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Jeilu O, Alexandersson E, Johansson E, Simachew A, Gessesse A. A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation. Sci Rep 2024; 14:10012. [PMID: 38693138 PMCID: PMC11063200 DOI: 10.1038/s41598-024-60645-y] [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: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.
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Affiliation(s)
- Oliyad Jeilu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden.
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia.
| | - Erik Alexandersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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Hu C, Wang Y, Wang W, Cui W, Jia X, Mayo KH, Zhou Y, Su J, Yuan Y. A trapped covalent intermediate as a key catalytic element in the hydrolysis of a GH3 β-glucosidase: An X-ray crystallographic and biochemical study. Int J Biol Macromol 2024; 265:131131. [PMID: 38527679 DOI: 10.1016/j.ijbiomac.2024.131131] [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: 01/10/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
Glycoside hydrolases (GHs) are industrially important enzymes that hydrolyze glycosidic bonds in glycoconjugates. In this study, we found a GH3 β-glucosidase (CcBgl3B) from Cellulosimicrobium cellulans sp. 21 was able to selectively hydrolyze the β-1,6-glucosidic bond linked glucose of ginsenosides. X-ray crystallographic studies of the ligand complex ginsenoside-specific β-glucosidase provided a novel finding that support the catalytic mechanism of GH3. The substrate was clearly identified within the catalytic center of wild-type CcBgl3B, revealing that the C1 atom of the glucose was covalently bound to the Oδ1 group of the conserved catalytic nucleophile Asp264 as an enzyme-glycosyl intermediate. The glycosylated Asp264 could be identified by mass spectrometry. Through site-directed mutagenesis studies with Asp264, it was found that the covalent intermediate state formed by Asp264 and the substrate was critical for catalysis. In addition, Glu525 variants (E525A, E525Q and E525D) showed no or marginal activity against pNPβGlc; thus, this residue could supply a proton for the reaction. Overall, our study provides an insight into the catalytic mechanism of the GH3 enzyme CcBgl3B.
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Affiliation(s)
- Chenxing Hu
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Yibing Wang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Weiyang Wang
- College of Life Science and Technology, Changchun University of Science & Technology, Changchun, Jilin 130022, China
| | - Wanli Cui
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Xinyue Jia
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, 6-155 Jackson Hall, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yifa Zhou
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Jiyong Su
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China.
| | - Ye Yuan
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China.
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Guo Y, Sun S, Gu M, Zhang L, Cheng L, Li Z, Li C, Ban X, Hong Y, Gu Z. Optimization and analysis of dual-enzymatic synthesis for the production of linear glucan. Int J Biol Macromol 2024; 259:129299. [PMID: 38211915 DOI: 10.1016/j.ijbiomac.2024.129299] [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: 10/11/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Linear α-glucan (LG), a linear polymer linked by α-1,4 bonds, has received increasing attention for its potential applications in synthetic polymer production. Notably, the functionality of LG is strongly influenced by its degree of polymerization (DP). In this study, SP and GP were successfully constructed and expressed. The reaction of enzymatic co-polymerization into LG was investigated. The preferred reaction was carried out at 37 °C and pH 7.4 for 72 h, with a maximum conversion rate of 25 %. Afterwards, two approaches were used to modulate the molecular structures of LGs. Firstly, LGs with distinct molecular weights ranging from 1062.33 ± 16.04 g/mol to 5679 ± 80.29 g/mol were obtained by adjusting the substrate/primer ratio during the LG synthesis process. Secondly, two distinct products could be produced by altering the enzyme addition method: short-chain LG with a DP < 10 (64.34 ± 0.54 %) or long-chain LG with a DP > 45 (45.57 ± 2.18 %). Additionally, theoretical synthesis model was constructed which subdivided the reaction into three stages to evaluate this dual-enzyme cooperative system. These findings have significant implications in promoting the application of LG in the fields of biomedicine and material science.
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Affiliation(s)
- Yue Guo
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shenglin Sun
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong Province 271018, China
| | - Mingfei Gu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liyue Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Li Cheng
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Yan Hong
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China; Jiaxing Institute of Future Food, Jiaxing 314050, China.
| | - Zhengbiao Gu
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China.
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Serra GM, Siqueira AS, de Molfetta FA, Santos AV, Xavier LP. In Silico Analysis of a GH3 β-Glucosidase from Microcystis aeruginosa CACIAM 03. Microorganisms 2023; 11:microorganisms11040998. [PMID: 37110421 PMCID: PMC10146135 DOI: 10.3390/microorganisms11040998] [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: 12/13/2022] [Revised: 02/02/2023] [Accepted: 02/28/2023] [Indexed: 04/29/2023] Open
Abstract
Cyanobacteria are rich sources of secondary metabolites and have the potential to be excellent industrial enzyme producers. β-glucosidases are extensively employed in processing biomass degradation as they mediate the most crucial step of bioconversion of cellobiose (CBI), hence controlling the efficiency and global rate of biomass hydrolysis. However, the production and availability of these enzymes derived from cyanobacteria remains limited. In this study, we evaluated the β-glucosidase from Microcystis aeruginosa CACIAM 03 (MaBgl3) and its potential for bioconversion of cellulosic biomass by analyzing primary/secondary structures, predicting physicochemical properties, homology modeling, molecular docking, and simulations of molecular dynamics (MD). The results showed that MaBgl3 derives from an N-terminal domain folded as a distorted β-barrel, which contains the conserved His-Asp catalytic dyad often found in glycosylases of the GH3 family. The molecular docking results showed relevant interactions with Asp81, Ala271 and Arg444 residues that contribute to the binding process during MD simulation. Moreover, the MD simulation of the MaBgl3 was stable, shown by analyzing the root mean square deviation (RMSD) values and observing favorable binding free energy in both complexes. In addition, experimental data suggest that MaBgl3 could be a potential enzyme for cellobiose-hydrolyzing degradation.
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Affiliation(s)
- Gustavo Marques Serra
- Laboratório de Biotecnologia de Enzimas e Biotransformações, Instituto de Ciências Biológicas, Universidade Federal do Pará-UFPA, Belém 66075-110, Brazil
| | - Andrei Santos Siqueira
- Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará-UFPA, Belém 66075-110, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará-UFPA, Belém 66075-10, Brazil
| | - Agenor Valadares Santos
- Laboratório de Biotecnologia de Enzimas e Biotransformações, Instituto de Ciências Biológicas, Universidade Federal do Pará-UFPA, Belém 66075-110, Brazil
| | - Luciana Pereira Xavier
- Laboratório de Biotecnologia de Enzimas e Biotransformações, Instituto de Ciências Biológicas, Universidade Federal do Pará-UFPA, Belém 66075-110, Brazil
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Wang Y, Zhang X, Lin Y, Lin H. The electron transport mechanism of downflow Leersia hexandra Swartz constructed wetland-microbial fuel cell when used to treat Cr(VI) and p-chlorophenol. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:37929-37945. [PMID: 36576625 DOI: 10.1007/s11356-022-24872-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Constructed wetland-microbial fuel cells are used to treat heavy metal and/or refractory organic wastewater. However, the electron transport mechanism of downflow Leersia hexandra constructed wetland-microbial fuel cells (DLCW-MFCs) is poorly understood when used to treat composite-polluted wastewater containing Cr(VI) and p-chlorophenol (4-CP) (C&P). In this study, metagenomics and in situ electrochemical techniques were used to investigate the electrochemical properties and the electricigens and their dominant gene functions. The DLCW-MFC was used to treat C&P and single-pollutant wastewater containing Cr(VI) (SC) and 4-CP (SP). The results showed that C&P had a higher current response and charge transfer capability and lower solution resistance plus charge transfer resistance. The anode bacteria solution of C&P contained more electron carriers (RF, FMN, FAD, CoQ10, and Cyt c). Metagenomic sequencing indicated that the total relative abundance of the microorganisms associated with electricity production (Desulfovibrio, Pseudomonas, Azospirillum, Nocardia, Microbacterium, Delftia, Geobacter, Acinetobacter, Bacillus, and Clostridium) was the highest in C&P (4.24%). However, Microbacterium was abundant in SP (0.12%), which exerted antagonistic effects on other electricigens. Among the 10 electricigens based on gene annotation, C&P had a higher overall relative abundance of the Unigene gene annotated to the KO pathway and CAZy level B compared with SC and SP, which were 1.31% and 0.582% respectively. Unigene153954 (ccmC), Unigene357497 (coxB), and Unigene1033667 (ubiG) were related to the electron carrier Cyt c, electron transfer, and CoQ biosynthesis, respectively. These were annotated to Desulfovibrio, Delftia, and Pseudomonas, respectively. Unigene161312 (AA1) used phenols and other substrates as electron donors and was annotated to Pseudomonas. Other functional carbohydrate enzyme genes (e.g., GT2, GT4, and GH31) used carbohydrates as donors and were annotated to other electricigens. This study provides a theoretical basis for electron transfer to promote the development of CW-MFCs.
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Affiliation(s)
- Yian Wang
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, 541000, Guilin, China
| | - Xuehong Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, 541000, Guilin, China
| | - Yi Lin
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, 541000, Guilin, China
| | - Hua Lin
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China.
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, 541000, Guilin, China.
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Chen C, Chen S, Wang B. A glance at the gut microbiota and the functional roles of the microbes based on marmot fecal samples. Front Microbiol 2023; 14:1035944. [PMID: 37125200 PMCID: PMC10140447 DOI: 10.3389/fmicb.2023.1035944] [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: 10/12/2022] [Accepted: 03/13/2023] [Indexed: 05/02/2023] Open
Abstract
Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.
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Affiliation(s)
- Chuizhe Chen
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Shu Chen
- Medical Laboratory Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Bo Wang
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- *Correspondence: Bo Wang,
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Abstract
Improving the availability of representative isolates from the coral microbiome is essential for investigating symbiotic mechanisms and applying beneficial microorganisms to improve coral health. However, few studies have explored the diversity of bacteria which can be isolated from a single species. Here, we isolated a total of 395 bacterial strains affiliated with 49 families across nine classes from the coral Pocillopora damicornis. Identification results showed that most of the strains represent potential novel bacterial species or genera. We also sequenced and assembled the genomes of 118 of these isolates, and then the putative functions of these isolates were identified based on genetic signatures derived from the genomes and this information was combined with isolate-specific phenotypic data. Genomic information derived from the isolates identified putative functions including nitrification and denitrification, dimethylsulfoniopropionate transformation, and supply of fixed carbon, amino acids, and B vitamins which may support their eukaryotic partners. Furthermore, the isolates contained genes associated with chemotaxis, biofilm formation, quorum sensing, membrane transport, signal transduction, and eukaryote-like repeat-containing and cell-cell attachment proteins, all of which potentially help the bacterium establish association with the coral host. Our work expands on the existing culture collection of coral-associated bacteria and provides important information on the metabolic potential of these isolates which can be used to refine understanding of the role of bacteria in coral health and are now available to be applied to novel strategies aimed at improving coral resilience through microbiome manipulation. IMPORTANCE Microbes underpin the health of corals which are the building blocks of diverse and productive reef ecosystems. Studying the culturable fraction of coral-associated bacteria has received less attention in recent times than using culture-independent molecular methods. However, the genomic and phenotypic characterization of isolated strains allows assessment of their functional role in underpinning coral health and identification of beneficial microbes for microbiome manipulation. Here, we isolated 395 bacterial strains from tissues of Pocillopora damicornis with many representing potentially novel taxa and therefore providing a significant contribution to coral microbiology through greatly enlarging the existing cultured coral-associated bacterial bank. Through analysis of the genomes obtained in this study for the coral-associated bacteria and coral host, we elucidate putative metabolic linkages and symbiotic establishment. The results of this study will help to elucidate the role of specific isolates in coral health and provide beneficial microbes for efforts aimed at improving coral health.
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Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. Int J Mol Sci 2022; 23:ijms23063043. [PMID: 35328479 PMCID: PMC8950772 DOI: 10.3390/ijms23063043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.
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Itoh T. Structures and functions of carbohydrate-active enzymes of chitinolytic bacteria Paenibacillus sp. str. FPU-7. Biosci Biotechnol Biochem 2021; 85:1314-1323. [PMID: 33792636 DOI: 10.1093/bbb/zbab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/22/2021] [Indexed: 11/14/2022]
Abstract
Chitin and its derivatives have valuable potential applications in various fields that include medicine, agriculture, and food industries. Paenibacillus sp. str. FPU-7 is one of the most potent chitin-degrading bacteria identified. This review introduces the chitin degradation system of P. str. FPU-7. In addition to extracellular chitinases, P. str. FPU-7 uses a unique multimodular chitinase (ChiW) to hydrolyze chitin to oligosaccharides on the cell surface. Chitin oligosaccharides are converted to N-acetyl-d-glucosamine by β-N-acetylhexosaminidase (PsNagA) in the cytosol. The functions and structures of ChiW and PsNagA are also summarized. The genome sequence of P. str. FPU-7 provides opportunities to acquire novel enzymes. Genome mining has identified a novel alginate lyase, PsAly. The functions and structure of PsAly are reviewed. These findings will inform further improvement of the sustainable conversion of polysaccharides to functional materials.
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
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Lin MC, Kuo HW, Kao MR, Lin WD, Li CW, Hung KS, Yang SC, Yu SM, Ho THD. From simple and specific zymographic detections to the annotation of a fungus Daldinia caldariorum D263 that encodes a wide range of highly bioactive cellulolytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:120. [PMID: 34020690 PMCID: PMC8140500 DOI: 10.1186/s13068-021-01959-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Lignocellulolytic enzymes are essential for agricultural waste disposal and production of renewable bioenergy. Many commercialized cellulase mixtures have been developed, mostly from saprophytic or endophytic fungal species. The cost of complete cellulose digestion is considerable because a wide range of cellulolytic enzymes is needed. However, most fungi can only produce limited range of highly bioactive cellulolytic enzymes. We aimed to investigate a simple yet specific method for discovering unique enzymes so that fungal species producing a diverse group of cellulolytic enzymes can be identified. RESULTS The culture medium of an endophytic fungus, Daldinia caldariorum D263, contained a complete set of cellulolytic enzymes capable of effectively digesting cellulose residues into glucose. By taking advantage of the unique product inhibition property of β-glucosidases, we have established an improved zymography method that can easily distinguish β-glucosidase and exoglucanase activity. Our zymography method revealed that D263 can secrete a wide range of highly bioactive cellulases. Analyzing the assembled genome of D263, we found over 100 potential genes for cellulolytic enzymes that are distinct from those of the commercially used fungal species Trichoderma reesei and Aspergillus niger. We further identified several of these cellulolytic enzymes by mass spectrometry. CONCLUSIONS The genome of Daldinia caldariorum D263 has been sequenced and annotated taking advantage of a simple yet specific zymography method followed by mass spectrometry analysis, and it appears to encode and secrete a wide range of bioactive cellulolytic enzymes. The genome and cellulolytic enzyme secretion of this unique endophytic fungus should be of value for identifying active cellulolytic enzymes that can facilitate conversion of agricultural wastes to fermentable sugars for the industrial production of biofuels.
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Affiliation(s)
- Meng-Chun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsion-Wen Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan, ROC
| | - Mu-Rong Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Chen-Wei Li
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Kuo-Sheng Hung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Sheng-Chih Yang
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC.
- Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan, ROC.
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Franceus J, Lormans J, Cools L, D’hooghe M, Desmet T. Evolution of Phosphorylases from N-Acetylglucosaminide Hydrolases in Family GH3. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jolien Lormans
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Lore Cools
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Matthias D’hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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De Anda V, Chen LX, Dombrowski N, Hua ZS, Jiang HC, Banfield JF, Li WJ, Baker BJ. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nat Commun 2021; 12:2404. [PMID: 33893309 PMCID: PMC8065059 DOI: 10.1038/s41467-021-22736-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.
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Affiliation(s)
- Valerie De Anda
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Den Burg, Netherlands
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China.
| | - Brett J Baker
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA.
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13
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Awad FN. Glycoside phosphorylases for carbohydrate synthesis: An insight into the diversity and potentiality. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2020.101886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Nieto-Domínguez M, Fernández de Toro B, de Eugenio LI, Santana AG, Bejarano-Muñoz L, Armstrong Z, Méndez-Líter JA, Asensio JL, Prieto A, Withers SG, Cañada FJ, Martínez MJ. Thioglycoligase derived from fungal GH3 β-xylosidase is a multi-glycoligase with broad acceptor tolerance. Nat Commun 2020; 11:4864. [PMID: 32978392 PMCID: PMC7519651 DOI: 10.1038/s41467-020-18667-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022] Open
Abstract
The synthesis of customized glycoconjugates constitutes a major goal for biocatalysis. To this end, engineered glycosidases have received great attention and, among them, thioglycoligases have proved useful to connect carbohydrates to non-sugar acceptors. However, hitherto the scope of these biocatalysts was considered limited to strong nucleophilic acceptors. Based on the particularities of the GH3 glycosidase family active site, we hypothesized that converting a suitable member into a thioglycoligase could boost the acceptor range. Herein we show the engineering of an acidophilic fungal β-xylosidase into a thioglycoligase with broad acceptor promiscuity. The mutant enzyme displays the ability to form O-, N-, S- and Se- glycosides together with sugar esters and phosphoesters with conversion yields from moderate to high. Analyses also indicate that the pKa of the target compound was the main factor to determine its suitability as glycosylation acceptor. These results expand on the glycoconjugate portfolio attainable through biocatalysis.
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Affiliation(s)
- Manuel Nieto-Domínguez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Beatriz Fernández de Toro
- NMR and Molecular Recognition Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Laura I de Eugenio
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular recognition group, Instituto de Química Orgánica General (CSIC), C/Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Lara Bejarano-Muñoz
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Zach Armstrong
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Juan Antonio Méndez-Líter
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular recognition group, Instituto de Química Orgánica General (CSIC), C/Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Alicia Prieto
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Stephen G Withers
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Francisco Javier Cañada
- NMR and Molecular Recognition Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María Jesús Martínez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain.
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15
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Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253. Sci Rep 2020; 10:1329. [PMID: 31992772 PMCID: PMC6987092 DOI: 10.1038/s41598-020-58015-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/07/2020] [Indexed: 11/08/2022] Open
Abstract
The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: β-N-acetyl-glucosaminidases, β-1,4-glucosidases/β-xylosidases and macrolide β-glucosidases. The RmNag3 with additional β-lactamase domain clustered with the deepest rooted GH3-lineage of β-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed β-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide β-glucosidases from Actinomycetes. The β-xylosidases, RmXyl3A and RmXyl3B, and the β-glucosidases RmBgl3A and RmBgl3C clustered within the major β-glucosidases/β-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed β-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed β-1,4-glucosidase/β-xylosidase activity while RmBgl3C was active on pNP-β-Glc and β-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252TRmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.
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16
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Mahasenan KV, Batuecas MT, De Benedetti S, Kim C, Rana N, Lee M, Hesek D, Fisher JF, Sanz-Aparicio J, Hermoso JA, Mobashery S. Catalytic Cycle of Glycoside Hydrolase BglX from Pseudomonas aeruginosa and Its Implications for Biofilm Formation. ACS Chem Biol 2020; 15:189-196. [PMID: 31877028 PMCID: PMC7995829 DOI: 10.1021/acschembio.9b00754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BglX is a heretofore uncharacterized periplasmic glycoside hydrolase (GH) of the human pathogen Pseudomonas aeruginosa. X-ray analysis identifies it as a protein homodimer. The two active sites of the homodimer comprise catalytic residues provided by each monomer. This arrangement is seen in <2% of the hydrolases of known structure. In vitro substrate profiling shows BglX is a catalyst for β-(1→2) and β-(1→3) saccharide hydrolysis. Saccharides with β-(1→4) or β-(1→6) bonds, and the β-(1→4) muropeptides from the cell-wall peptidoglycan, are not substrates. Additional structural insights from X-ray analysis (including structures of a mutant enzyme-derived Michaelis complex, two transition-state mimetics, and two enzyme-product complexes) enabled the comprehensive description of BglX catalysis. The half-chair (4H3) conformation of the transition-state oxocarbenium species, the approach of the hydrolytic water molecule to the oxocarbenium species, and the stepwise release of the two reaction products were also visualized. The substrate pattern for BglX aligns with the [β-(1→2)-Glc]x and [β-(1→3)-Glc]x periplasmic osmoregulated periplasmic glucans, and possibly with the Psl exopolysaccharides, of P. aeruginosa. Both polysaccharides are implicated in biofilm formation. Accordingly, we show that inactivation of the bglX gene of P. aeruginosa PAO1 attenuates biofilm formation.
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Affiliation(s)
- Kiran V Mahasenan
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - María T Batuecas
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Stefania De Benedetti
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Choon Kim
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Neha Rana
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Mijoon Lee
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Dusan Hesek
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Jed F Fisher
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
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17
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Teze D, Coines J, Raich L, Kalichuk V, Solleux C, Tellier C, André-Miral C, Svensson B, Rovira C. A Single Point Mutation Converts GH84 O-GlcNAc Hydrolases into Phosphorylases: Experimental and Theoretical Evidence. J Am Chem Soc 2020; 142:2120-2124. [DOI: 10.1021/jacs.9b09655] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 224, DK-2800 Kongens Lyngby, Denmark
- UFIP, CNRS, Université de Nantes, 44300 Nantes, France
| | - Joan Coines
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Lluís Raich
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | | | | | | | | | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 224, DK-2800 Kongens Lyngby, Denmark
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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18
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Guo X, Hansen BØ, Moeller SR, Harholt J, Mravec J, Willats W, Petersen BL, Ulvskov P. Extensin arabinoside chain length is modulated in elongating cotton fibre. Cell Surf 2019; 5:100033. [PMID: 32743148 PMCID: PMC7388976 DOI: 10.1016/j.tcsw.2019.100033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/18/2019] [Accepted: 10/23/2019] [Indexed: 01/02/2023] Open
Abstract
Cotton fibre provides a unicellular model system for studying cell expansion and secondary cell wall deposition. Mature cotton fibres are mainly composed of cellulose while the walls of developing fibre cells contain a variety of polysaccharides and proteoglycans required for cell expansion. This includes hydroxyproline-rich glycoproteins (HRGPs) comprising the subgroup, extensins. In this study, extensin occurrence in cotton fibres was assessed using carbohydrate immunomicroarrays, mass spectrometry and monosaccharide profiling. Extensin amounts in three species appeared to correlate with fibre quality. Fibre cell expression profiling of the four cotton cultivars, combined with extensin arabinoside chain length measurements during fibre development, demonstrated that arabinoside side-chain length is modulated during development. Implications and mechanisms of extensin side-chain length dynamics during development are discussed.
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Key Words
- AGPs, arabinogalactan proteins
- CoMPP
- CoMPP, comprehensive microarray polymer profiling
- Cotton fibre
- Cotton fibre quality
- CrRLK1L, Catharanthus roseus receptor-like1-like kinase
- DPA, days post anthesis
- EXTs, extensins
- ExAD, arabinosyltransferase named after the mutant Extensin Arabinose Deficient
- Extensin arabinoside metabolism
- GH, glycoside hydrolase
- HPAT, hydroxyproline arabinosyltransferase
- HRGP
- HRGPs, hydroxyproline-rich glycoproteins
- Hyp-Aran, extensin side-chain of length n
- LRX, leucine-rich repeat extensins
- PCW, primary cell wall
- RRA, arabinosyltransferase named after the mutant Reduced Residual Arabinose
- SCW, secondary cell wall
- SGT, serine galactosyltransferase
- Transcriptomics
- XEG113, arabinosyltransferase named after the mutant Xyloglucan Endo-Glucanase resistant mutant 113
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Affiliation(s)
- Xiaoyuan Guo
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Bjørn Øst Hansen
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam 14476, Germany
| | - Svenning Rune Moeller
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jesper Harholt
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - William Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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19
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Itoh T, Araki T, Nishiyama T, Hibi T, Kimoto H. Structural and functional characterization of a glycoside hydrolase family 3 β-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7. J Biochem 2019; 166:503-515. [DOI: 10.1093/jb/mvz072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/11/2019] [Indexed: 11/14/2022] Open
Abstract
AbstractChitin, a β-1,4-linked homopolysaccharide of N-acetyl-d-glucosamine (GlcNAc), is one of the most abundant biopolymers on Earth. Paenibacillus sp. str. FPU-7 produces several different chitinases and converts chitin into N,N′-diacetylchitobiose ((GlcNAc)2) in the culture medium. However, the mechanism by which the Paenibacillus species imports (GlcNAc)2 into the cytoplasm and divides it into the monomer GlcNAc remains unclear. The gene encoding Paenibacillus β-N-acetyl-d-glucosaminidase (PsNagA) was identified in the Paenibacillus sp. str. FPU-7 genome using an expression cloning system. The deduced amino acid sequence of PsNagA suggests that the enzyme is a part of the glycoside hydrolase family 3 (GH3). Recombinant PsNagA was successfully overexpressed in Escherichia coli and purified to homogeneity. As assessed by gel permeation chromatography, the enzyme exists as a 57-kDa monomer. PsNagA specifically hydrolyses chitin oligosaccharides, (GlcNAc)2–4, 4-nitrophenyl N-acetyl β-d-glucosamine (pNP-GlcNAc) and pNP-(GlcNAc)2–6, but has no detectable activity against 4-nitrophenyl β-d-glucose, 4-nitrophenyl β-d-galactosamine and colloidal chitin. In this study, we present a 1.9 Å crystal structure of PsNagA bound to GlcNAc. The crystal structure reveals structural features related to substrate recognition and the catalytic mechanism of PsNagA. This is the first study on the structural and functional characterization of a GH3 β-N-acetyl-d-glucosaminidase from Paenibacillus sp.
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Tomomitsu Araki
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Tomohiro Nishiyama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Takao Hibi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Hisashi Kimoto
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
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20
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The hydrolase LpqI primes mycobacterial peptidoglycan recycling. Nat Commun 2019; 10:2647. [PMID: 31201321 PMCID: PMC6572805 DOI: 10.1038/s41467-019-10586-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Growth and division by most bacteria requires remodelling and cleavage of their cell wall. A byproduct of this process is the generation of free peptidoglycan (PG) fragments known as muropeptides, which are recycled in many model organisms. Bacteria and hosts can harness the unique nature of muropeptides as a signal for cell wall damage and infection, respectively. Despite this critical role for muropeptides, it has long been thought that pathogenic mycobacteria such as Mycobacterium tuberculosis do not recycle their PG. Herein we show that M. tuberculosis and Mycobacterium bovis BCG are able to recycle components of their PG. We demonstrate that the core mycobacterial gene lpqI, encodes an authentic NagZ β-N-acetylglucosaminidase and that it is essential for PG-derived amino sugar recycling via an unusual pathway. Together these data provide a critical first step in understanding how mycobacteria recycle their peptidoglycan. Bacterial growth and division require remodelling of the cell wall, which generates free peptidoglycan fragments. Here, Moynihan et al. show that Mycobacterium tuberculosis can recycle components of their peptidoglycan, and characterise a crucial enzyme required for this process.
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21
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Tanaka N, Nakajima M, Narukawa-Nara M, Matsunaga H, Kamisuki S, Aramasa H, Takahashi Y, Sugimoto N, Abe K, Terada T, Miyanaga A, Yamashita T, Sugawara F, Kamakura T, Komba S, Nakai H, Taguchi H. Identification, characterization, and structural analyses of a fungal endo-β-1,2-glucanase reveal a new glycoside hydrolase family. J Biol Chem 2019; 294:7942-7965. [PMID: 30926603 DOI: 10.1074/jbc.ra118.007087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/20/2019] [Indexed: 11/06/2022] Open
Abstract
endo-β-1,2-Glucanase (SGL) is an enzyme that hydrolyzes β-1,2-glucans, which play important physiological roles in some bacteria as a cyclic form. To date, no eukaryotic SGL has been identified. We purified an SGL from Talaromyces funiculosus (TfSGL), a soil fungus, to homogeneity and then cloned the complementary DNA encoding the enzyme. TfSGL shows no significant sequence similarity to any known glycoside hydrolase (GH) families, but shows significant similarity to certain eukaryotic proteins with unknown functions. The recombinant TfSGL (TfSGLr) specifically hydrolyzed linear and cyclic β-1,2-glucans to sophorose (Glc-β-1,2-Glc) as a main product. TfSGLr hydrolyzed reducing-end-modified β-1,2-gluco-oligosaccharides to release a sophoroside with the modified moiety. These results indicate that TfSGL is an endo-type enzyme that preferably releases sophorose from the reducing end of substrates. Stereochemical analysis demonstrated that TfSGL is an inverting enzyme. The overall structure of TfSGLr includes an (α/α)6 toroid fold. The substrate-binding mode was revealed by the structure of a Michaelis complex of an inactive TfSGLr mutant with a β-1,2-glucoheptasaccharide. Mutational analysis and action pattern analysis of β-1,2-gluco-oligosaccharide derivatives revealed an unprecedented catalytic mechanism for substrate hydrolysis. Glu-262 (general acid) indirectly protonates the anomeric oxygen at subsite -1 via the 3-hydroxy group of the Glc moiety at subsite +2, and Asp-446 (general base) activates the nucleophilic water via another water. TfSGLr is apparently different from a GH144 SGL in the reaction and substrate recognition mechanism based on structural comparison. Overall, we propose that TfSGL and closely-related enzymes can be classified into a new family, GH162.
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Affiliation(s)
- Nobukiyo Tanaka
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Masahiro Nakajima
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510,
| | - Megumi Narukawa-Nara
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Hiroki Matsunaga
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Shinji Kamisuki
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510.,the School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5201
| | - Hiroki Aramasa
- the Faculty of Agriculture, Niigata University, Niigata 950-2181
| | - Yuta Takahashi
- the Faculty of Agriculture, Niigata University, Niigata 950-2181
| | - Naohisa Sugimoto
- the Faculty of Agriculture, Niigata University, Niigata 950-2181
| | - Koichi Abe
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510.,the Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Tohru Terada
- the Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Akimasa Miyanaga
- the Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551
| | | | - Fumio Sugawara
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Takashi Kamakura
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Shiro Komba
- the Food Component Analysis Unit, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Hiroyuki Nakai
- the Faculty of Agriculture, Niigata University, Niigata 950-2181
| | - Hayao Taguchi
- From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
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22
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Itoh T, Kimoto H. Bacterial Chitinase System as a Model of Chitin Biodegradation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:131-151. [PMID: 31102245 DOI: 10.1007/978-981-13-7318-3_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chitin, a structural polysaccharide of β-1,4-linked N-acetyl-D-glucosamine residues, is the second most abundant natural biopolymer after cellulose. The metabolism of chitin affects the global carbon and nitrogen cycles, which are maintained by marine and soil-dwelling bacteria. The degradation products of chitin metabolism serve as important nutrient sources for the chitinolytic bacteria. Chitinolytic bacteria have elaborate enzymatic systems for the degradation of the recalcitrant chitin biopolymer. This chapter introduces chitin degradation and utilization systems of the chitinolytic bacteria. These bacteria secrete many chitin-degrading enzymes, including processive chitinases, endo-acting non-processive chitinases, lytic polysaccharide monooxygenases, and N-acetyl-hexosaminidases. Bacterial chitinases play a fundamental role in the degradation of chitin. Enzymatic properties, catalytic mechanisms, and three-dimensional structures of chitinases have been extensively studied by many scientists. These enzymes can be exploited to produce a range of chitin-derived products, e.g., biocontrol agents against many plant pathogenic fungi and insects. We introduce bacterial chitinases in terms of their reaction modes and structural features.
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Affiliation(s)
- Takafumi Itoh
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195, Japan.
| | - Hisashi Kimoto
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195, Japan
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23
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Oliveira ESD, Junges Â, Sbaraini N, Andreis FC, Thompson CE, Staats CC, Schrank A. Molecular evolution and transcriptional profile of GH3 and GH20 β-N-acetylglucosaminidases in the entomopathogenic fungus Metarhizium anisopliae. Genet Mol Biol 2018; 41:843-857. [PMID: 30534852 PMCID: PMC6415606 DOI: 10.1590/1678-4685-gmb-2017-0363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/23/2018] [Indexed: 01/15/2023] Open
Abstract
Cell walls are involved in manifold aspects of fungi maintenance. For several fungi, chitin synthesis, degradation and recycling are essential processes required for cell wall biogenesis; notably, the activity of β-N-acetylglucosaminidases (NAGases) must be present for chitin utilization. For entomopathogenic fungi, such as Metarhizium anisopliae, chitin degradation is also used to breach the host cuticle during infection. In view of the putative role of NAGases as virulence factors, this study explored the transcriptional profile and evolution of putative GH20 NAGases (MaNAG1 and MaNAG2) and GH3 NAGases (MaNAG3 and MaNAG4) identified in M. anisopliae. While MaNAG2 orthologs are conserved in several ascomycetes, MaNAG1 clusters only with Aspergilllus sp. and entomopathogenic fungal species. By contrast, MaNAG3 and MaNAG4 were phylogenetically related with bacterial GH3 NAGases. The transcriptional profiles of M. anisopliae NAGase genes were evaluated in seven culture conditions showing no common regulatory patterns, suggesting that these enzymes may have specific roles during the Metarhizium life cycle. Moreover, the expression of MaNAG3 and MaNAG4 regulated by chitinous substrates is the first evidence of the involvement of putative GH3 NAGases in physiological cell processes in entomopathogens, indicating their potential influence on cell differentiation during the M. anisopliae life cycle.
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Affiliation(s)
- Eder Silva de Oliveira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ângela Junges
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Nicolau Sbaraini
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fábio Carrer Andreis
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | | | - Augusto Schrank
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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24
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Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins M, Springate CMK, Burke JE, Withers SG, Boraston AB. Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29. J Biol Chem 2018; 293:18296-18308. [PMID: 30282808 DOI: 10.1074/jbc.ra118.005134] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Indexed: 11/06/2022] Open
Abstract
Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes: MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Psychromonas Using carbohydrate-PAGE, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 α-l-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine side chain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.
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Affiliation(s)
- Chelsea Vickers
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Feng Liu
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada, and
| | - Kento Abe
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Orly Salama-Alber
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Meredith Jenkins
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | | | - John E Burke
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Stephen G Withers
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada, and
| | - Alisdair B Boraston
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada,.
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25
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Ho LA, Winogrodzki JL, Debowski AW, Madden Z, Vocadlo DJ, Mark BL, Stubbs KA. A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to β-lactams in Pseudomonas aeruginosa. Chem Commun (Camb) 2018; 54:10630-10633. [PMID: 30178799 DOI: 10.1039/c8cc05281f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of a potent mechanism-based inactivator of NagZ, an enzyme critical to the production of inducible AmpC β-lactamase in Gram-negative bacteria, is presented. This inactivator significantly reduces MIC values for important β-lactams against a clinically relevant strain of Pseudomonas aeruginosa.
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Affiliation(s)
- Louisa A Ho
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
| | - Judith L Winogrodzki
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
| | - Aleksandra W Debowski
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia. and School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Zarina Madden
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
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26
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Broeker J, Mechelke M, Baudrexl M, Mennerich D, Hornburg D, Mann M, Schwarz WH, Liebl W, Zverlov VV. The hemicellulose-degrading enzyme system of the thermophilic bacterium Clostridium stercorarium: comparative characterisation and addition of new hemicellulolytic glycoside hydrolases. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:229. [PMID: 30159029 PMCID: PMC6106730 DOI: 10.1186/s13068-018-1228-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/14/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND The bioconversion of lignocellulosic biomass in various industrial processes, such as the production of biofuels, requires the degradation of hemicellulose. Clostridium stercorarium is a thermophilic bacterium, well known for its outstanding hemicellulose-degrading capability. Its genome comprises about 50 genes for partially still uncharacterised thermostable hemicellulolytic enzymes. These are promising candidates for industrial applications. RESULTS To reveal the hemicellulose-degrading potential of 50 glycoside hydrolases, they were recombinantly produced and characterised. 46 of them were identified in the secretome of C. stercorarium cultivated on cellobiose. Xylanases Xyn11A, Xyn10B, Xyn10C, and cellulase Cel9Z were among the most abundant proteins. The secretome of C. stercorarium was active on xylan, β-glucan, xyloglucan, galactan, and glucomannan. In addition, the recombinant enzymes hydrolysed arabinan, mannan, and galactomannan. 20 enzymes are newly described, degrading xylan, galactan, arabinan, mannan, and aryl-glycosides of β-d-xylose, β-d-glucose, β-d-galactose, α-l-arabinofuranose, α-l-rhamnose, β-d-glucuronic acid, and N-acetyl-β-d-glucosamine. The activities of three enzymes with non-classified glycoside hydrolase (GH) family modules were determined. Xylanase Xyn105F and β-d-xylosidase Bxl31D showed activities not described so far for their GH families. 11 of the 13 polysaccharide-degrading enzymes were most active at pH 5.0 to pH 6.5 and at temperatures of 57-76 °C. Investigation of the substrate and product specificity of arabinoxylan-degrading enzymes revealed that only the GH10 xylanases were able to degrade arabinoxylooligosaccharides. While Xyn10C was inhibited by α-(1,2)-arabinosylations, Xyn10D showed a degradation pattern different to Xyn10B and Xyn10C. Xyn11A released longer degradation products than Xyn10B. Both tested arabinose-releasing enzymes, Arf51B and Axh43A, were able to hydrolyse single- as well as double-arabinosylated xylooligosaccharides. CONCLUSIONS The obtained results lead to a better understanding of the hemicellulose-degrading capacity of C. stercorarium and its involved enzyme systems. Despite similar average activities measured by depolymerisation tests, a closer look revealed distinctive differences in the activities and specificities within an enzyme class. This may lead to synergistic effects and influence the enzyme choice for biotechnological applications. The newly characterised glycoside hydrolases can now serve as components of an enzyme platform for industrial applications in order to reconstitute synthetic enzyme systems for complete and optimised degradation of defined polysaccharides and hemicellulose.
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Affiliation(s)
- Jannis Broeker
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Matthias Mechelke
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Melanie Baudrexl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Denise Mennerich
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Daniel Hornburg
- Present Address: School of Medicine, Stanford University, Stanford, CA 94305 USA
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
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27
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Yang S, Gao X, Meng J, Zhang A, Zhou Y, Long M, Li B, Deng W, Jin L, Zhao S, Wu D, He Y, Li C, Liu S, Huang Y, Zhang H, Zou L. Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas. Front Microbiol 2018; 9:1717. [PMID: 30108570 PMCID: PMC6080571 DOI: 10.3389/fmicb.2018.01717] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/10/2018] [Indexed: 11/13/2022] Open
Abstract
To obtain full details of gut microbiota, including bacteria, fungi, bacteriophages, and helminths, in giant pandas (GPs), we created a comprehensive microbial genome database and used metagenomic sequences to align against the database. We delineated a detailed and different gut microbiota structures of GPs. A total of 680 species of bacteria, 198 fungi, 185 bacteriophages, and 45 helminths were found. Compared with 16S rRNA sequencing, the dominant bacterium phyla not only included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria but also Cyanobacteria and other eight phyla. Aside from Ascomycota, Basidiomycota, and Glomeromycota, Mucoromycota, and Microsporidia were the dominant fungi phyla. The bacteriophages were predominantly dsDNA Myoviridae, Siphoviridae, Podoviridae, ssDNA Inoviridae, and Microviridae. For helminths, phylum Nematoda was the dominant. In addition to previously described parasites, another 44 species of helminths were found in GPs. Also, differences in abundance of microbiota were found between the captive, semiwild, and wild GPs. A total of 1,739 genes encoding cellulase, β-glucosidase, and cellulose β-1,4-cellobiosidase were responsible for the metabolism of cellulose, and 128,707 putative glycoside hydrolase genes were found in bacteria/fungi. Taken together, the results indicated not only bacteria but also fungi, bacteriophages, and helminths were diverse in gut of giant pandas, which provided basis for the further identification of role of gut microbiota. Besides, metagenomics revealed that the bacteria/fungi in gut of GPs harbor the ability of cellulose and hemicellulose degradation.
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Affiliation(s)
- Shengzhi Yang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xin Gao
- Department of Nutrition and Food Science, University of Maryland, College Park, College Park, MD, United States
| | - Jianghong Meng
- Department of Nutrition and Food Science, University of Maryland, College Park, College Park, MD, United States
| | - Anyun Zhang
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Yingmin Zhou
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Mei Long
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Bei Li
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wenwen Deng
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lei Jin
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Siyue Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Daifu Wu
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Yongguo He
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Caiwu Li
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya’an, China
| | - Yan Huang
- The China Conservation and Research Center for the Giant Panda, Wolong, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), Wolong, China
| | - Hemin Zhang
- The China Conservation and Research Center for the Giant Panda, Wolong, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), Wolong, China
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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28
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Marton K, Flajšman M, Radišek S, Košmelj K, Jakše J, Javornik B, Berne S. Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion. PLoS One 2018; 13:e0198971. [PMID: 29894496 PMCID: PMC5997321 DOI: 10.1371/journal.pone.0198971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022] Open
Abstract
The vascular plant pathogen Verticillium nonalfalfae causes Verticillium wilt in several important crops. VnaSSP4.2 was recently discovered as a V. nonalfalfae virulence effector protein in the xylem sap of infected hop. Here, we expanded our search for candidate secreted effector proteins (CSEPs) in the V. nonalfalfae predicted secretome using a bioinformatic pipeline built on V. nonalfalfae genome data, RNA-Seq and proteomic studies of the interaction with hop. The secretome, rich in carbohydrate active enzymes, proteases, redox proteins and proteins involved in secondary metabolism, cellular processing and signaling, includes 263 CSEPs. Several homologs of known fungal effectors (LysM, NLPs, Hce2, Cerato-platanins, Cyanovirin-N lectins, hydrophobins and CFEM domain containing proteins) and avirulence determinants in the PHI database (Avr-Pita1 and MgSM1) were found. The majority of CSEPs were non-annotated and were narrowed down to 44 top priority candidates based on their likelihood of being effectors. These were examined by spatio-temporal gene expression profiling of infected hop. Among the highest in planta expressed CSEPs, five deletion mutants were tested in pathogenicity assays. A deletion mutant of VnaUn.279, a lethal pathotype specific gene with sequence similarity to SAM-dependent methyltransferase (LaeA), had lower infectivity and showed highly reduced virulence, but no changes in morphology, fungal growth or conidiation were observed. Several putative secreted effector proteins that probably contribute to V. nonalfalfae colonization of hop were identified in this study. Among them, LaeA gene homolog was found to act as a potential novel virulence effector of V. nonalfalfae. The combined results will serve for future characterization of V. nonalfalfae effectors, which will advance our understanding of Verticillium wilt disease.
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Affiliation(s)
- Kristina Marton
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Marko Flajšman
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Katarina Košmelj
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Branka Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sabina Berne
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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29
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Macdonald SS, Patel A, Larmour VLC, Morgan-Lang C, Hallam SJ, Mark BL, Withers SG. Structural and mechanistic analysis of a β-glycoside phosphorylase identified by screening a metagenomic library. J Biol Chem 2018; 293:3451-3467. [PMID: 29317495 DOI: 10.1074/jbc.ra117.000948] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/04/2018] [Indexed: 11/06/2022] Open
Abstract
Glycoside phosphorylases have considerable potential as catalysts for the assembly of useful glycans for products ranging from functional foods and prebiotics to novel materials. However, the substrate diversity of currently identified phosphorylases is relatively small, limiting their practical applications. To address this limitation, we developed a high-throughput screening approach using the activated substrate 2,4-dinitrophenyl β-d-glucoside (DNPGlc) and inorganic phosphate for identifying glycoside phosphorylase activity and used it to screen a large insert metagenomic library. The initial screen, based on release of 2,4-dinitrophenyl from DNPGlc in the presence of phosphate, identified the gene bglP, encoding a retaining β-glycoside phosphorylase from the CAZy GH3 family. Kinetic and mechanistic analysis of the gene product, BglP, confirmed a double displacement ping-pong mechanism involving a covalent glycosyl-enzyme intermediate. X-ray crystallographic analysis provided insights into the phosphate-binding mode and identified a key glutamine residue in the active site important for substrate recognition. Substituting this glutamine for a serine swapped the substrate specificity from glucoside to N-acetylglucosaminide. In summary, we present a high-throughput screening approach for identifying β-glycoside phosphorylases, which was robust, simple to implement, and useful in identifying active clones within a metagenomics library. Implementation of this screen enabled discovery of a new glycoside phosphorylase class and has paved the way to devising simple ways in which enzyme specificity can be encoded and swapped, which has implications for biotechnological applications.
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Affiliation(s)
- Spencer S Macdonald
- From the Departments of Chemistry and Biochemistry and.,the Genome Science and Technology Program.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, and
| | - Ankoor Patel
- the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2
| | - Veronica L C Larmour
- the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2
| | | | - Steven J Hallam
- the Genome Science and Technology Program.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, and.,Graduate Program in Bioinformatics, and.,the Department of Microbiology and Immunology and.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia V6T 1Z1
| | - Brian L Mark
- the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2
| | - Stephen G Withers
- From the Departments of Chemistry and Biochemistry and .,the Genome Science and Technology Program.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, and.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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30
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Xie C, Gong W, Zhu Z, Yan L, Hu Z, Peng Y. Comparative transcriptomics of Pleurotus eryngii reveals blue-light regulation of carbohydrate-active enzymes (CAZymes) expression at primordium differentiated into fruiting body stage. Genomics 2017; 110:201-209. [PMID: 28970048 DOI: 10.1016/j.ygeno.2017.09.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/10/2017] [Accepted: 09/27/2017] [Indexed: 02/03/2023]
Abstract
Blue light is an important environmental factor which could induce mushroom primordium differentiation and fruiting body development. However, the mechanisms of Pleurotus eryngii primordium differentiation and development induced by blue light are still unclear. The CAZymes (carbohydrate-active enzymes) play important roles in degradation of renewable lignocelluloses to provide carbohydrates for fungal growth, development and reproduction. In the present research, the expression profiles of genes were measured by comparison between the Pleurotus eryngii at primordium differentiated into fruiting body stage after blue light stimulation and dark using high-throughput sequencing approach. After assembly and compared to the Pleurotus eryngii reference genome, 11,343 unigenes were identified. 539 differentially expressed genes including white collar 2 type of transcription factor gene, A mating type protein gene, MAP kinase gene, oxidative phosphorylation associated genes, CAZymes genes and other metabolism related genes were identified during primordium differentiated into fruiting body stage after blue light stimulation. KEGG results showed that carbon metabolism, glycolysis/gluconeogenesis and biosynthesis of amino acids pathways were affected during blue light inducing primordia formation. Most importantly, 319 differentially expressed CAZymes participated in carbon metabolism were identified. The expression patterns of six representative CAZymes and laccase genes were further confirmed by qRT-PCR. Enzyme activity results indicated that the activities of CAZymes and laccase were affected in primordium differentiated into fruiting body under blue light stimulation. In conclusion, the comprehensive transcriptome and CAZymes of Pleurotus eryngii at primordium differentiated into fruiting body stage after blue light stimulation were obtained. The biological insights gained from this integrative system represent a valuable resource for future genomic studies on this commercially important mushroom.
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Affiliation(s)
- Chunliang Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Wenbing Gong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Zuohua Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Li Yan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Zhenxiu Hu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China.
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31
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Unusual active site location and catalytic apparatus in a glycoside hydrolase family. Proc Natl Acad Sci U S A 2017; 114:4936-4941. [PMID: 28396425 DOI: 10.1073/pnas.1701130114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The human gut microbiota use complex carbohydrates as major nutrients. The requirement for an efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that these bacteria represent a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis, we focused on enzymes that hydrolyze rhamnosidic bonds, as cleavage of these linkages is chemically challenging and there is a paucity of information on l-rhamnosidases. Here we screened the activity of enzymes derived from the human gut microbiota bacterium Bacteroides thetaiotaomicron, which are up-regulated in response to rhamnose-containing glycans. We identified an α-l-rhamnosidase, BT3686, which is the founding member of a glycoside hydrolase (GH) family, GH145. In contrast to other rhamnosidases, BT3686 cleaved l-Rha-α1,4-d-GlcA linkages through a retaining double-displacement mechanism. The crystal structure of BT3686 showed that the enzyme displayed a type A seven-bladed β-propeller fold. Mutagenesis and crystallographic studies, including the structure of BT3686 in complex with the reaction product GlcA, revealed a location for the active site among β-propeller enzymes cited on the posterior surface of the rhamnosidase. In contrast to the vast majority of GH, the catalytic apparatus of BT3686 does not comprise a pair of carboxylic acid residues but, uniquely, a single histidine functions as the only discernable catalytic amino acid. Intriguingly, the histidine, His48, is not invariant in GH145; however, when engineered into structural homologs lacking the imidazole residue, α-l-rhamnosidase activity was established. The potential contribution of His48 to the catalytic activity of BT3686 is discussed.
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Vadlamani G, Stubbs KA, Désiré J, Blériot Y, Vocadlo DJ, Mark BL. Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress β-lactam antibiotic resistance. Protein Sci 2017; 26:1161-1170. [PMID: 28370529 DOI: 10.1002/pro.3166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 11/10/2022]
Abstract
NagZ is an N-acetyl-β-d-glucosaminidase that participates in the peptidoglycan (PG) recycling pathway of Gram-negative bacteria by removing N-acetyl-glucosamine (GlcNAc) from PG fragments that have been excised from the cell wall during growth. The 1,6-anhydromuramoyl-peptide products generated by NagZ activate β-lactam resistance in many Gram-negative bacteria by inducing the expression of AmpC β-lactamase. Blocking NagZ activity can thereby suppress β-lactam antibiotic resistance in these bacteria. The NagZ active site is dynamic and it accommodates distortion of the glycan substrate during catalysis using a mobile catalytic loop that carries a histidine residue which serves as the active site general acid/base catalyst. Here, we show that flexibility of this catalytic loop also accommodates structural differences in small molecule inhibitors of NagZ, which could be exploited to improve inhibitor specificity. X-ray structures of NagZ bound to the potent yet non-selective N-acetyl-β-glucosaminidase inhibitor PUGNAc (O-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino-N-phenylcarbamate), and two NagZ-selective inhibitors - EtBuPUG, a PUGNAc derivative bearing a 2-N-ethylbutyryl group, and MM-156, a 3-N-butyryl trihydroxyazepane, revealed that the phenylcarbamate moiety of PUGNAc and EtBuPUG completely displaces the catalytic loop from the NagZ active site to yield a catalytically incompetent form of the enzyme. In contrast, the catalytic loop was found positioned in the catalytically active conformation within the NagZ active site when bound to MM-156, which lacks the phenylcarbamate extension. Displacement of the catalytic loop by PUGNAc and its N-acyl derivative EtBuPUG alters the active site conformation of NagZ, which presents an additional strategy to improve the potency and specificity of NagZ inhibitors.
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Affiliation(s)
- Grishma Vadlamani
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3T2N2
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Jérôme Désiré
- IC2MP, UMR CNRS 7285, Équipe "Synthèse Organique" Groupe Glycochimie, Université de Poitiers, 4 rue Michel Brunet, 86073, Poitiers cedex 9, France
| | - Yves Blériot
- IC2MP, UMR CNRS 7285, Équipe "Synthèse Organique" Groupe Glycochimie, Université de Poitiers, 4 rue Michel Brunet, 86073, Poitiers cedex 9, France
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5S 1P6
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3T2N2
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Slámová K, Bojarová P. Engineered N-acetylhexosamine-active enzymes in glycoscience. Biochim Biophys Acta Gen Subj 2017; 1861:2070-2087. [PMID: 28347843 DOI: 10.1016/j.bbagen.2017.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 01/17/2023]
Abstract
BACKGROUND In recent years, enzymes modifying N-acetylhexosamine substrates have emerged in numerous theoretical studies as well as practical applications from biology, biomedicine, and biotechnology. Advanced enzyme engineering techniques converted them into potent synthetic instruments affording a variety of valuable glycosides. SCOPE OF REVIEW This review presents the diversity of engineered enzymes active with N-acetylhexosamine carbohydrates: from popular glycoside hydrolases and glycosyltransferases to less known oxidases, epimerases, kinases, sulfotransferases, and acetylases. Though hydrolases in natura, engineered chitinases, β-N-acetylhexosaminidases, and endo-β-N-acetylglucosaminidases were successfully employed in the synthesis of defined natural and derivatized chitooligomers and in the remodeling of N-glycosylation patterns of therapeutic antibodies. The genes of various N-acetylhexosaminyltransferases were cloned into metabolically engineered microorganisms for producing human milk oligosaccharides, Lewis X structures, and human-like glycoproteins. Moreover, mutant N-acetylhexosamine-active glycosyltransferases were applied, e.g., in the construction of glycomimetics and complex glycostructures, industrial production of low-lactose milk, and metabolic labeling of glycans. In the synthesis of biotechnologically important compounds, several innovative glycoengineered systems are presented for an efficient bioproduction of GlcNAc, UDP-GlcNAc, N-acetylneuraminic acid, and of defined glycosaminoglycans. MAJOR CONCLUSIONS The above examples demonstrate that engineering of N-acetylhexosamine-active enzymes was able to solve complex issues such as synthesis of tailored human-like glycoproteins or industrial-scale production of desired oligosaccharides. Due to the specific catalytic mechanism, mutagenesis of these catalysts was often realized through rational solutions. GENERAL SIGNIFICANCE Specific N-acetylhexosamine glycosylation is crucial in biological, biomedical and biotechnological applications and a good understanding of its details opens new possibilities in this fast developing area of glycoscience.
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Affiliation(s)
- Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic.
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Nakajima M, Tanaka N, Furukawa N, Nihira T, Kodutsumi Y, Takahashi Y, Sugimoto N, Miyanaga A, Fushinobu S, Taguchi H, Nakai H. Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans. Sci Rep 2017; 7:42671. [PMID: 28198470 PMCID: PMC5309861 DOI: 10.1038/srep42671] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/11/2017] [Indexed: 11/25/2022] Open
Abstract
Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique β-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain. In the complex structure of LpSOGP with sophorose, sophorose binds at subsites +1 to +2. Notably, the Glc moiety at subsite +1 is flipped compared with the corresponding ligands in other GH94 enzymes. This inversion suggests the great distortion of the glycosidic bond between subsites −1 and +1, which is likely unfavorable for substrate binding. Compensation for this disadvantage at subsite +2 can be accounted for by the small distortion of the glycosidic bond in the sophorose molecule. Therefore, the binding mode at subsites +1 and +2 defines the substrate specificity of LpSOGP, which provides mechanistic insights into the substrate specificity of a phosphorylase acting on β-1,2-glucooligosaccharides.
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Affiliation(s)
- Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Nobukiyo Tanaka
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Nayuta Furukawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan.,Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Takanori Nihira
- Graduate School of Science &Technology, Niigata University, Niigata, Japan
| | - Yuki Kodutsumi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Yuta Takahashi
- Graduate School of Science &Technology, Niigata University, Niigata, Japan
| | - Naohisa Sugimoto
- Graduate School of Science &Technology, Niigata University, Niigata, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Hayao Taguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Hiroyuki Nakai
- Graduate School of Science &Technology, Niigata University, Niigata, Japan
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van Wyk N, Drancourt M, Henrissat B, Kremer L. Current perspectives on the families of glycoside hydrolases ofMycobacterium tuberculosis: their importance and prospects for assigning function to unknowns. Glycobiology 2016; 27:112-122. [DOI: 10.1093/glycob/cww099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 08/28/2016] [Accepted: 09/26/2016] [Indexed: 11/14/2022] Open
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Ducatti DRB, Carroll MA, Jakeman DL. On the phosphorylase activity of GH3 enzymes: A β-N-acetylglucosaminidase from Herbaspirillum seropedicae SmR1 and a glucosidase from Saccharopolyspora erythraea. Carbohydr Res 2016; 435:106-112. [PMID: 27744113 DOI: 10.1016/j.carres.2016.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/21/2016] [Accepted: 09/21/2016] [Indexed: 10/21/2022]
Abstract
A phosphorolytic activity has been reported for beta-N-acetylglucosaminidases from glycoside hydrolase family 3 (GH3) giving an interesting explanation for an unusual histidine as catalytic acid/base residue and suggesting that members from this family may be phosphorylases [J. Biol. Chem. 2015, 290, 4887]. Here, we describe the characterization of Hsero1941, a GH3 beta-N-acetylglucosaminidase from the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae SmR1. The enzyme has significantly higher activity against pNP-beta-D-GlcNAcp (Km = 0.24 mM, kcat = 1.2 s-1, kcat/Km = 5.0 mM-1s-1) than pNP-beta-D-Glcp (Km = 33 mM, kcat = 3.3 × 10-3 s-1, kcat/Km = 9 × 10-4 mM-1s-1). The presence of phosphate failed to significantly modify the kinetic parameters of the reaction. The enzyme showed a broad aglycone site specificity, being able to hydrolyze sugar phosphates beta-D-GlcNAc 1P and beta-D-Glc 1P, albeit at a fraction of the rate of hydrolysis of aryl glycosides. GH3 beta-glucosidase EryBI, that does not have a histidine as the general acid/base residue, also hydrolyzed beta-D-Glc 1P, at comparable rates to Hsero1941. These data indicate that Hsero1941 functions primarily as a hydrolase and that phosphorolytic activity is likely adventitious. The prevalence of histidine as a general acid/base residue is not predictive, nor correlative, with GH3 beta-N-acetylglucosaminidases having phosphorolytic activity.
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Affiliation(s)
- Diogo R B Ducatti
- College of Pharmacy, Dalhousie University, 5968 College Street, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada; Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Centro Politécnico, CEP 81-531-990, P.O. Box 19046, Curitiba, Paraná, Brazil
| | - Madison A Carroll
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| | - David L Jakeman
- College of Pharmacy, Dalhousie University, 5968 College Street, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada; Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada.
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Abstract
Bacterial-bacterial interactions play a critical role in promoting biofilm formation. Here we show that NagZ, a protein associated with peptidoglycan recycling, has moonlighting activity that allows it to modulate biofilm accumulation by Neisseria gonorrhoeae. We characterize the biochemical properties of NagZ and demonstrate its ability to function as a dispersing agent for biofilms formed on abiotic surfaces. We extend these observations to cell culture and tissue explant models and show that in nagZ mutants, the biofilms formed in cell culture and on human tissues contain significantly more biomass than those formed by a wild-type strain. Our results demonstrate that an enzyme thought to be restricted to peptidoglycan recycling is able to disperse preformed biofilms.
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38
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Kappel L, Gaderer R, Flipphi M, Seidl-Seiboth V. The N-acetylglucosamine catabolic gene cluster in Trichoderma reesei is controlled by the Ndt80-like transcription factor RON1. Mol Microbiol 2016; 99:640-57. [PMID: 26481444 PMCID: PMC4950302 DOI: 10.1111/mmi.13256] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2015] [Indexed: 11/28/2022]
Abstract
Chitin is an important structural constituent of fungal cell walls composed of N-acetylglucosamine (GlcNAc) monosaccharides, but catabolism of GlcNAc has not been studied in filamentous fungi so far. In the yeast Candida albicans, the genes encoding the three enzymes responsible for stepwise conversion of GlcNAc to fructose-6-phosphate are clustered. In this work, we analysed GlcNAc catabolism in ascomycete filamentous fungi and found that the respective genes are also clustered in these fungi. In contrast to C. albicans, the cluster often contains a gene for an Ndt80-like transcription factor, which we named RON1 (regulator of N-acetylglucosamine catabolism 1). Further, a gene for a glycoside hydrolase 3 protein related to bacterial N-acetylglucosaminidases can be found in the GlcNAc gene cluster in filamentous fungi. Functional analysis in Trichoderma reesei showed that the transcription factor RON1 is a key activator of the GlcNAc gene cluster and essential for GlcNAc catabolism. Furthermore, we present an evolutionary analysis of Ndt80-like proteins in Ascomycota. All GlcNAc cluster genes, as well as the GlcNAc transporter gene ngt1, and an additional transcriptional regulator gene, csp2, encoding the homolog of Neurospora crassa CSP2/GRHL, were functionally characterised by gene expression analysis and phenotypic characterisation of knockout strains in T. reesei.
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Affiliation(s)
- Lisa Kappel
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Romana Gaderer
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
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Su H, Sheng X, Liu Y. Insights into the catalytic mechanism of N-acetylglucosaminidase glycoside hydrolase from Bacillus subtilis: a QM/MM study. Org Biomol Chem 2016; 14:3432-42. [DOI: 10.1039/c6ob00320f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
QM/MM calculations on NagZs fromBacillus subtilisfurther confirm NagZs to be glycoside phosphorylases rather than glycoside hydrolases.
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Affiliation(s)
- Hao Su
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Xiang Sheng
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
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40
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Qin Z, Xiao Y, Yang X, Mesters JR, Yang S, Jiang Z. A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase. Sci Rep 2015; 5:18292. [PMID: 26669854 PMCID: PMC4680927 DOI: 10.1038/srep18292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/16/2015] [Indexed: 11/17/2022] Open
Abstract
Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions — a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins.
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Affiliation(s)
- Zhen Qin
- College of Food Science and Nutritional Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
| | - Yibei Xiao
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Xinbin Yang
- College of Food Science and Nutritional Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
| | - Jeroen R Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
| | - Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
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Kitaoka M. Diversity of phosphorylases in glycoside hydrolase families. Appl Microbiol Biotechnol 2015; 99:8377-90. [PMID: 26293338 DOI: 10.1007/s00253-015-6927-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/05/2015] [Indexed: 01/02/2023]
Abstract
Phosphorylases are useful catalysts for the practical preparation of various sugars. The number of known specificities was 13 in 2002 and is now 30. The drastic increase in available genome sequences has facilitated the discovery of novel activities. Most of these novel phosphorylase activities have been identified through the investigations of glycoside hydrolase families containing known phosphorylases. Here, the diversity of phosphorylases in each family is described in detail.
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Affiliation(s)
- Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
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