This study screens and isolates thermophilic bacteria and thermozymes from the Golan hot springs in Karakocan, Elazig, Turkey. The study also characterizes thermophilic bacteria and their thermozymes to understand their features and applications better. Golan hot spring water samples at 50 °C yielded 12 isolates. GKE 02, 07, 08, and 10 produce amylase, GKE 04, 08, and 11 cellulase, and GKE 06 xylanase. One isolate (GKE 08) displayed both amylolytic and cellulolytic activity on agar plates. GKE 02 had the highest plate assay amylolytic index (2.3) and amylase activity (67.87 U/ml). Plate assay indicates GKE 08 has 1.5 amylolytic index, 1.1 cellulolytic index, 38.57 U/ml amylase, and 6.81 U/ml cellulase. GKE 04 had the greatest cellulolytic index (1.7) and cellulase activity (27.46). GKE 06, the only xylanase producer, has 19.67 U/ml activity and 1.4 plate assay index. The investigation also included determining the optimal pH and temperature conditions for each enzyme. 16S rDNA gene sequencing revealed seven thermozyme-producing bacteria Bacillus, Geobacillus, and Thermomonas. Thermomonas hydrothermalis genome annotation showed glycosyl hydrolase genes for amylolytic and cellulolytic activity. The findings of this study on thermophilic bacteria and thermostable enzyme synthesis in the Golan hot springs are promising, particularly for T. hydrothermalis, which has limited research on its potential as a thermozyme producer.
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Affiliation(s)
- Songül Yaşar Yildiz
- Bioengineering Department, Faculty of Engineering and Natural Sciences, Istanbul Medeniyet University, Istanbul, 34700, Turkey.
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Ashcroft E, Munoz-Munoz J. A review of the principles and biotechnological applications of glycoside hydrolases from extreme environments. Int J Biol Macromol 2024; 259:129227. [PMID: 38185295 DOI: 10.1016/j.ijbiomac.2024.129227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
It is apparent that Biocatalysts are shaping the future by providing a more sustainable approach to established chemical processes. Industrial processes rely heavily on the use of toxic compounds and high energy or pH reactions, factors that both contributes to the worsening climate crisis. Enzymes found in bacterial systems and other microorganisms, from the glaciers of the Arctic to the sandy deserts of Abu Dhabi, provide key tools and understanding as to how we can progress in the biotechnology sector. These extremophilic bacteria harness the adaptive enzymes capable of withstanding harsh reaction conditions in terms of stability and reactivity. Carbohydrate-active enzymes, including glycoside hydrolases or carbohydrate esterases, are extremely beneficial for the presence and future of biocatalysis. Their involvement in the industry spans from laundry detergents to paper and pulp treatment by degrading oligo/polysaccharides into their monomeric products in almost all detrimental environments. This includes exceedingly high temperatures, pHs or even in the absence of water. In this review, we discuss the structure and function of different glycoside hydrolases from extremophiles, and how they can be applied to industrial-scale reactions to replace the use of harsh chemicals, reduce waste, or decrease energy consumption.
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Affiliation(s)
- Ellie Ashcroft
- Microbial Enzymology Lab, Department of Applied Sciences, Ellison Building A, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.
| | - Jose Munoz-Munoz
- Microbial Enzymology Lab, Department of Applied Sciences, Ellison Building A, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.
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He F, Gao YW, Ye ZX, Huang HJ, Tian CH, Zhang CX, Chen JP, Li JM, Lu JB. Comparative transcriptomic analysis of salivary glands between the zoophytophagous Cyrtorhinus lividipennis and the phytozoophagous Apolygus lucorum. BMC Genomics 2024; 25:53. [PMID: 38212677 PMCID: PMC10785411 DOI: 10.1186/s12864-023-09956-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/31/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Saliva plays a crucial role in shaping the feeding behavior of insects, involving processes such as food digestion and the regulation of interactions between insects and their hosts. Cyrtorhinus lividipennis serves as a predominant natural enemy of rice pests, while Apolygus lucorum, exhibiting phytozoophagous feeding behavior, is a destructive agricultural pest. In this study, a comparative transcriptome analysis, incorporating the published genomes of C.lividipennis and A.lucorum, was conducted to reveal the role of salivary secretion in host adaptation. RESULTS In contrast to A.lucorum, C.lividipennis is a zoophytophagous insect. A de novo genome analysis of C.lividipennis yielded 19,706 unigenes, including 16,217 annotated ones. On the other hand, A.lucorum had altogether 20,111 annotated genes, as obtained from the published official gene set (20,353 unigenes). Functional analysis of the top 1,000 salivary gland (SG)-abundant genes in both insects revealed that the SG was a dynamically active tissue engaged in protein synthesis and secretion. Predictions of other tissues and signal peptides were compared. As a result, 94 and 157 salivary proteins were identified in C.lividipennis and A.lucorum, respectively, and were categorized into 68 and 81 orthogroups. Among them, 26 orthogroups were shared, potentially playing common roles in digestion and detoxification, including several venom serine proteases. Furthermore, 42 and 55 orthogroups were exclusive in C.lividipennis and A.lucorum, respectively, which were exemplified by a hyaluronidase in C.lividipennis that was associated with predation, while polygalacturonases in A.lucorum were involved in mesophyll-feeding patterns. CONCLUSIONS Findings in this study provide a comprehensive insight into saliva secretions in C.lividipennis and A.lucorum via a transcriptome approach, reflecting the intricate connections between saliva secretions and feeding behaviors. It is found that conserved salivary secretions are involved in shaping the overlapping feeding patterns, while a plethora of unique salivary secretions may drive the evolution of specific feeding behaviors crucial for their survival. These results enhance our understanding of the feeding mechanisms in different insects from the perspective of saliva and contribute to future environmentally friendly pest control by utilizing predatory insects.
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Affiliation(s)
- Fang He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Yang-Wei Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Cai-Hong Tian
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
- Institute of Insect Science, Zhejiang University, 310058, Hangzhou, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Jia-Bao Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China.
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Hrmova M, Zimmer J, Bulone V, Fincher GB. Enzymes in 3D: Synthesis, remodelling, and hydrolysis of cell wall (1,3;1,4)-β-glucans. PLANT PHYSIOLOGY 2023; 194:33-50. [PMID: 37594400 PMCID: PMC10762513 DOI: 10.1093/plphys/kiad415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/09/2023] [Indexed: 08/19/2023]
Abstract
Recent breakthroughs in structural biology have provided valuable new insights into enzymes involved in plant cell wall metabolism. More specifically, the molecular mechanism of synthesis of (1,3;1,4)-β-glucans, which are widespread in cell walls of commercially important cereals and grasses, has been the topic of debate and intense research activity for decades. However, an inability to purify these integral membrane enzymes or apply transgenic approaches without interpretative problems associated with pleiotropic effects has presented barriers to attempts to define their synthetic mechanisms. Following the demonstration that some members of the CslF sub-family of GT2 family enzymes mediate (1,3;1,4)-β-glucan synthesis, the expression of the corresponding genes in a heterologous system that is free of background complications has now been achieved. Biochemical analyses of the (1,3;1,4)-β-glucan synthesized in vitro, combined with 3-dimensional (3D) cryogenic-electron microscopy and AlphaFold protein structure predictions, have demonstrated how a single CslF6 enzyme, without exogenous primers, can incorporate both (1,3)- and (1,4)-β-linkages into the nascent polysaccharide chain. Similarly, 3D structures of xyloglucan endo-transglycosylases and (1,3;1,4)-β-glucan endo- and exohydrolases have allowed the mechanisms of (1,3;1,4)-β-glucan modification and degradation to be defined. X-ray crystallography and multi-scale modeling of a broad specificity GH3 β-glucan exohydrolase recently revealed a previously unknown and remarkable molecular mechanism with reactant trajectories through which a polysaccharide exohydrolase can act with a processive action pattern. The availability of high-quality protein 3D structural predictions should prove invaluable for defining structures, dynamics, and functions of other enzymes involved in plant cell wall metabolism in the immediate future.
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Affiliation(s)
- Maria Hrmova
- School of Agriculture, Food and Wine, and the Waite Research Institute, University of Adelaide, Glen Osmond, South Australia 5064, Australia
| | - Jochen Zimmer
- Howard Hughes Medical Institute and Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Vincent Bulone
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Alba Nova University Centre, 106 91 Stockholm, Sweden
| | - Geoffrey B Fincher
- School of Agriculture, Food and Wine, and the Waite Research Institute, University of Adelaide, Glen Osmond, South Australia 5064, Australia
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Dagher SF, Vaishnav A, Stanley CB, Meilleur F, Edwards BFP, Bruno-Bárcena JM. Structural analysis and functional evaluation of the disordered ß-hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis. Front Bioeng Biotechnol 2023; 11:1291245. [PMID: 38162180 PMCID: PMC10755861 DOI: 10.3389/fbioe.2023.1291245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024] Open
Abstract
Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1-110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region's impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%-97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.
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Affiliation(s)
- Suzanne F. Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States
| | | | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Brian F. P. Edwards
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States
| | - José M. Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Colombini L, Santoro F, Tirziu M, Lazzeri E, Morelli L, Pozzi G, Iannelli F. The mobilome of Lactobacillus crispatus M247 includes two novel genetic elements: Tn 7088 coding for a putative bacteriocin and the siphovirus prophage ΦM247. Microb Genom 2023; 9:001150. [PMID: 38085804 PMCID: PMC10763512 DOI: 10.1099/mgen.0.001150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Lactobacillus crispatus is a member of the vaginal and gastrointestinal human microbiota. Here we determined the complete genome sequence of the probiotic strain M247 combining Nanopore and Illumina technologies. The M247 genome is organized in one circular chromosome of 2 336 109 bp, with a GC content of 37.04 % and 2303 ORFs, of which 1962 could be annotated. Analysis of the M247 mobilome, which accounts for 14 % of the whole genome, revealed the presence of: (i) Tn7088, a novel 14 105 bp long integrative and mobilizable element (IME) containing 16 ORFs; (ii) ΦM247, a novel 42 510 bp long siphovirus prophage containing 52 ORFs; (iii) three clustered regularly interspaced short palindromic repeats (CRISPRs); and (iv) 226 insertion sequences (ISs) belonging to 14 different families. Tn7088 has a modular organization including a mobilization module encoding FtsK homologous proteins and a relaxase, an integration/excision module coding for an integrase and an excisionase, and an adaptation module coding for a class I bacteriocin and homologous to the listeriolysin S (lls) locus of Listeria monocytogenes. Genome-wide homology search analysis showed the presence of Tn7088-like elements in 12 out of 23 L. crispatus complete public genomes. Mobilization and integration/excision modules are essentially conserved, while the adaptation module is variable since it is the target site for the integration of different ISs. Prophage ΦM247 contains genes for phage structural proteins, DNA replication and packaging, lysogenic and lytic cycles. ΦM247-like prophages are present in seven L. crispatus complete genomes, with sequence variability mainly due to the integration of ISs. PCR and sequencing showed that the Tn7088 IME excises from the M247 chromosome producing a circular form at a concentration of 4.32×10-5 copies per chromosome, and reconstitution of the Tn7088 chromosomal target site occurred at 6.65×10-4 copies per chromosome. The ΦM247 prophage produces an excised form and a reconstituted target site at a level of 3.90×10-5 and 2.48×10-5 copies per chromosome, respectively. This study identified two novel genetic elements in L. crispatus. Tn7088 represents the first example of an IME carrying a biosynthetic gene cluster for a class I bacteriocin in L. crispatus.
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Affiliation(s)
- Lorenzo Colombini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Mariana Tirziu
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Elisa Lazzeri
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lorenzo Morelli
- Università Cattolica del Sacro Cuore, Department of Food Science and Technologies for a Sustainable Agri-food Supply Chain (DiSTAS), University of Piacenza, 53100 Piacenza, Italy
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
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Kwain S, Dominy BN, Whitehead KJ, Miller BA, Whitehead DC. Exploring the interactive mechanism of acarbose with the amylase SusG in the starch utilization system of the human gut symbiont Bacteroides thetaiotaomicron through molecular modeling. Chem Biol Drug Des 2023; 102:486-499. [PMID: 37062591 DOI: 10.1111/cbdd.14251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/15/2023] [Accepted: 04/04/2023] [Indexed: 04/18/2023]
Abstract
The α-amylase, SusG, is a principal component of the Bacteroides thetaiotaomicron (Bt) starch utilization system (Sus) used to metabolize complex starch molecules in the human gastrointestinal (GI) tract. We previously reported the non-microbicidal growth inhibition of Bt by the acarbose-mediated arrest of the Sus as a potential therapeutic strategy. Herein, we report a computational approach using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation to explore the interactive mechanism between acarbose and SusG at the atomic level in an effort to understand how acarbose shuts down the Bt Sus. The docking analysis reveals that acarbose binds orthosterically to SusG with a binding affinity of -8.3 kcal/mol. The MD simulation provides evidence of conformational variability of acarbose at the active site of SusG and also suggests that acarbose interacts with the main catalytic residues via a general acid-base double-displacement catalytic mechanism. These results suggest that small molecule competitive inhibition against the SusG protein could impact the entire Bt Sus and eliminate or reduce the system's ability to metabolize starch. This computational strategy could serve as a potential avenue for structure-based drug design to discover other small molecules capable of inhibiting the Sus of Bt with high potency, thus providing a holistic approach for selective modulation of the GI microbiota.
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Affiliation(s)
- Samuel Kwain
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Brian N Dominy
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Kristi J Whitehead
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Brock A Miller
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Daniel C Whitehead
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
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12
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Li F, Hou CFD, Lokareddy RK, Yang R, Forti F, Briani F, Cingolani G. High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217. Nat Commun 2023; 14:4052. [PMID: 37422479 PMCID: PMC10329688 DOI: 10.1038/s41467-023-39756-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023] Open
Abstract
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4.
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Affiliation(s)
- Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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13
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Wang L, Jing M, Gu S, Li D, Dai X, Chen Z, Chen J. Genome-Wide Investigation of BAM Gene Family in Annona atemoya: Evolution and Expression Network Profiles during Fruit Ripening. Int J Mol Sci 2023; 24:10516. [PMID: 37445694 DOI: 10.3390/ijms241310516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
β-amylase proteins (BAM) are important to many aspects of physiological process such as starch degradation. However, little information was available about the BAM genes in Annona atemoya, an important tropical fruit. Seven BAM genes containing the conservative domain of glycoside hydrolase family 14 (PF01373) were identified with Annona atemoya genome, and these BAM genes can be divided into four groups. Subcellular localization analysis revealed that AaBAM3 and AaBAM9 were located in the chloroplast, and AaBAM1.2 was located in the cell membrane and the chloroplast. The AaBAMs belonging to Subfamily I contribute to starch degradation have the higher expression than those belonging to Subfamily II. The analysis of the expression showed that AaBAM3 may function in the whole fruit ripening process, and AaBAM1.2 may be important to starch degradation in other organs. Temperature and ethylene affect the expression of major AaBAM genes in Subfamily I during fruit ripening. These expressions and subcellular localization results indicating β-amylase play an important role in starch degradation.
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Affiliation(s)
- Luli Wang
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Minmin Jing
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Shuailei Gu
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Dongliang Li
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Xiaohong Dai
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Zhihui Chen
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Jingjing Chen
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
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14
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Velayutham M, Sarkar P, Karuppiah KM, Arumugam P, Shajahan S, Abu Haija M, Ahamad T, Arasu MV, Al-Dhabi NA, Choi KC, Guru A, Arockiaraj J. PS9, Derived from an Aquatic Fungus Virulent Protein, Glycosyl Hydrolase, Arrests MCF-7 Proliferation by Regulating Intracellular Reactive Oxygen Species and Apoptotic Pathways. ACS OMEGA 2023; 8:18543-18553. [PMID: 37273629 PMCID: PMC10233697 DOI: 10.1021/acsomega.3c00336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 06/06/2023]
Abstract
One of the most common diseases in women is breast cancer, which has the highest death globally. Surgery, chemotherapy, hormone treatments, and radiation are the current treatment options for breast cancer. However, these options have several adverse side effects. Recently, peptide-based drugs have gained attention as anticancer therapy. Studies report that peptides from biological toxins such as venom and virulent pathogenic molecules have potential therapeutic effects against multiple diseases, including cancers. This study reports on the in vitro anticancer effect of a short peptide, PS9, derived from a virulent protein, glycosyl hydrolase, of an aquatic fungus, Aphanomyces invadans. This peptide arrests MCF-7 proliferation by regulating intercellular reactive oxygen species (ROS) and apoptotic pathways. Based on the potential for the anticancer effect of PS9, from the in silico analysis, in vitro analyses using MCF-7 cells were executed. PS9 showed a dose-dependent activity; its IC50 value was 25.27-43.28 μM at 24 h. The acridine orange/ethidium bromide (AO/EtBr) staining, to establish the status of apoptosis in MCF-7 cells, showed morphologies for early and late apoptosis and necrotic cell death. The 2,7-dichlorodihydrofluorescein diacetate (DCFDA) staining and biochemical analyses showed a significant increase in reactive oxygen species (ROS). Besides, PS9 has been shown to regulate the caspase-mediated apoptotic pathway. PS9 is nontoxic, in vitro, and in vivo zebrafish larvae. Together, PS9 may have an anticancer effect in vitro.
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Affiliation(s)
- Manikandan Velayutham
- Department
of Medical Biotechnology and Integrative Physiology, Institute of
Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai 602105, Tamil Nadu, India
| | - Purabi Sarkar
- Department
of Molecular Medicine, School of Allied Healthcare and Sciences, Jain Deemed-to-be University, Whitefield, Bangalore 560066, Karnataka, India
| | - Kanchana M. Karuppiah
- Department
of Medical Research, Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Chennai 603203, Tamil Nadu, India
| | - Priyadharsan Arumugam
- Department
of Conservative Dentistry and Endodontics, Saveetha Dental College
and Hospitals, SIMATS, Chennai 600077, Tamil Nadu, India
| | - Shanavas Shajahan
- Department
of Conservative Dentistry and Endodontics, Saveetha Dental College
and Hospitals, SIMATS, Chennai 600077, Tamil Nadu, India
- Department
of Chemistry, Khalifa University of Science
and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Mohammad Abu Haija
- Department
of Chemistry, Khalifa University of Science
and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
- Center for
Catalysis and Separations, Khalifa University
of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Tansir Ahamad
- Department
of Chemistry, College of Science, King Saud
University, Riyadh 11451, Saudi Arabia
| | - Mariadhas Valan Arasu
- Department
of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department
of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ki-Choon Choi
- Grassland
and Forage Division, National Institute
of Animal Science, RDA, Seonghwan-Eup, Cheonan-Si, Chungnam 330-801, Republic of Korea
| | - Ajay Guru
- Department
of Conservative Dentistry and Endodontics, Saveetha Dental College
and Hospitals, SIMATS, Chennai 600077, Tamil Nadu, India
| | - Jesu Arockiaraj
- Department
of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chennai 603203, Tamil Nadu, India
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15
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Yang M, Ma Y, Si X, Liu X, Geng X, Wen X, Li G, Zhang L, Yang C, Zhang Z. Analysis of the Glycoside Hydrolase Family 1 from Wild Jujube Reveals Genes Involved in the Degradation of Jujuboside A. Genes (Basel) 2023; 14:1135. [PMID: 37372316 DOI: 10.3390/genes14061135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Jujubosides are the major medicinal ingredients of Ziziphi Spinosae Semen (the seed of wild jujube). To date, a complete understanding of jujuboside's metabolic pathways has not been attained. This study has systematically identified 35 β-glucosidase genes belonging to the glycoside hydrolase family 1 (GH1) using bioinformatic methods based on the wild jujube genome. The conserved domains and motifs of the 35 putative β-glucosidases, along with the genome locations and exon-intron structures of 35 β-glucosidase genes were revealed. The potential functions of the putative proteins encoded by the 35 β-glucosidase genes are suggested based on their phylogenetic relationships with Arabidopsis homologs. Two wild jujube β-glucosidase genes were heterologously expressed in Escherichia coli, and the recombinant proteins were able to convert jujuboside A (JuA) into jujuboside B (JuB). Since it has been previously reported that JuA catabolites, including JuB and other rare jujubosides, may play crucial roles in the jujuboside's pharmacological activity, it is suggested that these two proteins can be used to enhance the utilization potential of jujubosides. This study provides new insight into the metabolism of jujubosides in wild jujube. Furthermore, the characterization of β-glucosidase genes is expected to facilitate investigations involving the cultivation and breeding of wild jujube.
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Affiliation(s)
- Mingjun Yang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Yimian Ma
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xupeng Si
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Xiaofeng Liu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Xin Geng
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xin Wen
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Guoqiong Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Liping Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Chengmin Yang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Zheng Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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16
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Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
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17
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Lipsh-Sokolik R, Khersonsky O, Schröder SP, de Boer C, Hoch SY, Davies GJ, Overkleeft HS, Fleishman SJ. Combinatorial assembly and design of enzymes. Science 2023; 379:195-201. [PMID: 36634164 DOI: 10.1126/science.ade9434] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The design of structurally diverse enzymes is constrained by long-range interactions that are necessary for accurate folding. We introduce an atomistic and machine learning strategy for the combinatorial assembly and design of enzymes (CADENZ) to design fragments that combine with one another to generate diverse, low-energy structures with stable catalytic constellations. We applied CADENZ to endoxylanases and used activity-based protein profiling to recover thousands of structurally diverse enzymes. Functional designs exhibit high active-site preorganization and more stable and compact packing outside the active site. Implementing these lessons into CADENZ led to a 10-fold improved hit rate and more than 10,000 recovered enzymes. This design-test-learn loop can be applied, in principle, to any modular protein family, yielding huge diversity and general lessons on protein design principles.
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Affiliation(s)
- R Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - O Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - S P Schröder
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - C de Boer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S-Y Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - G J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, UK
| | - H S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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18
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Structural and functional insights into the glycoside hydrolase family 30 xylanase of the rumen bacterium Ruminococcus flavefaciens. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Nikam PB, Salunkhe JD, Marathe KR, Alghuthaymi MA, Abd-Elsalam KA, Patil SV. Rhizobium pusense-Mediated Selenium Nanoparticles-Antibiotics Combinations against Acanthamoeba sp. Microorganisms 2022; 10:microorganisms10122502. [PMID: 36557755 PMCID: PMC9785558 DOI: 10.3390/microorganisms10122502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Severe ocular infections by Acanthamoeba sp. lead to keratitis, resulting in irreversible vision loss in immune-compromised individuals. When a protozoal infection spreads to neural tissues, it causes granulomatous encephalitis, which can be fatal. Treatment often takes longer due to the transition of amoeba from trophozoites to cyst stages, cyst being the dormant form of Acanthamoeba. A prolonged use of therapeutic agents, such as ciprofloxacin (Cipro), results in severe side effects; thus, it is critical to improve the therapeutic efficacy of these widely used antibiotics, possibly by limiting the drug-sensitive protozoal-phase transition to cyst formation. Owing to the biomedical potential of selenium nanoparticles (SeNPs), we evaluated the synergistic effects of ciprofloxacin and Rhizobium pusense-biogenic SeNPs combination. SeNPs synthesized using Rhizobium pusense isolated from root nodules were characterized using UV-Visible spectrophotometer, FT-IR, SEM with EDX, particle size analysis, and Zeta potential. The combination was observed to reduce the sub-lethal dose of Cipro, which may help reduce its side effects. The selenium and ciprofloxacin (SeNPs-Cipro) combination reduced the LC50 by 33.43%. The anti-protozoal efficacy of SeNPs-Cipro was found to transduce through decreased protozoal-cyst formations and the inhibition of the galactosidase and protease enzymes of trophozoites. Furthermore, high leakage of sugar, proteins, and amino acids during the SeNPs-Cipro treatment was one primary reason for killing the trophozoites. These experimental results may be helpful in the further pre-clinical evaluation of SeNPs-Cipro to combat protozoal infections. Future studies for combinations of SeNPs with other antibiotics need to be conducted to know the potential of SeNPs against antibiotic resistance in Acanthamoeba.
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Affiliation(s)
- Pradnya B. Nikam
- Department of Biochemistry, School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425001, India
| | - Jitendra D. Salunkhe
- Department of Biochemistry, School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425001, India
| | - Kiran R. Marathe
- Department of Biochemistry, School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425001, India
| | - Mousa A. Alghuthaymi
- Biology Department, Science and Humanities College, Shaqra University, Alquwayiyah 11971, Saudi Arabia
| | - Kamel A. Abd-Elsalam
- Plant Pathology Research Institute, Agricultural Research Center, Giza 12619, Egypt
- Correspondence: (K.A.A.-E.); or (S.V.P.); Tel.: +91-0257-2257421–25 (S.V.P.)
| | - Satish V. Patil
- Department of Biochemistry, School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425001, India
- Correspondence: (K.A.A.-E.); or (S.V.P.); Tel.: +91-0257-2257421–25 (S.V.P.)
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20
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St John FJ, Crooks C, Kim Y, Tan K, Joachimiak A. The first crystal structure of a xylobiose-bound xylobiohydrolase with high functional specificity from the bacterial glycoside hydrolase 30 subfamily 10. FEBS Lett 2022; 596:2449-2464. [PMID: 35876256 DOI: 10.1002/1873-3468.14454] [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: 05/25/2022] [Revised: 07/05/2022] [Accepted: 07/09/2022] [Indexed: 11/05/2022]
Abstract
Xylobiose is a prebiotic sugar that has applications in functional foods. This report describes the first X-ray crystallographic structure models of apo and xylobiose bound forms of a xylobiohydrolase (XBH) from Acetivibrio clariflavus. This xylan active enzyme, a member of the recently described glycoside hydrolase family 30 (GH30) subfamily 10 phylogenetic clade has been shown to strictly release xylobiose as its primary hydrolysis product. Inspection of the apo-structure reveals a glycone region X2 binding slot. When X2 binds, the nonreducing xylose in the -2 subsite is highly coordinated with numerous hydrogen bond contacts while contacts in the -1 subsite mostly reflect interactions typical for GH30 and enzymes in clan A of the carbohydrate-active enzymes database (CAZy). This structure provides an explanation for the high functional specificity of this new bacterial GH30 XBH subfamily.
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Affiliation(s)
- Franz J St John
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, Madison, WI, 53726, USA
| | - Casey Crooks
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, Madison, WI, 53726, USA
| | - Youngchang Kim
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Il, 60439, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Il, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Il, 60439, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
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21
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Su X, Meng F, Liu Y, Jiang W, Wang Z, Wu L, Guo X, Yao X, Wu J, Sun Z, Zha L, Gui S, Peng D, Xing S. Molecular Cloning and Functional Characterization of a β-Glucosidase Gene to Produce Platycodin D in Platycodon grandiflorus. FRONTIERS IN PLANT SCIENCE 2022; 13:955628. [PMID: 35860532 PMCID: PMC9289601 DOI: 10.3389/fpls.2022.955628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Platycodin D (PD) is a deglycosylated triterpene saponin with much higher pharmacological activity than glycosylated platycoside E (PE). Extensive studies in vitro showed that the transformation of platycoside E to platycodin D can be achieved using β-glucosidase extracted from several bacteria. However, whether similar enzymes in Platycodon grandiflorus could convert platycoside E to platycodin D, as well as the molecular mechanism underlying the deglycosylation process of platycodon E, remain unclear. Here, we identified a β-glucosidase in P. grandiflorus from our previous RNA-seq analysis, with a full-length cDNA of 1,488 bp encoding 495 amino acids. Bioinformatics and phylogenetic analyses showed that β-glucosidases in P. grandiflorus have high homology with other plant β-glucosidases. Subcellular localization showed that there is no subcellular preference for its encoding gene. β-glucosidase was successfully expressed as 6 × His-tagged fusion protein in Escherichia coli BL21 (DE3). Western blot analysis yielded a recombinant protein of approximately 68 kDa. In vitro enzymatic reactions determined that β-glucosidase was functional and could convert PE to PD. RT-qPCR analysis showed that the expression level of β-glucosidase was higher at night than during the day, with the highest expression level between 9:00 and 12:00 at night. Analysis of the promoter sequence showed many light-responsive cis-acting elements, suggesting that the light might regulate the gene. The results will contribute to the further study of the biosynthesis and metabolism regulation of triterpenoid saponins in P. grandiflorus.
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Affiliation(s)
- Xinglong Su
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
| | - Fei Meng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yingying Liu
- College of Humanities and International Education Exchange, Anhui University of Chinese Medicine, Hefei, China
| | - Weimin Jiang
- College of Life Sciences and Environment, Hengyang Normal University, Hengyang, China
| | - Zhaojian Wang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Liping Wu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaohu Guo
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaoyan Yao
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jing Wu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Zongping Sun
- Engineering Technology Research Center of Anti-aging, Chinese Herbal Medicine, Fuyang Normal University, Fuyang, China
| | - Liangping Zha
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
| | - Shuangying Gui
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Pharmaceutical Preparation Technology and Application, Anhui University of Chinese Medicine, Hefei, China
| | - Daiyin Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- MOE-Anhui, Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Shihai Xing
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
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22
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Shin NR, Doucet D, Pauchet Y. Duplication of horizontally acquired GH5_2 enzymes played a central role in the evolution of longhorned beetles. Mol Biol Evol 2022; 39:msac128. [PMID: 35763818 PMCID: PMC9246334 DOI: 10.1093/molbev/msac128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/14/2022] Open
Abstract
The rise of functional diversity through gene duplication contributed to the adaption of organisms to various environments. Here we investigate the evolution of putative cellulases of the subfamily 2 of glycoside hydrolase family 5 (GH5_2) in the Cerambycidae (longhorned beetles), a megadiverse assemblage of mostly xylophagous beetles. Cerambycidae originally acquired GH5_2 from a bacterial donor through horizontal gene transfer (HGT), and extant species harbor multiple copies that arose from gene duplication. We ask how these digestive enzymes contributed to the ability of these beetles to feed on wood. We analyzed 113 GH5_2, including the functional characterization of 52 of them, derived from 25 species covering most subfamilies of Cerambycidae. Ancestral gene duplications led to five well-defined groups with distinct substrate specificity, allowing these beetles to break down, in addition to cellulose, polysaccharides that are abundant in plant cell walls (PCWs), namely, xyloglucan, xylan, and mannans. Resurrecting the ancestral enzyme originally acquired by HGT, we show it was a cellulase that was able to break down glucomannan and xylan. Finally, recent gene duplications further expanded the catalytic repertoire of cerambycid GH5_2, giving rise to enzymes that favor transglycosylation over hydrolysis. We suggest that HGT and gene duplication, which shaped the evolution of GH5_2, played a central role in the ability of cerambycid beetles to use a PCW-rich diet and may have contributed to their successful radiation.
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Affiliation(s)
- Na Ra Shin
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Daniel Doucet
- Great Lakes Forestry Centre, Natural Resources Canada, Canadian Forest Service, Sault Ste. Marie, ON P6A 2E5, Canada
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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23
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Kadziński L, Łyżeń R, Bury K, Banecki B. Modeling and Optimization of β-Galactosidase Entrapping in Polydimethylsiloxane-Modified Silica Composites. Int J Mol Sci 2022; 23:ijms23105395. [PMID: 35628204 PMCID: PMC9141798 DOI: 10.3390/ijms23105395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 02/05/2023] Open
Abstract
Protein entrapment has multiple applications in enzymatic hydrolysis, drug delivery, etc. Here, we report the studies that successfully utilized the Box–Behnken design to model and optimize the parameters of β-galactosidase entrapment in sol–gel-derived silica composites. We have also demonstrated the influence of polymer–polydimethylsiloxane as a composite modifying agent on the activity of entrapped enzymes. We have determined how different sol-gel process parameters influence the activity of entrapped enzymes. The highest impact on β-galactosidase activity was exerted by the water:tetramethoxysilane ratio, followed by polydimethylsiloxane content. Optimized synthesis parameters have been utilized to obtain a composite with maximum β-galactosidase activity. Performed porosity studies have shown that the addition of polydimethylsiloxane increased the pore diameter. Microscopy studies demonstrated that polydimethylsiloxane-modified composites are softer and less rough. Studies of β-galactosidase activity using the o-NPG test showed statistically significant shifts in the enzyme temperature and pH profiles compared to the soluble form. An improvement in the reusability of the enzyme and a significant increase in the thermal stability was also observed. When lactose was used, a strong correlation was observed between the substrate concentration and the type of the catalyzed reaction. Moreover, we have demonstrated that the yields and rates of both lactose hydrolysis and galactooligosaccharides formation were correlated with reaction temperature and with the presence of polydimethylsiloxane. All these findings provide the opportunity for industrial use of optimized PDMS-modified silica composites in lactose elimination from dairy products, e.g., milk or whey.
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24
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Metabolomic and transcriptional profiling of oleuropein bioconversion into hydroxytyrosol during table olive fermentation by Lactiplantibacillus plantarum. Appl Environ Microbiol 2022; 88:e0201921. [PMID: 35170988 PMCID: PMC8939334 DOI: 10.1128/aem.02019-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
This study aims to elucidate the mechanisms responsible for the bioconversion of oleuropein into low-molecular-weight phenolic compounds in two selected Lactiplantibacillus plantarum strains, namely, C11C8 and F3.5, under stress brine conditions and at two different temperatures (16°C and 30°C). For this purpose, we adopted an experimental strategy that combined high-resolution mass spectrometry, in silico functional analysis of glycoside hydrolase family 1 (GH1)-encoding candidate genes, and gene expression studies. The oleuropein hydrolysis products and the underlying enzymatic steps were identified, and a novel putative bgl gene was detected, using seven strains belonging to the same species as controls. According to metabolomic analysis, a new intermediate compound (decarboxymethyl dialdehydic form of oleuropein aglycone) was revealed. In addition, strain C11C8 showed a decrease in the oleuropein content greater than that of the F3.5 strain (30% versus 15%) at a temperature of 16°C. The highest increase in hydroxytyrosol was depicted by strain C11C8 at a temperature of 30°C. PCR assays and sequencing analyses revealed that both strains possess bglH1, bglH2, and bglH3 genes. Furthermore, a reverse transcription-PCR (RT-PCR) assay showed that bglH3 is the only gene transcribed under all tested conditions, while bglH2 is switched off in strain C11C8 grown at cold temperatures, and no transcription was detected for the bglH1 gene. The bglH3 gene encodes a 6-phospho-β-glucosidase, suggesting how phospho-β-glucosidase activity could belong to the overall metabolic strategy undertaken by L. plantarum to survive in an environment poor in free sugars, like table olives. IMPORTANCE In the present study, a new candidate gene, bglH3, responsible for the β-glucosidase-positive phenotype in L. plantarum was detected, providing the basis for the future marker-assisted selection of L. plantarum starter strains with a β-glucosidase-positive phenotype. Furthermore, the ability of selected strains to hydrolyze oleuropein at low temperatures is important for application as starter cultures on an industrial scale.
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25
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Neis A, da Silva Pinto L. Glycosyl hydrolases family 5, subfamily 5: Relevance and structural insights for designing improved biomass degrading cocktails. Int J Biol Macromol 2021; 193:980-995. [PMID: 34666133 DOI: 10.1016/j.ijbiomac.2021.10.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Endoglucanases are carbohydrate-degrading enzymes widely used for bioethanol production as part of the enzymatic cocktail. However, family 5 subfamily 5 (GH5_5) endoglucanases are still poorly explored in depth. The Trichoderma reesei representative is the most studied enzyme, presenting catalytic activity in acidic media and mild temperature conditions. Though biochemically similar, its modular structure and synergy with other components vary greatly compared to other GH5_5 members and there is still a lack of specific studies regarding their interaction with other cellulases and application on novel and better mixtures. In this regard, the threedimensional structure elucidation is a highly valuable tool to both uncover basic catalytic mechanisms and implement engineering techniques, proved by the high success rate GH5_5 endoglucanases show. GH5_5 enzymes must be carefully evaluated to fully uncover their potential in biomass-degrading cocktails: the optimal industrial conditions, synergy with other cellulases, structural studies, and enzyme engineering approaches. We aimed to provide the current understanding of these main topics, collecting all available information about characterized GH5_5 endoglucanases function, structure, and bench experiments, in order to suggest future directions to a better application of these enzymes in the industry.
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Affiliation(s)
- Alessandra Neis
- Laboratório de Bioinformática e Proteômica (BioPro Lab), Centro de Desenvolvimento Tecnológico, Campus Universitário, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Caixa Postal 96010-900, Brazil.
| | - Luciano da Silva Pinto
- Laboratório de Bioinformática e Proteômica (BioPro Lab), Centro de Desenvolvimento Tecnológico, Campus Universitário, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Caixa Postal 96010-900, Brazil.
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26
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Moroz OV, Blagova E, Lebedev AA, Sánchez Rodríguez F, Rigden DJ, Tams JW, Wilting R, Vester JK, Longhin E, Hansen GH, Krogh KBRM, Pache RA, Davies GJ, Wilson KS. Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions. Acta Crystallogr D Struct Biol 2021; 77:1564-1578. [PMID: 34866612 DOI: 10.1107/s2059798321010949] [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: 06/03/2021] [Accepted: 10/20/2021] [Indexed: 11/10/2022] Open
Abstract
β-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some β-galactosidases also catalyse the formation of galactooligosaccharides by transglycosylation. Both reactions have industrial importance: lactose hydrolysis is used to produce lactose-free milk, while galactooligosaccharides have been shown to act as prebiotics. For some multi-domain β-galactosidases, the hydrolysis/transglycosylation ratio can be modified by the truncation of carbohydrate-binding modules. Here, an analysis of BbgIII, a multidomain β-galactosidase from Bifidobacterium bifidum, is presented. The X-ray structure has been determined of an intact protein corresponding to a gene construct of eight domains. The use of evolutionary covariance-based predictions made sequence docking in low-resolution areas of the model spectacularly easy, confirming the relevance of this rapidly developing deep-learning-based technique for model building. The structure revealed two alternative orientations of the CBM32 carbohydrate-binding module relative to the GH2 catalytic domain in the six crystallographically independent chains. In one orientation the CBM32 domain covers the entrance to the active site of the enzyme, while in the other orientation the active site is open, suggesting a possible mechanism for switching between the two activities of the enzyme, namely lactose hydrolysis and transgalactosylation. The location of the carbohydrate-binding site of the CBM32 domain on the opposite site of the module to where it comes into contact with the catalytic GH2 domain is consistent with its involvement in adherence to host cells. The role of the CBM32 domain in switching between hydrolysis and transglycosylation modes offers protein-engineering opportunities for selective β-galactosidase modification for industrial purposes in the future.
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Affiliation(s)
- Olga V Moroz
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elena Blagova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Andrey A Lebedev
- CCP4, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | | | | | | | - Elena Longhin
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | | | | | - Roland A Pache
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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27
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Horikoshi S, Saburi W, Yu J, Matsuura H, Cairns JRK, Yao M, Mori H. Substrate specificity of glycoside hydrolase family 1 β-glucosidase AtBGlu42 from Arabidopsis thaliana and its molecular mechanism. Biosci Biotechnol Biochem 2021; 86:231-245. [PMID: 34965581 DOI: 10.1093/bbb/zbab200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/13/2021] [Indexed: 11/15/2022]
Abstract
Plants possess many glycoside hydrolase family 1 (GH1) β-glucosidases, which physiologically function in cell wall metabolism and activation of bioactive substances, but most remain uncharacterized. One GH1 isoenzyme AtBGlu42 in Arabidopsis thaliana has been identified to hydrolyze scopolin using the gene deficient plants, but no enzymatic properties were obtained. Its sequence similarity to another functionally characterized enzyme Os1BGlu4 in rice suggests that AtBGlu42 also acts on oligosaccharides. Here, we show that the recombinant AtBGlu42 possesses high kcat/Km not only on scopolin, but also on various β-glucosides, cellooligosaccharides, and laminarioligosaccharides. Of the cellooligosaccharides, cellotriose was the most preferred. The crystal structure, determined at 1.7 Å resolution, suggests that Arg342 gives unfavorable binding to cellooligosaccharides at subsite +3. The mutants R342Y and R342A showed the highest preference on cellotetraose or cellopentaose with increased affinities at subsite +3, indicating that the residues at this position have an important role for chain length specificity.
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Affiliation(s)
- Shu Horikoshi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - James R Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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28
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Pongsapipatana N, Charoenwattanasatien R, Pramanpol N, Nguyen TH, Haltrich D, Nitisinprasert S, Keawsompong S. Crystallization, structural characterization and kinetic analysis of a GH26 β-mannanase from Klebsiella oxytoca KUB-CW2-3. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1425-1436. [PMID: 34726170 DOI: 10.1107/s2059798321009992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/25/2021] [Indexed: 11/10/2022]
Abstract
β-Mannanase (EC 3.2.1.78) is an enzyme that cleaves within the backbone of mannan-based polysaccharides at β-1,4-linked D-mannose residues, resulting in the formation of mannooligosaccharides (MOS), which are potential prebiotics. The GH26 β-mannanase KMAN from Klebsiella oxytoca KUB-CW2-3 shares 49-72% amino-acid sequence similarity with β-mannanases from other sources. The crystal structure of KMAN at a resolution of 2.57 Å revealed an open cleft-shaped active site. The enzyme structure is based on a (β/α)8-barrel architecture, which is a typical characteristic of clan A glycoside hydrolase enzymes. The putative catalytic residues Glu183 and Glu282 are located on the loop connected to β-strand 4 and at the end of β-strand 7, respectively. KMAN digests linear MOS with a degree of polymerization (DP) of between 4 and 6, with high catalytic efficiency (kcat/Km) towards DP6 (2571.26 min-1 mM-1). The predominant end products from the hydrolysis of locust bean gum, konjac glucomannan and linear MOS are mannobiose and mannotriose. It was observed that KMAN requires at least four binding sites for the binding of substrate molecules and hydrolysis. Molecular docking of mannotriose and galactosyl-mannotetraose to KMAN confirmed its mode of action, which prefers linear substrates to branched substrates.
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Affiliation(s)
- Nawapan Pongsapipatana
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Ratana Charoenwattanasatien
- Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Nuttawan Pramanpol
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathumthani 12120, Thailand
| | - Thu Ha Nguyen
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Sunee Nitisinprasert
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Suttipun Keawsompong
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
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29
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Ecological factors influence balancing selection on leaf chemical profiles of a wildflower. Nat Ecol Evol 2021; 5:1135-1144. [PMID: 34140651 PMCID: PMC8325631 DOI: 10.1038/s41559-021-01486-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/07/2021] [Indexed: 02/05/2023]
Abstract
Balancing selection is frequently invoked as a mechanism that maintains variation within and across populations. However, there are few examples of balancing selection operating on loci underpinning complex traits, which frequently display high levels of variation. We investigated mechanisms that may maintain variation in a focal polymorphism-leaf chemical profiles of a perennial wildflower (Boechera stricta, Brassicaceae)-explicitly interrogating multiple ecological and genetic processes including spatial variation in selection, antagonistic pleiotropy and frequency-dependent selection. A suite of common garden and greenhouse experiments showed that the alleles underlying variation in chemical profile have contrasting fitness effects across environments, implicating two ecological drivers of selection on chemical profile: herbivory and drought. Phenotype-environment associations and molecular genetic analyses revealed additional evidence of past selection by these drivers. Together, these data are consistent with balancing selection on chemical profile, probably caused by pleiotropic effects of secondary chemical biosynthesis genes on herbivore defence and drought response.
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30
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Li H, Hu Q, Hong X, Jiang Z, Ni H, Li Q, Zhu Y. Molecular cloning and characterization of a thermostable and halotolerant endo-β-1,4-glucanase from Microbulbifer sp. ALW1. 3 Biotech 2021; 11:250. [PMID: 33968593 PMCID: PMC8088414 DOI: 10.1007/s13205-021-02801-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/19/2021] [Indexed: 01/20/2023] Open
Abstract
The bacterium Microbulbifer sp. ALW1 was previously characterized with the capability to break down the cell wall of brown algae into fine pieces. The biological functions of strain ALW1 were yet to be elucidated. In this study, a gene, namely MaCel5A, was isolated from the ALW1 strain genome, encoding an endo-β-1,4-glucanase. MaCel5A was phylogenetically categorized under the glycoside hydrolase family GH5, with the highest identity to a putative cellulase of Microbulbifer thermotolerans. The recombinant MaCel5A protein purified from heterologous expression in E. coli exhibited maximum activity at 50 °C and pH 6.0, respectively, and functioned selectively toward carboxymethyl cellulose and barley β-glucan. Recombinant MaCel5A demonstrated considerable tolerance to the exposure to high temperature up to 80 °C for 30 min retaining 49% residual activity. In addition, MaCel5A showed moderate stability against pH 5.0-11.0 and strong stability in the presence of nonionic surfactant. MaCel5A exhibited strong halo-stability and halotolerance. The activity of the enzyme increased about tenfold at 0.5 M NaCl, and about fivefold even at 4.0 M NaCl compared to the enzyme activity without the addition of salt. The two conserved glutamic acid residues in MaCel5A featured the typical catalytic acid/base and nucleophile machinery of glycoside hydrolases. These characteristics highlight the industrial application potential of MaCel5A.
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Affiliation(s)
- Hebin Li
- Department of Pharmacy, Xiamen Medical College, Xiamen, 361008 China
| | - Qingsong Hu
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
| | - Xuan Hong
- Department of Pharmacy, Xiamen Medical College, Xiamen, 361008 China
| | - Zedong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021 China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021 China
| | - Qingbiao Li
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021 China
| | - Yanbing Zhu
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021 China
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31
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Jafari S, Ryde U, Irani M. QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues. J Chem Theory Comput 2021; 17:1822-1841. [PMID: 33543623 PMCID: PMC8023669 DOI: 10.1021/acs.jctc.0c01121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Myrosinase from Sinapis alba hydrolyzes glycosidic
bonds of β-d-S-glucosides. The enzyme
shows an enhanced activity in the presence of l-ascorbic
acid. In this work, we employed combined quantum mechanical and molecular
mechanical (QM/MM) calculations and molecular dynamics simulations
to study the catalytic reaction of wild-type myrosinase and its E464A,
Q187A, and Q187E mutants. Test calculations show that a proper QM
region to study the myrosinase reaction must contain the whole substrate,
models of Gln-187, Glu-409, Gln-39, His-141, Asn-186, Tyr-330, Glu-464,
Arg-259, and a water molecule. Furthermore, to make the deglycosylation
step possible, Arg-259 must be charged, Glu-464 must be protonated
on OE2, and His-141 must be protonated on the NE2 atom. The results
indicate that assigning proper protonation states of the residues
is more important than the size of the model QM system. Our model
reproduces the anomeric retaining characteristic of myrosinase and
also reproduces the experimental fact that ascorbate increases the
rate of the reaction. A water molecule in the active site, positioned
by Gln-187, helps the aglycon moiety of the substrate to stabilize
the buildup of negative charge during the glycosylation reaction and
this in turn makes the moiety a better leaving group. The water molecule
also lowers the glycosylation barrier by ∼9 kcal/mol. The results
indicate that the Q187E and E464A mutants but not the Q187A mutant
can perform the glycosylation step. However, the energy profiles for
the deglycosylation step of the mutants are not similar to that of
the wild-type enzyme. The Glu-464 residue lowers the barriers of the
glycosylation and deglycosylation steps. The ascorbate ion can act
as a general base in the reaction of the wild-type enzyme only if
the Glu-464 and His-141 residues are properly protonated.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
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Li K, Jiang C, Tan H, Li J, Xu Y, Tang D, Zhao X, Liu Q, Li J, Yin H. Identification and characterization of a novel glucomannanase from Paenibacillus polymyxa. 3 Biotech 2021; 11:129. [PMID: 33680694 PMCID: PMC7892656 DOI: 10.1007/s13205-021-02676-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/01/2021] [Indexed: 10/22/2022] Open
Abstract
Konjac glucomannan oligosaccharide has attracted much attention due to its broad biological activities. Specific glucomannan degrading enzymes are effective tools for the production of oligosaccharides from konjac glucomannan. However, there are still few reports of commercial enzymes that can specifically degrade konjac glucomannan. The gene ppgluB encoding a glucomannanase consisting of 553 amino acids (61.5 kDa) from Paenibacillus polymyxa 3-3 was cloned and heterologous expressed in Escherichia coli BL21 (DE3). The recombinant PpGluB showed high specificity for the degradation of konjac glucomannan. Moreover, the hydrolytic products of PpGluB degrade konjac glucomannan were a series of oligosaccharides with degrees of polymerisation of 2-12. Furthermore, the biochemical properties indicated that PpGluB is the optimal active at 45 to 55 °C and pH 5.0-6.0, and shows highly pH stability over a very broad pH range. The present characteristics indicated that PpGluB is a potential tool to be used to produce oligosaccharides from konjac glucomannan.
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Affiliation(s)
- Kuikui Li
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Chaofeng Jiang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Haidong Tan
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Junyan Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Yali Xu
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
| | - Dejian Tang
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
| | - Xiaoming Zhao
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Qishun Liu
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Jianguo Li
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
- Ankang Agro-Tech Extension and Service Center, Ankang, 725000 Shaanxi China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
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Xylanases of glycoside hydrolase family 30 - An overview. Biotechnol Adv 2021; 47:107704. [PMID: 33548454 DOI: 10.1016/j.biotechadv.2021.107704] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 12/22/2022]
Abstract
Xylan is the most abundant hemicellulose in nature and as such it is a huge source of renewable carbon. Its bioconversion requires a battery of xylanolytic enzymes. Of them the most important are the endo-β-1,4-xylanases which depolymerize the polysaccharide into smaller fragments. Most of the xylanases are members of glycoside hydrolase (GH) families 10 and 11, although they are classified in some other GH families. The relatively new xylanases of GH30 are of special interest. Initially, they appeared to be specific glucuronoxylanases, however, other specificities were found later among prokaryotic and in particular eukaryotic enzymes. This review gives an overview of the substrate and product specificities observed for the GH30 xylanases characterized to date. An emphasis is given to the structure-activity relationship in order to explain how minor differences in catalytic centre and its vicinity can alter catalytic properties from the endoxylanase into the reducing end xylose releasing exoxylanase or into the non-reducing end xylobiohydrolase. Biotechnological potential of the GH30 xylanases is also considered.
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Baiya S, Pengthaisong S, Kitjaruwankul S, Ketudat Cairns JR. Structural analysis of rice Os4BGlu18 monolignol β-glucosidase. PLoS One 2021; 16:e0241325. [PMID: 33471829 PMCID: PMC7817009 DOI: 10.1371/journal.pone.0241325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/28/2020] [Indexed: 01/07/2023] Open
Abstract
Monolignol glucosides are storage forms of monolignols, which are polymerized to lignin to strengthen plant cell walls. The conversion of monolignol glucosides to monolignols is catalyzed by monolignol β-glucosidases. Rice Os4BGlu18 β-glucosidase catalyzes hydrolysis of the monolignol glucosides, coniferin, syringin, and p-coumaryl alcohol glucoside more efficiently than other natural substrates. To understand more clearly the basis for substrate specificity of a monolignol β-glucosidase, the structure of Os4BGlu18 was determined by X-ray crystallography. Crystals of Os4BGlu18 and its complex with δ-gluconolactone diffracted to 1.7 and 2.1 Å resolution, respectively. Two protein molecules were found in the asymmetric unit of the P212121 space group of their isomorphous crystals. The Os4BGlu18 structure exhibited the typical (β/α)8 TIM barrel of glycoside hydrolase family 1 (GH1), but the four variable loops and two disulfide bonds appeared significantly different from other known structures of GH1 β-glucosidases. Molecular docking studies of the Os4BGlu18 structure with monolignol substrate ligands placed the glycone in a similar position to the δ-gluconolactone in the complex structure and revealed the interactions between protein and ligands. Molecular docking, multiple sequence alignment, and homology modeling identified amino acid residues at the aglycone-binding site involved in substrate specificity for monolignol β-glucosides. Thus, the structural basis of substrate recognition and hydrolysis by monolignol β-glucosidases was elucidated.
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Affiliation(s)
- Supaporn Baiya
- Faculty of Science at Sriracha, Kasetsart University, Sriracha Campus, Sriracha, Chonburi, Thailand
| | - Salila Pengthaisong
- School of Chemistry, Institute of Science and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Sunan Kitjaruwankul
- Faculty of Science at Sriracha, Kasetsart University, Sriracha Campus, Sriracha, Chonburi, Thailand
| | - James R. Ketudat Cairns
- School of Chemistry, Institute of Science and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
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Pilot-Scale Production of Chito-Oligosaccharides Using an Innovative Recombinant Chitosanase Preparation Approach. Polymers (Basel) 2021; 13:polym13020290. [PMID: 33477553 PMCID: PMC7831125 DOI: 10.3390/polym13020290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/03/2022] Open
Abstract
For pilot-scale production of chito-oligosaccharides, it must be cost-effective to prepare designable recombinant chitosanase. Herein, an efficient method for preparing recombinant Bacillus chitosanase from Escherichia coli by elimination of undesirable substances as a precipitate is proposed. After an optimized culture with IPTG (Isopropyl β-d-1-thiogalactopyranoside) induction, the harvested cells were resuspended, disrupted by sonication, divided by selective precipitation, and stored using the same solution conditions. Several factors involved in these procedures, including ion types, ionic concentration, pH, and bacterial cell density, were examined. The optimal conditions were inferred to be pH = 4.5, 300 mM sodium dihydrogen phosphate, and cell density below 1011 cells/mL. Finally, recombinant chitosanase was purified to >70% homogeneity with an activity recovery and enzyme yield of 90% and 106 mg/L, respectively. When 10 L of 5% chitosan was hydrolyzed with 2500 units of chitosanase at ambient temperature for 72 h, hydrolyzed products having molar masses of 833 ± 222 g/mol with multiple degrees of polymerization (chito-dimer to tetramer) were obtained. This work provided an economical and eco-friendly preparation of recombinant chitosanase to scale up the hydrolysis of chitosan towards tailored oligosaccharides in the near future.
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36
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Are Physicochemical Properties Shaping the Allergenic Potency of Animal Allergens? Clin Rev Allergy Immunol 2021; 62:1-36. [DOI: 10.1007/s12016-020-08826-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 12/31/2022]
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37
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Dong S, Liu YJ, Zhou H, Xiao Y, Xu J, Cui Q, Wang X, Feng Y. Structural insight into a GH1 β-glucosidase from the oleaginous microalga, Nannochloropsis oceanica. Int J Biol Macromol 2020; 170:196-206. [PMID: 33347927 DOI: 10.1016/j.ijbiomac.2020.12.128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 11/28/2022]
Abstract
Marine microalgae are promising sources of novel glycoside hydrolases (GHs), which have great value in biotechnical and industrial applications. Although many GH1 family β-glucosidases have been extensively studied, studies on β-glucosidases from microalgae are rare, and no structure of algal GH1 β-glucosidase has been reported. Here, we report the biochemical and structural study of a GH1 β-glucosidase BGLN1 from Nannochloropsis oceanica, an oleaginous microalga. Phylogenetic analysis of BGLN1, together with the known structures of GH1 β-glucosidases, has indicated that BGLN1 is branched at the root of the eukaryotic part of the phylogenetic tree. BGLN1 showed higher activity against laminaribiose compared to cello-oligosaccharides. Unlike most of the other GH1 β-glucosidases, BGLN1 is partially inhibited by metal ions. The crystal structure of BGLN1 revealed that BGLN1 adopts a typical (α/β)8-barrel fold with variations in loops and N-terminal regions. BGLN1 contains extra residues at the N-terminus, which are essential for maintaining protein stability. BGLN1 has a more acidic substrate-binding pocket than other β-glucosidases, and the variations beyond the conserved -1 site determine the substrate specificity. These results indicate that GH enzymes from microalgae may have unique structural and functional features, which will provide new insight into carbohydrate synthesis and metabolism in marine microalgae.
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Affiliation(s)
- Sheng Dong
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Zhou
- Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Xiao
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Xu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xinquan Wang
- Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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38
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Lakshmi SA, Shafreen RB, Priyanga A, Shiburaj S, Pandian SK. A highly divergent α-amylase from Streptomyces spp.: An evolutionary perspective. Int J Biol Macromol 2020; 163:2415-2428. [PMID: 32961188 DOI: 10.1016/j.ijbiomac.2020.09.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/01/2020] [Accepted: 09/15/2020] [Indexed: 11/18/2022]
Abstract
The present study deals with the genetic changes observed in the protein sequence of an α-amylase from Streptomyces spp. and its structural homologs from Pseudoalteromonas haloplanktis, invertebrates and mammals. The structural homologs are renowned for their important features such as chloride binding triad and a serine-protease like catalytic triad (a triad which is reported to be strictly conserved in all chloride-dependent α-amylases). These conserved regions are essential for allosteric activation of enzyme and conformational stability, respectively. An evaluation of these distinctive features in Streptomyces α-amylases revealed the role of mutations in conserved regions and evolution of chloride-independent α-amylases in Streptomyces spp. Besides, the study also discovers a highly divergent α-amylase from Streptomyces spp. which varies greatly even within the homologs of the same genus. Another very important feature is the number of disulfide bridges in which the structural homologs own eight Cys residues to form four disulfide bridges whereas Streptomyces α-amylases possess only seven Cys to form three disulfide bridges. The study also highlights the unique evolution of carbohydrate binding module 20 domain (CBM20 also known as raw starch binding domain or E domain) in Streptomyces α-amylases which is completely absent in α-amylases of other structural homologs.
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Affiliation(s)
- Selvaraj Alagu Lakshmi
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630003, Tamil Nadu, India
| | | | - Appasamy Priyanga
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630003, Tamil Nadu, India
| | - Sugathan Shiburaj
- Division of Microbiology, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Palode, Thiruvananthapuram, Kerala 695562, India; Department of Botany, University of Kerala, Kariavattom, Thiruvananthapuram, Kerala 695581, India
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39
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Kaira GS, Kapoor M. Molecular advancements on over-expression, stability and catalytic aspects of endo-β-mannanases. Crit Rev Biotechnol 2020; 41:1-15. [PMID: 33032458 DOI: 10.1080/07388551.2020.1825320] [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] [Indexed: 10/23/2022]
Abstract
The hydrolysis of mannans by endo-β-mannanases continues to gather significance as exemplified by its commercial applications in food, feed, and a rekindled interest in biorefineries. The present review provides a comprehensive account of fundamental research and fascinating insights in the field of endo-β-mannanase engineering in order to improve over-expression and to decipher molecular determinants governing activity-stability during harsh conditions, substrate recognition, polysaccharide specificity, endo/exo mode of action and multi-functional activities in the modular polypeptide. In-depth analysis of the available literature has also been made on rational and directed evolution approaches, which have translated native endo-β-mannanases into superior biocatalysts for satisfying industrial requirements.
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Affiliation(s)
- Gaurav Singh Kaira
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mukesh Kapoor
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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40
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Thakur CJ, Saini S, Notra A, Chauhan B, Arya S, Gupta R, Thakur J, Kumar V. Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2020; 9:129-139. [PMID: 33313333 PMCID: PMC7727763 DOI: 10.22099/mbrc.2020.36894.1495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Chloroflexus aurantiacus J-10-f1 is an anoxygenic, photosynthetic, facultative autotrophic gram negative bacterium found from hot spring at a temperature range of 50-60°C. It can sustain itself in dark only if oxygen is available thereby exhibiting a dark orange color, however display a dark green color when grown in sunlight. Genome of the organism contains total of 3853 proteins out of which 785 (~20%) proteins are uncharacterised or hypothetical proteins (HPs). Therefore in this work we have characterized the 785 hypothetical proteins of Chloroflexus aurantiacus J-10-f1 using bioinformatics tools and databases. HPs annotated by more than five domain prediction tools were filtered and named high confidence-hypothetical proteins (HC-HPs). These HC-HPs were further annotated by calculating their physiochemical properties, homologous, subcellular locations, signal peptides and transmembrane regions. We found most of the HC-HPs were involved in photosynthesis, carbohydrate metabolism, biofuel production and cellulose synthesis processes. Furthermore, few of these HC-HPs could provide resistance to bacteria at high temperature due to their thermophilic nature. Hence these HC-HPs have the potential to be used in industrial as well as in biomedical needs. To conclude, the bioinformatics approach used in this study provides an insight to better understand the nature and role of Chloroflexus aurantiacus J-10-f1 hypothetical proteins.
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Affiliation(s)
- Chander Jyoti Thakur
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India,Corresponding Author: Department of Bioinformatics, GGDSD College, Chandigarh, India. Tel: +91 8699776533 ; Fax: +91 172 2661077, E. mail:
| | - Sandeep Saini
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India,Department of Biophysics, Panjab University, Sector 25, 160014, Chandigarh, India
| | - Aayushi Notra
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Bhavanshu Chauhan
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Sarthak Arya
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Rishabh Gupta
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Jyotsna Thakur
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Varinder Kumar
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
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41
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Guerrero EB, de Villegas RMD, Soria MA, Santangelo MP, Campos E, Talia PM. Characterization of two GH5 endoglucanases from termite microbiome using synthetic metagenomics. Appl Microbiol Biotechnol 2020; 104:8351-8366. [DOI: 10.1007/s00253-020-10831-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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42
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Bernardes JS, Eberle RJ, Vieira FRJ, Coronado MA. A comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains. J Biomol Struct Dyn 2020; 39:6974-6986. [PMID: 32779519 DOI: 10.1080/07391102.2020.1805017] [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] [Indexed: 10/23/2022]
Abstract
Corynebacterium pseudotuberculosis is a pathogenic bacterium with great veterinary and economic importance. It is classified into two biovars: ovis, nitrate-negative, that causes lymphadenitis in small ruminants and equi, nitrate-positive, causing ulcerative lymphangitis in equines. With the explosive growth of available genomes of several strains, pan-genome analysis has opened new opportunities for understanding the dynamics and evolution of C. pseudotuberculosis. However, few pan-genomic studies have compared biovars equi and ovis. Such studies have considered a reduced number of strains and compared entire genomes. Here we conducted an original pan-genome analysis based on protein sequences and their functional domains. We considered 53 C. pseudotuberculosis strains from both biovars isolated from different hosts and countries. We have analysed conserved domains, common domains more frequently found in each biovar and biovar-specific (unique) domains. Our results demonstrated that biovar equi is more variable; there is a significant difference in the number of proteins per strains, probably indicating the occurrence of more gene loss/gain events. Moreover, strains of biovar equi presented a higher number of biovar-specific domains, 77 against only eight in biovar ovis, most of them are associated with virulence mechanisms. With this domain analysis, we have identified functional differences among strains of biovars ovis and equi that could be related to niche-adaptation and probably help to better understanding mechanisms of virulence and pathogenesis. The distribution patterns of functional domains identified in this work might have impacts on bacterial physiology and lifestyle, encouraging the development of new diagnoses, vaccines, and treatments for C. pseudotuberculosis diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Juliana S Bernardes
- Laboratoire de Biologie Computationelle et Quantitative, UMR 7238, CNRS, Sorbonne Université, Paris, France
| | - Raphael J Eberle
- Multiuser Center for Biomolecular Innovation, Department of Physics, Instituto de Biociências, Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, Brazil
| | - Fabio R J Vieira
- Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France
| | - Mônika A Coronado
- Multiuser Center for Biomolecular Innovation, Department of Physics, Instituto de Biociências, Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, Brazil.,Institute of Biological Information Processing (IBI-7: Strucutral Biochemistry), Forschungszentrum Juelich, Juelich, Germany
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43
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Ureta MM, Martins GN, Figueira O, Pires PF, Castilho PC, Gomez-Zavaglia A. Recent advances in β-galactosidase and fructosyltransferase immobilization technology. Crit Rev Food Sci Nutr 2020; 61:2659-2690. [PMID: 32590905 DOI: 10.1080/10408398.2020.1783639] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The highly demanding conditions of industrial processes may lower the stability and affect the activity of enzymes used as biocatalysts. Enzyme immobilization emerged as an approach to promote stabilization and easy removal of enzymes for their reusability. The aim of this review is to go through the principal immobilization strategies addressed to achieve optimal industrial processes with special care on those reported for two types of enzymes: β-galactosidases and fructosyltransferases. The main methods used to immobilize these two enzymes are adsorption, entrapment, covalent coupling and cross-linking or aggregation (no support is used), all of them having pros and cons. Regarding the support, it should be cost-effective, assure the reusability and an easy recovery of the enzyme, increasing its stability and durability. The discussion provided showed that the type of enzyme, its origin, its purity, together with the type of immobilization method and the support will affect the performance during the enzymatic synthesis. Enzymes' immobilization involves interdisciplinary knowledge including enzymology, nanotechnology, molecular dynamics, cellular physiology and process design. The increasing availability of facilities has opened a variety of possibilities to define strategies to optimize the activity and re-usability of β-galactosidases and fructosyltransferases, but there is still great place for innovative developments.
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Affiliation(s)
- Maria Micaela Ureta
- Center for Research and Development in Food Cryotechnology (CIDCA, CCT-CONICET La Plata), La Plata, Argentina
| | | | - Onofre Figueira
- CQM - Centro de Química da Madeira, Universidade da Madeira, Funchal, Portugal
| | - Pedro Filipe Pires
- CQM - Centro de Química da Madeira, Universidade da Madeira, Funchal, Portugal
| | | | - Andrea Gomez-Zavaglia
- Center for Research and Development in Food Cryotechnology (CIDCA, CCT-CONICET La Plata), La Plata, Argentina
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44
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Immunoreactive Proteins in the Esophageal Gland Cells of Anisakis Simplex Sensu Stricto Detected by MALDI-TOF/TOF Analysis. Genes (Basel) 2020; 11:genes11060683. [PMID: 32580523 PMCID: PMC7349779 DOI: 10.3390/genes11060683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 01/15/2023] Open
Abstract
In plant and animal nematode parasites, proteins derived from esophageal gland cells have been shown to be important in the host-nematodes relationship but little is known about the allergenic potential of these proteins in the genus Anisakis. Taking into account the increase of anisakiasis and allergies related to these nematodes, immunoreactive properties of gland cell proteins were investigated. Two hundred ventricles were manually dissected from L3 stage larvae of Aniskakis simplex s.s. to allow direct protein analysis. Denaturing gel electrophoresis followed by monochromatic silver staining which revealed the presence of differential (enriched) proteins when compared to total nematode extracts. Such comparison was performed by means of 1D and 2D electrophoresis. Pooled antisera from Anisakis spp.-allergic patients were used in western blots revealing the presence of 13 immunoreactive bands in the ventricular extracts in 1D, with 82 spots revealed in 2D. The corresponding protein bands and spots were excised from the silver-stained gel and protein assignation was made by MALDI-TOF/TOF. A total of 13 (including proteoforms) were unambiguously identified. The majority of these proteins are known to be secreted by nematodes into the external environment, of which three are described as being major allergens in other organisms with different phylogenetic origin and one is an Anisakis simplex allergen.
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45
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Mangiagalli M, Lapi M, Maione S, Orlando M, Brocca S, Pesce A, Barbiroli A, Camilloni C, Pucciarelli S, Lotti M, Nardini M. The co-existence of cold activity and thermal stability in an Antarctic GH42 β-galactosidase relies on its hexameric quaternary arrangement. FEBS J 2020; 288:546-565. [PMID: 32363751 DOI: 10.1111/febs.15354] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 11/28/2022]
Abstract
To survive in cold environments, psychrophilic organisms produce enzymes endowed with high specific activity at low temperature. The structure of these enzymes is usually flexible and mostly thermolabile. In this work, we investigate the structural basis of cold adaptation of a GH42 β-galactosidase from the psychrophilic Marinomonas ef1. This enzyme couples cold activity with astonishing robustness for a psychrophilic protein, for it retains 23% of its highest activity at 5 °C and it is stable for several days at 37 °C and even 50 °C. Phylogenetic analyses indicate a close relationship with thermophilic β-galactosidases, suggesting that the present-day enzyme evolved from a thermostable scaffold modeled by environmental selective pressure. The crystallographic structure reveals the overall similarity with GH42 enzymes, along with a hexameric arrangement (dimer of trimers) not found in psychrophilic, mesophilic, and thermophilic homologues. In the quaternary structure, protomers form a large central cavity, whose accessibility to the substrate is promoted by the dynamic behavior of surface loops, even at low temperature. A peculiar cooperative behavior of the enzyme is likely related to the increase of the internal cavity permeability triggered by heating. Overall, our results highlight a novel strategy of enzyme cold adaptation, based on the oligomerization state of the enzyme, which effectively challenges the paradigm of cold activity coupled with intrinsic thermolability. DATABASE: Structural data are available in the Protein Data Bank database under the accession number 6Y2K.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Michela Lapi
- Department of Biosciences, University of Milano, Italy
| | - Serena Maione
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | | | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Italy
| | | | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
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46
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Santos CR, Costa PACR, Vieira PS, Gonzalez SET, Correa TLR, Lima EA, Mandelli F, Pirolla RAS, Domingues MN, Cabral L, Martins MP, Cordeiro RL, Junior AT, Souza BP, Prates ÉT, Gozzo FC, Persinoti GF, Skaf MS, Murakami MT. Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol 2020; 16:920-929. [PMID: 32451508 DOI: 10.1038/s41589-020-0554-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/22/2020] [Indexed: 11/09/2022]
Abstract
The fundamental and assorted roles of β-1,3-glucans in nature are underpinned on diverse chemistry and molecular structures, demanding sophisticated and intricate enzymatic systems for their processing. In this work, the selectivity and modes of action of a glycoside hydrolase family active on β-1,3-glucans were systematically investigated combining sequence similarity network, phylogeny, X-ray crystallography, enzyme kinetics, mutagenesis and molecular dynamics. This family exhibits a minimalist and versatile (α/β)-barrel scaffold, which can harbor distinguishing exo or endo modes of action, including an ancillary-binding site for the anchoring of triple-helical β-1,3-glucans. The substrate binding occurs via a hydrophobic knuckle complementary to the canonical curved conformation of β-1,3-glucans or through a substrate conformational change imposed by the active-site topology of some fungal enzymes. Together, these findings expand our understanding of the enzymatic arsenal of bacteria and fungi for the breakdown and modification of β-1,3-glucans, which can be exploited for biotechnological applications.
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Affiliation(s)
- Camila R Santos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Pedro A C R Costa
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Plínio S Vieira
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | | | - Thamy L R Correa
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Evandro A Lima
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Fernanda Mandelli
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Lucelia Cabral
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Marcele P Martins
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Rosa L Cordeiro
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Atílio T Junior
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Beatriz P Souza
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Érica T Prates
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Fabio C Gozzo
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil.
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47
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Dashnyam P, Lin HY, Chen CY, Gao S, Yeh LF, Hsieh WC, Tu Z, Lin CH. Substituent Position of Iminocyclitols Determines the Potency and Selectivity for Gut Microbial Xenobiotic-Reactivating Enzymes. J Med Chem 2020; 63:4617-4627. [PMID: 32105467 DOI: 10.1021/acs.jmedchem.9b01918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Selective inhibitors of gut bacterial β-glucuronidases (GUSs) are of particular interest in the prevention of xenobiotic-induced toxicities. This study reports the first structure-activity relationships on potency and selectivity of several iminocyclitols (2-7) for the GUSs. Complex structures of Ruminococcus gnavus GUS with 2-7 explained how charge, conformation, and substituent of iminocyclitols affect their potency and selectivity. N1 of uronic isofagomine (2) made strong electrostatic interactions with two catalytic glutamates of GUSs, resulting in the most potent inhibition (Ki ≥ 11 nM). C6-propyl analogue of 2 (6) displayed 700-fold selectivity for opportunistic bacterial GUSs (Ki = 74 nM for E. coli GUS and 51.8 μM for RgGUS). In comparison with 2, there was 200-fold enhancement in the selectivity, which was attributed to differential interactions between the propyl group and loop 5 residues of the GUSs. The results provide useful insights to develop potent and selective inhibitors for undesired GUSs.
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Affiliation(s)
- Punsaldulam Dashnyam
- Institute of Biological Chemistry, Academia Sinica, No 128, Academia Road, Taipei 11529, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,National Chung-Hsing University, Taichung 40227, Taiwan.,Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Hsien-Ya Lin
- Institute of Biological Chemistry, Academia Sinica, No 128, Academia Road, Taipei 11529, Taiwan
| | - Chia-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, No 128, Academia Road, Taipei 11529, Taiwan
| | - Shijay Gao
- Institute of Biological Chemistry, Academia Sinica, No 128, Academia Road, Taipei 11529, Taiwan
| | - Lun-Fu Yeh
- Institute of Biological Chemistry, Academia Sinica, No 128, Academia Road, Taipei 11529, Taiwan
| | - Wei-Che Hsieh
- Institute of Biological Chemistry, Academia Sinica, No 128, Academia Road, Taipei 11529, Taiwan
| | - Zhijay Tu
- Institute of Biological Chemistry, Academia Sinica, No 128, Academia Road, Taipei 11529, Taiwan
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, No 128, Academia Road, Taipei 11529, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,National Chung-Hsing University, Taichung 40227, Taiwan.,Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan.,Department of Chemistry and Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
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48
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Zarafeta D, Galanopoulou AP, Leni ME, Kaili SI, Chegkazi MS, Chrysina ED, Kolisis FN, Hatzinikolaou DG, Skretas G. XynDZ5: A New Thermostable GH10 Xylanase. Front Microbiol 2020; 11:545. [PMID: 32390953 PMCID: PMC7193231 DOI: 10.3389/fmicb.2020.00545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
Xylanolytic enzymes have a broad range of applications in industrial biotechnology as biocatalytic components of various processes and products, such as food additives, bakery products, coffee extraction, agricultural silage and functional foods. An increasing market demand has driven the growing interest for the discovery of xylanases with specific industrially relevant characteristics, such as stability at elevated temperatures and in the presence of other denaturing factors, which will facilitate their incorporation into industrial processes. In this work, we report the discovery and biochemical characterization of a new thermostable GH10 xylanase, termed XynDZ5, exhibiting only 26% amino acid sequence identity to the closest characterized xylanolytic enzyme. This new enzyme was discovered in an Icelandic hot spring enrichment culture of a Thermoanaerobacterium species using a recently developed bioinformatic analysis platform. XynDZ5 was produced recombinantly in Escherichia coli, purified and characterized biochemically. This analysis revealed that it acts as an endo-1,4-β-xylanase that performs optimally at 65–75°C and pH 7.5. The enzyme is capable of retaining high levels of catalytic efficiency after several hours of incubation at high temperatures, as well as in the presence of significant concentrations of a range of metal ions and denaturing agents. Interestingly, the XynDZ5 biochemical profile was found to be atypical, as it also exhibits significant exo-activity. Computational modeling of its three-dimensional structure predicted a (β/α)8 TIM barrel fold, which is very frequently encountered among family GH10 enzymes. This modeled structure has provided clues about structural features that may explain aspects of its catalytic performance. Our results suggest that XynDZ5 represents a promising new candidate biocatalyst appropriate for several high-temperature biotechnological applications in the pulp, paper, baking, animal-feed and biofuel industries.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia P Galanopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Evangelia Leni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Stavroula I Kaili
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Magda S Chegkazi
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitris G Hatzinikolaou
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
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49
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Sieriebriennikov B, Sun S, Lightfoot JW, Witte H, Moreno E, Rödelsperger C, Sommer RJ. Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell. PLoS Genet 2020; 16:e1008687. [PMID: 32282814 PMCID: PMC7179942 DOI: 10.1371/journal.pgen.1008687] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/23/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Environment shapes development through a phenomenon called developmental plasticity. Deciphering its genetic basis has potential to shed light on the origin of novel traits and adaptation to environmental change. However, molecular studies are scarce, and little is known about molecular mechanisms associated with plasticity. We investigated the gene regulatory network controlling predatory vs. non-predatory dimorphism in the nematode Pristionchus pacificus and found that it consists of genes of extremely different age classes. We isolated mutants in the conserved nuclear hormone receptor nhr-1 with previously unseen phenotypic effects. They disrupt mouth-form determination and result in animals combining features of both wild-type morphs. In contrast, mutants in another conserved nuclear hormone receptor nhr-40 display altered morph ratios, but no intermediate morphology. Despite divergent modes of control, NHR-1 and NHR-40 share transcriptional targets, which encode extracellular proteins that have no orthologs in Caenorhabditis elegans and result from lineage-specific expansions. An array of transcriptional reporters revealed co-expression of all tested targets in the same pharyngeal gland cell. Major morphological changes in this gland cell accompanied the evolution of teeth and predation, linking rapid gene turnover with morphological innovations. Thus, the origin of feeding plasticity involved novelty at the level of genes, cells and behavior.
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Affiliation(s)
- Bogdan Sieriebriennikov
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shuai Sun
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - James W. Lightfoot
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eduardo Moreno
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ralf J. Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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50
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Grootaert H, Van Landuyt L, Hulpiau P, Callewaert N. Functional exploration of the GH29 fucosidase family. Glycobiology 2020; 30:735-745. [PMID: 32149359 DOI: 10.1093/glycob/cwaa023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/27/2020] [Accepted: 02/27/2020] [Indexed: 12/16/2022] Open
Abstract
The deoxy sugar l-fucose is frequently found as a glycan constituent on and outside living cells, and in mammals it is involved in a wide range of biological processes including leukocyte trafficking, histo-blood group antigenicity and antibody effector functions. The manipulation of fucose levels in those biomedically important systems may provide novel insights and therapeutic leads. However, despite the large established sequence diversity of natural fucosidases, so far, very few enzymes have been characterized. We explored the diversity of the α-l-fucosidase-containing CAZY family GH29 by bio-informatic analysis, and by the recombinant production and exploration for fucosidase activity of a subset of 82 protein sequences that represent the family's large sequence diversity. After establishing that most of the corresponding proteins can be readily expressed in E. coli, more than half of the obtained recombinant proteins (57% of the entire subset) showed activity towards the simple chromogenic fucosylated substrate 4-nitrophenyl α-l-fucopyranoside. Thirty-seven of these active GH29 enzymes (and the GH29 subtaxa that they represent) had not been characterized before. With such a sequence diversity-based collection available, it can easily be used to screen for fucosidase activity towards biomedically relevant fucosylated glycoproteins. As an example, the subset was used to screen GH29 members for activity towards the naturally occurring sialyl-Lewis x-type epitope on glycoproteins, and several such enzymes were identified. Together, the results provide a significant increase in the diversity of characterized GH29 enzymes, and the recombinant enzymes constitute a resource for the further functional exploration of this enzyme family.
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Affiliation(s)
- Hendrik Grootaert
- VIB Center for Medical Biotechnology, VIB, Zwijnaarde, Technologiepark 71, 9052 Ghent (Zwijnaarde), Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark 71, 9052 Ghent (Zwijnaarde), Belgium
| | - Linde Van Landuyt
- VIB Center for Medical Biotechnology, VIB, Zwijnaarde, Technologiepark 71, 9052 Ghent (Zwijnaarde), Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark 71, 9052 Ghent (Zwijnaarde), Belgium
| | - Paco Hulpiau
- VIB Center for Inflammation Research, VIB, Zwijnaarde, Technologiepark 71, 9052 Ghent (Zwijnaarde), Belgium
| | - Nico Callewaert
- VIB Center for Medical Biotechnology, VIB, Zwijnaarde, Technologiepark 71, 9052 Ghent (Zwijnaarde), Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark 71, 9052 Ghent (Zwijnaarde), Belgium
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