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Carbonaro M, Aulitto M, Mazurkewich S, Fraia AD, Contursi P, Limauro D, Larsbrink J, Fiorentino G. Genomic mining of Geobacillus stearothermophilus GF16 for xylose production from hemicellulose-rich biomasses using secreted enzymes. N Biotechnol 2024; 82:14-24. [PMID: 38688408 DOI: 10.1016/j.nbt.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The valorization of lignocellulosic biomass, derived from various bio-waste materials, has received considerable attention as a sustainable approach to improve production chains while reducing environmental impact. Microbial enzymes have emerged as key players in the degradation of polysaccharides, offering versatile applications in biotechnology and industry. Among these enzymes, glycoside hydrolases (GHs) play a central role. Xylanases, in particular, are used in a wide range of applications and are essential for the production of xylose, which can be fermented into bioethanol or find use in many other industries. Currently, fungal secretomes dominate as the main reservoir of lignocellulolytic enzymes, but thermophilic microorganisms offer notable advantages in terms of enzyme stability and production efficiency. Here we present the genomic characterization of Geobacillus stearothermophilus GF16 to identify genes encoding putative enzymes involved in lignocellulose degradation. Thermostable GHs secreted by G. stearothermophilus GF16 were investigated and found to be active on different natural polysaccharides and synthetic substrates, revealing an array of inducible GH activities. In particular, the concentrated secretome possesses significant thermostable xylanase and β-xylosidase activities (5 ×103 U/L and 1.7 ×105 U/L, respectively), highlighting its potential for application in biomass valorization. We assessed the hemicellulose hydrolysis capabilities of various agri-food wastes using the concentrated secretome of the strain cultivated on xylan. An impressive 300-fold increase in xylose release compared to a commercially available cocktail was obtained with the secretome, underscoring the remarkable efficacy of this approach.
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Affiliation(s)
- Miriam Carbonaro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Martina Aulitto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Alessia Di Fraia
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Patrizia Contursi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Danila Limauro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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Firrincieli A, Minuti A, Cappelletti M, Ferilli M, Ajmone-Marsan P, Bani P, Petruccioli M, Harfouche AL. Structural and functional analysis of the active cow rumen's microbial community provides a catalogue of genes and microbes participating in the deconstruction of cardoon biomass. Biotechnol Biofuels Bioprod 2024; 17:53. [PMID: 38589938 PMCID: PMC11003169 DOI: 10.1186/s13068-024-02495-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Ruminal microbial communities enriched on lignocellulosic biomass have shown considerable promise for the discovery of microorganisms and enzymes involved in digesting cell wall compounds, a key bottleneck in the development of second-generation biofuels and bioproducts, enabling a circular bioeconomy. Cardoon (Cynara cardunculus) is a promising inedible energy crop for current and future cellulosic biorefineries and the emerging bioenergy and bioproducts industries. The rumen microbiome can be considered an anaerobic "bioreactor", where the resident microbiota carry out the depolymerization and hydrolysis of plant cell wall polysaccharides (PCWPs) through the catalytic action of fibrolytic enzymes. In this context, the rumen microbiota represents a potential source of microbes and fibrolytic enzymes suitable for biofuel production from feedstocks. In this study, metatranscriptomic and 16S rRNA sequencing were used to profile the microbiome and to investigate the genetic features within the microbial community adherent to the fiber fractions of the rumen content and to the residue of cardoon biomass incubated in the rumen of cannulated cows. RESULTS The metatranscriptome of the cardoon and rumen fibre-adherent microbial communities were dissected in their functional and taxonomic components. From a functional point of view, transcripts involved in the methanogenesis from CO2 and H2, and from methanol were over-represented in the cardoon-adherent microbial community and were affiliated with the Methanobrevibacter and Methanosphaera of the Euryarchaeota phylum. Transcripts encoding glycoside hydrolases (GHs), carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), and glycoside transferases (GTs) accounted for 1.5% (6,957) of the total RNA coding transcripts and were taxonomically affiliated to major rumen fibrolytic microbes, such as Oscillospiraceae, Fibrobacteraceae, Neocallimastigaceae, Prevotellaceae, Lachnospiraceae, and Treponemataceae. The comparison of the expression profile between cardoon and rumen fiber-adherent microbial communities highlighted that specific fibrolytic enzymes were potentially responsible for the breakdown of cardoon PCWPs, which was driven by specific taxa, mainly Ruminococcus, Treponema, and Neocallimastigaceae. CONCLUSIONS Analysis of 16S rRNA and metatranscriptomic sequencing data revealed that the cow rumen microbiome harbors a repertoire of new enzymes capable of degrading PCWPs. Our results demonstrate the feasibility of using metatranscriptomics of enriched microbial RNA as a potential approach for accelerating the discovery of novel cellulolytic enzymes that could be harnessed for biotechnology. This research contributes a relevant perspective towards degrading cellulosic biomass and providing an economical route to the production of advanced biofuels and high-value bioproducts.
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Affiliation(s)
- Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Via San Camillo de Lellis Snc, 01100, Viterbo, Italy
| | - Andrea Minuti
- Department of Animal Science, Food and Nutrition, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Marco Ferilli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Via San Camillo de Lellis Snc, 01100, Viterbo, Italy
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
- CREI - Romeo and Enrica Invernizzi Research Center On Sustainable Dairy Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
| | - Paolo Bani
- Department of Animal Science, Food and Nutrition, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Maurizio Petruccioli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Via San Camillo de Lellis Snc, 01100, Viterbo, Italy
| | - Antoine L Harfouche
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Via San Camillo de Lellis Snc, 01100, Viterbo, Italy.
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Wang Z, Rehman A, Jia Y, Dai P, He S, Wang X, Li H, Wang L, Qayyum A, Peng Z, Du X. Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton. Gene 2023; 868:147374. [PMID: 36934785 DOI: 10.1016/j.gene.2023.147374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]
Abstract
Colored cotton is also called eco-cotton because of its natural color fiber. It is inferior in yield and quality than white cotton. The underlying regulatory genes involved in fiber quality and pigment synthesis are not well understood. This study aimed to investigate the transcriptomic and proteomic changes during fiber development in a brown cotton cultivar (Z161) and a white cotton cultivar. The differential proteins with the same expression trend as genes were significantly and positively correlated with corresponding fold changes in expression. Enrichment analysis revealed that Z161, enriched in fiber elongation genes related to flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism, and many more genes (proteins) are up-regulated. Moreover, 164 glycosyltransferases genes, 15 MYB-bHLH-WD40 genes, and other transcription factors such as C2H2 (12), ERF (11), and NAC (7) were preferentially expressed in Z161. Weighted correlation network analysis identified fatty acid synthesis and energy metabolism as the principal metabolic pathways in both cotton genotypes during fiber development. Identified 15 hub genes will provide important insights for genetic manipulation of fiber quality and pigment deposition balance in brown cotton fibers.
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Affiliation(s)
- Zhenzhen Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yinhua Jia
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Panhong Dai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Xiaoyang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Hongge Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China.
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
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Schmitz E, Leontakianakou S, Norlander S, Nordberg Karlsson E, Adlercreutz P. Lignocellulose degradation for the bioeconomy: The potential of enzyme synergies between xylanases, ferulic acid esterase and laccase for the production of arabinoxylo-oligosaccharides. Bioresour Technol 2022; 343:126114. [PMID: 34648963 DOI: 10.1016/j.biortech.2021.126114] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
The success of establishing bioeconomies replacing current economies based on fossil resources largely depends on our ability to degrade recalcitrant lignocellulosic biomass. This study explores the potential of employing various enzymes acting synergistically on previously pretreated agricultural side streams (corn bran, oat hull, soluble and insoluble oat bran). Degrees of synergy (oligosaccharide yield obtained with the enzyme combination divided by the sum of yields obtained with individual enzymes) of up to 88 were obtained. Combinations of a ferulic acid esterase and xylanases resulted in synergy on all substrates, while a laccase and xylanases only acted synergistically on the more recalcitrant substrates. Synergy between different xylanases (glycoside hydrolase (GH) families 5 and 11) was observed particularly on oat hulls, producing a yield of 57%. The synergistic ability of the enzymes was found to be partly due to the increased enzyme stability when in combination with the substrates.
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Affiliation(s)
- Eva Schmitz
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund, SE-22100, Sweden.
| | - Savvina Leontakianakou
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund, SE-22100, Sweden
| | - Siri Norlander
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund, SE-22100, Sweden
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund, SE-22100, Sweden
| | - Patrick Adlercreutz
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund, SE-22100, Sweden
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Wu MX, Zou Y, Yu YH, Chen BX, Zheng QW, Ye ZW, Wei T, Ye SQ, Guo LQ, Lin JF. Comparative transcriptome and proteome provide new insights into the regulatory mechanisms of the postharvest deterioration of Pleurotus tuoliensis fruitbodies during storage. Food Res Int 2021; 147:110540. [PMID: 34399517 DOI: 10.1016/j.foodres.2021.110540] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/05/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
The Pleurotus tuoliensis (Pt), a precious edible mushroom with high economic value, is widely popular for its rich nutrition and meaty texture. However, rapid postharvest deterioration depreciates the commercial value of Pt and severely restricts its marketing. By RNA-Seq transcriptomic and TMT-MS MS proteomic, we study the regulatory mechanisms of the postharvest storage of Pt fruitbodies at 25 ℃ for 0, 38, and 76 h (these three-time points recorded as groups A, B, and C, respectively). 2,008 DEGs (Differentially expressed genes) were identified, and all DEGs shared 265 factors with all DEPs (Differentially expressed proteins). Jointly, the DEGs and DEPs of two-omics showed that the category of the metabolic process contained the most DEGs and DEPs in the biological process by GO (Gene Ontology) classification. The top 17 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways with the highest sum of DEG and DEP numbers in groups B/A (38 h vs. 0 h) and C/A (76 h vs. 0 h) and pathways closely related to energy metabolism were selected for analysis and discussion. Actively expression of CAZymes (Carbohydrate active enzymes), represented by laccase, chitinase, and β-glucanase, directly leads to the softening of fruitbodies. The transcription factor Rlm1 of 1,3-β-glucan synthase attracted attention with a significant down-regulation of gene levels in the C/A group. Laccase also contributes, together with phenylalanine ammonia-lyase (PAL), to the discoloration reaction in the first 76 h of the fruitbodies. Significant expression of several crucial enzymes for EMP (Glycolysis), Fatty acid degradation, and Valine, leucine and isoleucine degradation at the gene or protein level supply substantial amounts of acetyl-CoA to the TCA cycle. Citrate synthase (CS), isocitrate dehydrogenase (ICDH), and three mitochondrial respiratory complexes intensify respiration and produce high levels of ROS (Reactive oxygen species) by significant up-regulation. In the ROS scavenging system, only Mn-SOD was significantly up-regulated at the gene level and was probably interacted with Hsp60 (Heat shock protein 60), which was significantly up-regulated at the protein level, to play a dominant role in antioxidation. Three types of stresses - cell wall stress, starvation, and oxidative stress - were suffered by Pt fruitbodies postharvest, resulting in cell cycle arrest and gene expression disorder.
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Affiliation(s)
- Mu-Xiu Wu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Yuan Zou
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Ying-Hao Yu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Bai-Xiong Chen
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Qian-Wang Zheng
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Zhi-Wei Ye
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Tao Wei
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Si-Qiang Ye
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Li-Qiong Guo
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China.
| | - Jun-Fang Lin
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China.
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Tõlgo M, Hüttner S, Rugbjerg P, Thuy NT, Thanh VN, Larsbrink J, Olsson L. Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172. Biotechnol Biofuels 2021; 14:131. [PMID: 34082802 PMCID: PMC8176577 DOI: 10.1186/s13068-021-01975-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Biomass-degrading enzymes with improved activity and stability can increase substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate low pH and high temperatures. Here, we aimed to illuminate the lignocellulose-degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail. RESULTS We sequenced and analyzed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. 10,128 predicted genes were found in total, which included 411 CAZy domains. Compared to other fungi, auxiliary activity (AA) domains were particularly enriched. A higher GC content was found in coding sequences compared to the overall genome, as well as a high GC3 content, which is hypothesized to contribute to thermophilicity. Primarily auxiliary activity (AA) family 9 lytic polysaccharide monooxygenase (LPMO) and glycoside hydrolase (GH) family 7 glucanase encoding genes were upregulated when LPH172 was cultivated on cellulosic substrates. Conventional hemicellulose encoding genes (GH10, GH11 and various CEs), as well as AA9 LPMOs, were upregulated when LPH172 was cultivated on xylan. The observed co-expression and co-upregulation of genes encoding AA9 LPMOs, other AA CAZymes, and (hemi)cellulases point to a complex and nuanced degradation strategy. CONCLUSIONS Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal that the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterization of potential new enzymes for industrial biomass saccharification.
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Affiliation(s)
- Monika Tõlgo
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Silvia Hüttner
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Peter Rugbjerg
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Nguyen Thanh Thuy
- Center for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Hanoi, Vietnam
| | - Vu Nguyen Thanh
- Center for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Hanoi, Vietnam
| | - Johan Larsbrink
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
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Fernandez-Julia PJ, Munoz-Munoz J, van Sinderen D. A comprehensive review on the impact of β-glucan metabolism by Bacteroides and Bifidobacterium species as members of the gut microbiota. Int J Biol Macromol 2021; 181:877-889. [PMID: 33864864 DOI: 10.1016/j.ijbiomac.2021.04.069] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/01/2021] [Accepted: 04/10/2021] [Indexed: 12/16/2022]
Abstract
β-glucans are polysaccharides which can be obtained from different sources, and which have been described as potential prebiotics. The beneficial effects associated with β-glucan intake are that they reduce energy intake, lower cholesterol levels and support the immune system. Nevertheless, the mechanism(s) of action underpinning these health effects related to β-glucans are still unclear, and the precise impact of β-glucans on the gut microbiota has been subject to debate and revision. In this review, we summarize the most recent advances involving structurally different types of β-glucans as fermentable substrates for Bacteroidetes (mainly Bacteroides) and Bifidobacterium species as glycan degraders. Bacteroides is one of the most abundant bacterial components of the human gut microbiota, while bifidobacteria are widely employed as a probiotic ingredient. Both are generalist glycan degraders capable of using a wide range of substrates: Bacteroides spp. are specialized as primary degraders in the metabolism of complex carbohydrates, whereas Bifidobacterium spp. more commonly metabolize smaller glycans, in particular oligosaccharides, sometimes through syntrophic interactions with Bacteroides spp., in which they act as secondary degraders.
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Affiliation(s)
- Pedro J Fernandez-Julia
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, Tyne & Wear, England, United Kingdom
| | - Jose Munoz-Munoz
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, Tyne & Wear, England, United Kingdom.
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland.
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Boersma AS, Kallscheuer N, Wiegand S, Rast P, Peeters SH, Mesman RJ, Heuer A, Boedeker C, Jetten MSM, Rohde M, Jogler M, Jogler C. Alienimonas californiensis gen. nov. sp. nov., a novel Planctomycete isolated from the kelp forest in Monterey Bay. Antonie Van Leeuwenhoek 2020; 113:1751-1766. [PMID: 31802338 DOI: 10.1007/s10482-019-01367-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022]
Abstract
Planctomycetes are environmentally and biotechnologically important bacteria and are often found in association with nutrient-rich (marine) surfaces. To allow a more comprehensive understanding of planctomycetal lifestyle and physiology we aimed at expanding the collection of axenic cultures with new isolates. Here, we describe the isolation and genomic and physiological characterisation of strain CA12T obtained from giant bladder kelp (Macrocystis pyrifera) in Monterey Bay, California, USA. 16S rRNA gene sequence and whole genome-based phylogenetic analysis showed that strain CA12T clusters within the family Planctomycetaceae and that it has a high 16S rRNA sequence similarity (82.3%) to Planctomicrobium piriforme DSM 26348T. The genome of strain CA12T has a length of 5,475,215 bp and a G+C content of 70.1%. The highest growth rates were observed at 27 °C and pH 7.5. Using different microscopic methods, we could show that CA12T is able to divide by consecutive polar budding, without completing a characteristic planctomycetal lifestyle switch. Based on our data, we suggest that the isolated strain represents a novel species within a novel genus. We thus propose the name Alienimonas gen. nov. with Alienimonas californiensis sp. nov. as type species of the novel genus and CA12T as type strain of the novel species.
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Affiliation(s)
- Alje S Boersma
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Patrick Rast
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Rob J Mesman
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Mareike Jogler
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Gilchrist CLM, Lacey HJ, Vuong D, Pitt JI, Lange L, Lacey E, Pilgaard B, Chooi YH, Piggott AM. Comprehensive chemotaxonomic and genomic profiling of a biosynthetically talented Australian fungus, Aspergillus burnettii sp. nov. Fungal Genet Biol 2020; 143:103435. [PMID: 32702474 DOI: 10.1016/j.fgb.2020.103435] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 01/09/2023]
Abstract
Aspergillus burnettii is a new species belonging to the A. alliaceus clade in Aspergillus subgenus Circumdati section Flavi isolated from peanut-growing properties in southern Queensland, Australia. A. burnettii is a fast-growing, floccose fungus with distinctive brown conidia and is a talented producer of biomass-degrading enzymes and secondary metabolites. Chemical profiling of A. burnettii revealed the metabolites ochratoxin A, kotanins, isokotanins, asperlicin E, anominine and paspalinine, which are common to subgenus Circumdati, together with burnettiene A, burnettramic acids, burnettides, and high levels of 14α-hydroxypaspalinine and hirsutide. The genome of A. burnettii was sequenced and an annotated draft genome is presented. A. burnettii is rich in secondary metabolite biosynthetic gene clusters, containing 51 polyketide synthases, 28 non-ribosomal peptide synthetases and 19 genes related to terpene biosynthesis. Functional annotation of digestive enzymes of A. burnettii and A. alliaceus revealed overlapping carbon utilisation profiles, consistent with a close phylogenetic relationship.
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Affiliation(s)
- Cameron L M Gilchrist
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Heather J Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - John I Pitt
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Lene Lange
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; BioEconomy, Research & Advisory, Karensgade 5, 2500 Valby, Copenhagen, Denmark
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia; Department of Molecular Sciences, Macquarie University, NSW 2109, Australia
| | - Bo Pilgaard
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
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10
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Wu D, Zheng J, Hu W, Zheng X, He Q, Linhardt RJ, Ye X, Chen S. Structure-activity relationship of Citrus segment membrane RG-I pectin against Galectin-3: The galactan is not the only important factor. Carbohydr Polym 2020; 245:116526. [PMID: 32718630 DOI: 10.1016/j.carbpol.2020.116526] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 11/25/2022]
Abstract
Rhamnogalacturonan I (RG-I) pectin are regarded as strong galectin-3 (Gal-3) antagonist because of galactan sidechains. The present study focused on discussing the effects of more structural regions in pectin on the anti-Gal-3 activity. The water-soluble pectin (WSP) recovered from citrus canning processing water was categorized as RG-I pectin. The controlled enzymatic hydrolysis was employed to sequentially remove the α-1,5-arabinan, homogalaturonan and β-1,4-galactan in WSP. The Gal-3-binding affinity KD (kd/ka) of WSP and debranched pectins were calculated to be 0.32 μM, 0.48 μM, 0.56 μM and 1.93 μM. Moreover, based on the more sensitive cell line (MCF-7) model, the IC30 value of WSP was lower than these of modified pectins, indicating decreased anti-Gal-3 activity. Our results suggested that the total amount of neutral sugar sidechains, the length of arabinan and cooperation between HG and RG-I played important roles in the anti-Gal-3 activity of WSP, not the Gal/Ara ratio or RG-I/HG ratio. These results provided a new insight into structure-activity relationship of citrus segment membrane RG-I as a galectin-3 antagonist and a new functional food.
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Affiliation(s)
- Dongmei Wu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
| | - Jiaqi Zheng
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
| | - Weiwei Hu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
| | - Xiaoliang Zheng
- Center for Molecular Medicine, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Qiaojun He
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Xingqian Ye
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China; Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo 315100, China
| | - Shiguo Chen
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China; Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo 315100, China.
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11
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Albesa-Jové D, Cifuente JO, Trastoy B, Guerin ME. Quick-soaking of crystals reveals unprecedented insights into the catalytic mechanism of glycosyltransferases. Methods Enzymol 2019; 621:261-279. [PMID: 31128783 DOI: 10.1016/bs.mie.2019.02.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycosyltransferases (GTs) catalyze the transfer of a sugar moiety from nucleotide-sugar or lipid-phospho-sugar donors to a wide range of acceptor substrates, generating a remarkable amount of structural diversity in biological systems. Glycosyl transfer reactions can proceed with either inversion or retention of the anomeric configuration with respect to the sugar donor substrate. In this chapter, we discuss the application of a quick soaking method of substrates and products into protein crystals to visualize native ternary complexes of retaining glycosyltransferases. The crystal structures provide different snapshots of the catalytic cycle, including the Michaelis complex. During this sequence of events, we visualize how the enzyme guides the substrates into the reaction center where the glycosyl transfer reaction takes place, and unveil the mechanism of product release, involving multiple conformational changes not only in the substrates and products but also in the enzyme. The methodology described here provides unprecedented insights into the catalytic mechanism of glycosyltransferases at the molecular level, and can be applied to the study a myriad of enzymatic mediated reactions.
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Affiliation(s)
- David Albesa-Jové
- Structural Biology Unit, CIC bioGUNE, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | | | - Marcelo E Guerin
- Structural Biology Unit, CIC bioGUNE, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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12
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You Y, Wang Z, Xu W, Wang C, Zhao X, Su Y. Phthalic acid esters disturbed the genetic information processing and improved the carbon metabolism in black soils. Sci Total Environ 2019; 653:212-222. [PMID: 30408669 DOI: 10.1016/j.scitotenv.2018.10.355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/26/2018] [Accepted: 10/27/2018] [Indexed: 06/08/2023]
Abstract
Phthalic acid esters (PAEs), such as dimethyl phthalate (DMP) and dibutyl phthalate (DBP), are widely distributed as environmental pollutants. In this study, the effects of these chemicals were investigated in black soils using a metagenomics approach. The results clearly showed that DMP or DBP increased the abundance of genes involved in transcription, replication and repair in black soils. In addition, the abundances of genes associated with metabolic functions was improved following treatment with DMP or DBP, including those involved in lipid transport and metabolism, carbohydrate transport and metabolism, and energy production and conversion. There could be many reasons for these observed changes. First, the DMP or DBP treatments increased the abundances of genes associated with the LuxR family, the UvrABC repair system, DNA replication pathways, the RNA polymerase complex and base excision repair. Second, the abundances of genes associated with isocitrate lyase regulator (IclR) family transcriptional regulators, lipid metabolism and carbohydrate active enzymes (CAZys) were altered by the DMP or DBP treatments. Finally, the DMP or DBP treatments also increased the emission load of CO2 and altered the fluorescence intensity of humic acid. Therefore, the results of this study suggested that DMP and DBP contamination altered the abundances of genes associated with genetic information processing and improved the carbon metabolism in black soils.
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Affiliation(s)
- Yimin You
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73072, USA.
| | - Weihui Xu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Chunlong Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Xiaosong Zhao
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Yunpeng Su
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
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13
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Badhan A, Huang J, Wang Y, Abbott DW, Di Falco M, Tsang A, McAllister T. Saccharification efficiencies of multi-enzyme complexes produced by aerobic fungi. N Biotechnol 2018; 46:1-6. [PMID: 29803771 DOI: 10.1016/j.nbt.2018.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 11/16/2022]
Abstract
In the present study, we have characterized high molecular weight multi-enzyme complexes in two commercial enzymes produced by Trichoderma reesei (Spezyme CP) and Penicillium funiculosum (Accellerase XC). We successfully identified 146-1000 kDa complexes using Blue native polyacrylamide gel electrophoresis (BN-PAGE) to fractionate the protein profile in both preparations. Identified complexes dissociated into lower molecular weight constituents when loaded on SDS PAGE. Unfolding of the secondary structure of multi-enzyme complexes with trimethylamine (pH >10) suggested that they were not a result of unspecific protein aggregation. Cellulase (CMCase) profiles of extracts of BN-PAGE fractionated protein bands confirmed cellulase activity within the multi-enzyme complexes. A microassay was used to identify protein bands that promoted high levels of glucose release from barley straw. Those with high saccharification yield were subjected to LC-MS analysis to identify the principal enzymatic activities responsible. The results suggest that secretion of proteins by aerobic fungi leads to the formation of high molecular weight multi-enzyme complexes that display activity against carboxymethyl cellulose and barley straw.
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Affiliation(s)
- Ajay Badhan
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Jiangli Huang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Yuxi Wang
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Adrian Tsang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Tim McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada.
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14
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Jurak E, Suzuki H, van Erven G, Gandier JA, Wong P, Chan K, Ho CY, Gong Y, Tillier E, Rosso MN, Kabel MA, Miyauchi S, Master ER. Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce. BMC Genomics 2018; 19:815. [PMID: 30424733 PMCID: PMC6234650 DOI: 10.1186/s12864-018-5210-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/30/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition. RESULTS Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi. CONCLUSIONS The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.
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Affiliation(s)
- E Jurak
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.,Department of Aquatic Biotechnology and Bioproduct Engineering, Groningen, The Netherlands
| | - H Suzuki
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - G van Erven
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - J A Gandier
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - P Wong
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - K Chan
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - C Y Ho
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Y Gong
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - E Tillier
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - M-N Rosso
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - M A Kabel
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - S Miyauchi
- Laboratory of Excellence ARBRE, INRA, Nancy, Lorraine, France.,Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - E R Master
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.
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15
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Andlar M, Rezić T, Marđetko N, Kracher D, Ludwig R, Šantek B. Lignocellulose degradation: An overview of fungi and fungal enzymes involved in lignocellulose degradation. Eng Life Sci 2018; 18:768-778. [PMID: 32624871 PMCID: PMC6999254 DOI: 10.1002/elsc.201800039] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/03/2018] [Accepted: 04/17/2018] [Indexed: 11/10/2022] Open
Abstract
This review aims to present current knowledge of the fungi involved in lignocellulose degradation with an overview of the various classes of lignocellulose-acting enzymes engaged in the pretreatment and saccharification step. Fungi have numerous applications and biotechnological potential for various industries including chemicals, fuel, pulp, and paper. The capability of fungi to degrade lignocellulose containing raw materials is due to their highly effective enzymatic system. Along with the hydrolytic enzymes consisting of cellulases and hemicellulases, responsible for polysaccharide degradation, they have a unique nonenzymatic oxidative system which together with ligninolytic enzymes is responsible for lignin modification and degradation. An overview of the enzymes classification is given by the Carbohydrate-Active enZymes (CAZy) database as the major database for the identification of the lignocellulolytic enzymes by their amino acid sequence similarity. Finally, the recently discovered novel class of recalcitrant polysaccharide degraders-lytic polysaccharide monooxygenases (LPMOs) are presented, because of these enzymes importance in the cellulose degradation process.
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Affiliation(s)
- Martina Andlar
- Department of Biochemical EngineeringFaculty of Food Technology and BiotechnologyUniversity of ZagrebZagrebCroatia
| | - Tonči Rezić
- Department of Biochemical EngineeringFaculty of Food Technology and BiotechnologyUniversity of ZagrebZagrebCroatia
| | - Nenad Marđetko
- Department of Biochemical EngineeringFaculty of Food Technology and BiotechnologyUniversity of ZagrebZagrebCroatia
| | - Daniel Kracher
- Department of Food Sciences and TechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Roland Ludwig
- Department of Food Sciences and TechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Božidar Šantek
- Department of Biochemical EngineeringFaculty of Food Technology and BiotechnologyUniversity of ZagrebZagrebCroatia
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16
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Hooker CA, Hillman ET, Overton JC, Ortiz-Velez A, Schacht M, Hunnicutt A, Mosier NS, Solomon KV. Hydrolysis of untreated lignocellulosic feedstock is independent of S-lignin composition in newly classified anaerobic fungal isolate, Piromyces sp. UH3-1. Biotechnol Biofuels 2018; 11:293. [PMID: 30386430 PMCID: PMC6203967 DOI: 10.1186/s13068-018-1292-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/15/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as anaerobic gut fungi. These gut fungi express a broad range of carbohydrate active enzymes and are native to the digestive tracts of ruminants and hindgut fermenters. In this study, we examine gut fungal performance on these substrates as a function of composition, and the ability of this isolate to degrade inhibitory high syringyl lignin-containing forestry residues. RESULTS We isolated a novel fungal specimen from a donkey in Independence, Indiana, United States. Phylogenetic analysis of the Internal Transcribed Spacer 1 sequence classified the isolate as a member of the genus Piromyces within the phylum Neocallimastigomycota (Piromyces sp. UH3-1, strain UH3-1). The isolate penetrates the substrate with an extensive rhizomycelial network and secretes many cellulose-binding enzymes, which are active on various components of lignocellulose. These activities enable the fungus to hydrolyze at least 58% of the glucan and 28% of the available xylan in untreated corn stover within 168 h and support growth on crude agricultural residues, food waste, and energy crops. Importantly, UH3-1 hydrolyzes high syringyl lignin-containing poplar that is inhibitory to many fungi with efficiencies equal to that of low syringyl lignin-containing poplar with no reduction in fungal growth. This behavior is correlated with slight remodeling of the fungal secretome whose composition adapts with substrate to express an enzyme cocktail optimized to degrade the available biomass. CONCLUSIONS Piromyces sp. UH3-1, a newly isolated anaerobic gut fungus, grows on diverse untreated substrates through production of a broad range of carbohydrate active enzymes that are robust to variations in substrate composition. Additionally, UH3-1 and potentially other anaerobic fungi are resistant to inhibitory lignin composition possibly due to changes in enzyme secretion with substrate. Thus, anaerobic fungi are an attractive platform for the production of enzymes that efficiently use mixed feedstocks of variable composition for second generation biofuels. More importantly, our work suggests that the study of anaerobic fungi may reveal naturally evolved strategies to circumvent common hydrolytic inhibitors that hinder biomass usage.
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Affiliation(s)
- Casey A. Hooker
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, 155 South Grant Street, West Lafayette, IN 47907-2114 USA
| | - Jonathan C. Overton
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Adrian Ortiz-Velez
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
| | - Makayla Schacht
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Abigail Hunnicutt
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
| | - Nathan S. Mosier
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Kevin V. Solomon
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
- Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, 155 South Grant Street, West Lafayette, IN 47907-2114 USA
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17
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Sen A, Tisa LS, Gtari M, Sarkar I. Contrasted evolutionary constraints on carbohydrate active enzymes (CAZymes) in selected Frankia strains. Antonie Van Leeuwenhoek 2019; 112:115-25. [PMID: 30291576 DOI: 10.1007/s10482-018-1173-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/29/2018] [Indexed: 10/28/2022]
Abstract
Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simpler form. In plant-host-associated microorganisms CAZymes are known to be involved in plant cell wall degradation. However, the biology and evolution of Frankia CAZymes are largely unknown. In the present study, we took a genomic approach to evaluate the presence and putative roles of CAZymes in Frankia. The CAZymes were found to be potentially highly expressed (PHX) proteins and contained more aromatic amino acids, which increased their biosynthetic energy cost. These energy rich amino acids were present in the active sites of CAZymes aiding in their carbohydrate binding capacity. Phylogenetic and evolutionary analyses showed that, in Frankia strains with the capacity to nodulate host plants, CAZymes were evolving slower than the other PHX genes, whereas similar genes from non-nodulating (or ineffectively nodulating) Frankia strains showed little variation in their evolutionary constraints compared to other PHX genes. Thus, the present study revealed the persistence of a strong purifying selection on CAZymes of Frankia indicating their crucial role.
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18
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Ogunmolu FE, Kaur I, Pasari N, Gupta M, Yazdani SS. Quantitative multiplexed profiling of Penicillium funiculosum secretome grown on polymeric cellulase inducers and glucose. J Proteomics 2018; 179:150-60. [PMID: 29597011 DOI: 10.1016/j.jprot.2018.03.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/16/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
Filamentous fungi respond to the need to secure utilisable carbon from their growth milieu by secreting unique extracellular proteins depending upon the types of polymeric substrates. We have here profiled the variations in the secretome pattern of a non-model hypercellulolytic fungus - Penicillium funiculosum, grown in minimal media containing four different polymeric cellulase inducers, i.e., Avicel, wheat bran, ammonium-pretreated wheat straw and Avicel & wheat bran, and glucose over its early and late log phases of growth. Of the 137 secreted proteins validated at 1% FDR, we identified the quantified proteins in three clusters as early, persistently or lately expressed. The type of carbon substrate present in the culture media significantly affected the levels of cellulolytic enzymes expression by the fungus. The top abundant proteins quantified in the secretome for Avicel and wheat bran were cellobiohydrolaseI [GH7-CBM1], cellobiohydrolaseII [GH6-CBM1], β-glucosidase [GH3], arabinofuranosidase [GH51] and β-xylosidase [GH3], with bicupin being highest in case of wheat straw. Our results further suggested that the fungus secreted the extracellular proteins in waves, such that the initial responders act to hydrolyse the composite substrates in the culture environment before the second wave of proteins which tend to be more tailored to the specific substrate in the cultivating media. BIOLOGICAL SIGNIFICANCE In this article, we have comprehensively examined the dynamics of the secretome of a non-model hypercellulolytic fungus produced in response to model and composite cellulase inducers. Our study has provided additional insights into how the fungus enzyme machinery responds to the presence of different polymeric cellulase inducers over the two different growth phases (early growth and late growth phase). The comprehensive typing and quantification of the different proteins present in the secretomes of the cellulolytic fungal strains in response to diverse nutrient sources hold many prospects in understanding the fungus unique enzyme machinery and dynamics for the downstream biotechnological applications.
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Spertino S, Boatti L, Icardi S, Manfredi M, Cattaneo C, Marengo E, Cavaletto M. Cellulomonas fimi secretomes: In vivo and in silico approaches for the lignocellulose bioconversion. J Biotechnol 2018; 270:21-29. [PMID: 29409863 DOI: 10.1016/j.jbiotec.2018.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 12/30/2017] [Accepted: 01/26/2018] [Indexed: 12/17/2022]
Abstract
Lignocellulose degradation is a challenging step for value added products and biofuels production. Cellulomonas fimi secretes complex mixtures of carbohydrate active enzymes (CAZymes) which synergistically degrade cellulose and hemicelluloses. Their characterization may provide new insights for enzymatic cocktails implementation. Bioinformatic analysis highlighted 1127 secreted proteins, constituting the in silico secretome, graphically represented in a 2DE map. According to Blast2GO functional annotation, many of these are involved in carbohydrates metabolism. In vivo secretomes were obtained, growing C. fimi on glucose, CMC or wheat straw for 24 h. Zymography revealed degradative activity on carbohydrates and proteomic analysis identified some CAZymes, only in secretomes obtained with CMC and wheat straw. An interaction between cellobiohydrolases is proposed as a strategy adopted by soluble multimodular cellulases. Such approach can be crucial for a better characterization and industrial exploitation of the synergism among C. fimi enzymes.
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Affiliation(s)
- Stefano Spertino
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy.
| | - Lara Boatti
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Sara Icardi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Marcello Manfredi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy; ISALIT S.r.l., Novara, Italy
| | - Chiara Cattaneo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Emilio Marengo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Maria Cavaletto
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
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20
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Gupta DK, Rühl M, Mishra B, Kleofas V, Hofrichter M, Herzog R, Pecyna MJ, Sharma R, Kellner H, Hennicke F, Thines M. The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes. BMC Genomics 2018; 19:48. [PMID: 29334897 PMCID: PMC5769442 DOI: 10.1186/s12864-017-4430-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 12/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology. RESULTS Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery. CONCLUSIONS The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.
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Affiliation(s)
- Deepak K Gupta
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany.,Project Group "Bioresources", Fraunhofer IME, Giessen, Germany
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Vanessa Kleofas
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Martin Hofrichter
- International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Robert Herzog
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Marek J Pecyna
- University of Applied Sciences Zittau/Görlitz, Zittau, Germany
| | - Rahul Sharma
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Harald Kellner
- International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Florian Hennicke
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Frankfurt a. M., Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany. .,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany. .,Department of Biology, Microbiology, Utrecht University, Utrecht, The Netherlands.
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany. .,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany.
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21
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Fogelqvist J, Tzelepis G, Bejai S, Ilbäck J, Schwelm A, Dixelius C. Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum. BMC Genomics 2018; 19:14. [PMID: 29298673 PMCID: PMC5753508 DOI: 10.1186/s12864-017-4407-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/21/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Brassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. In this study we report the draft genomes of 2 V. longisporum field isolates sequenced using the Illumina technology. Genomic characterization and lineage composition, followed by selected gene analysis to facilitate the comprehension of its genomic features and potential effector categories were performed. RESULTS The draft genomes of 2 Verticillium longisporum single spore isolates (VL1 and VL2) have an estimated ungapped size of about 70 Mb. The total number of protein encoding genes identified in VL1 was 20,793, whereas 21,072 gene models were predicted in VL2. The predicted genome size, gene contents, including the gene families coding for carbohydrate active enzymes were almost double the numbers found in V. dahliae and V. albo-atrum. Single nucleotide polymorphisms (SNPs) were frequently distributed in the two genomes but the distribution of heterozygosity and depth was not independent. Further analysis of potential parental lineages suggests that the V. longisporum genome is composed of two parts, A1 and D1, where A1 is more ancient than the parental lineage genome D1, the latter being more closer related to V. dahliae. Presence of the mating-type genes MAT1-1-1 and MAT1-2-1 in the V. longisporum genomes were confirmed. However, the MAT genes in V. dahliae, V. albo-atrum and V. longisporum have experienced extensive nucleotide changes at least partly explaining the present asexual nature of these fungal species. CONCLUSIONS The established draft genome of V. longisporum is comparatively large compared to other studied ascomycete fungi. Consequently, high numbers of genes were predicted in the two V. longisporum genomes, among them many secreted proteins and carbohydrate active enzyme (CAZy) encoding genes. The genome is composed of two parts, where one lineage is more ancient than the part being more closely related to V. dahliae. Dissimilar mating-type sequences were identified indicating possible ancient hybridization events.
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Affiliation(s)
- Johan Fogelqvist
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden
| | - Georgios Tzelepis
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden
| | - Sarosh Bejai
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden
| | - Jonas Ilbäck
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden
- Present Address: National Food Agency, P.O. Box 622, 75126, Uppsala, Sweden
| | - Arne Schwelm
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden.
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22
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Gharechahi J, Salekdeh GH. A metagenomic analysis of the camel rumen's microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation. Biotechnol Biofuels 2018; 11:216. [PMID: 30083229 PMCID: PMC6071333 DOI: 10.1186/s13068-018-1214-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/24/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND The diverse microbiome present in the rumen of ruminant animals facilitates the digestion of plant-based fiber. In this study, a shotgun metagenomic analysis of the microbes adhering to plant fiber in the camel rumen was undertaken to identify the key species contributing to lignocellulose degradation and short chain volatile fatty acids (VFA) fermentation. RESULTS The density of genes in the metagenome encoding glycoside hydrolases was estimated to be 25 per Mbp of assembled DNA, which is significantly greater than what has been reported in other sourced metagenomes, including cow rumen. There was also a substantial representation of sequences encoding scaffoldins, dockerins and cohesins, indicating the potential for cellulosome-mediated lignocellulose degradation. Binning of the assembled metagenome has enabled the definition of 65 high-quality genome bins which showed high diversity for lignocellulose degrading enzymes. Species associated to Bacteroidetes showed a high proportion of genes for debranching and oligosaccharide degrading enzymes, while those belonging to Firmicutes and Fibrobacteres were rich in cellulases and hemicellulases and thus these lineages were probably the key for ensuring the degradation of lignocellulose. The presence of many "polysaccharide utilization loci" (PULs) in Bacteroidetes genomes indicates their broad substrate specificity and high potential carbohydrate degradation ability. An analysis of VFA biosynthesis pathways showed that genes required for the synthesis of acetate were present in a range of species, except for Elusimicrobiota and Euryarchaeota. The production of propionate, exclusively via the succinate pathway, was carried out by species belonging to the phyla Bacteroidetes, Firmicutes, Spirochaetes and Fibrobacteres. Butyrate was generated via the butyrylCoA: acetate CoA-transferase pathway by Bacteroidetes and Lentisphaerae species, but generally via the butyrate kinase pathway by Firmicutes species. CONCLUSION The analysis confirmed the camel rumen's microbiome as a dense and yet largely untapped source of enzymes with the potential to be used in a range of biotechnological processes including biofuel, fine chemicals and food processing industries.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education, and Extension Organization, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, NSW Australia
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23
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Pontes MVA, Patyshakuliyeva A, Post H, Jurak E, Hildén K, Altelaar M, Heck A, Kabel MA, de Vries RP, Mäkelä MR. The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates. Fungal Genet Biol 2017; 112:12-20. [PMID: 29277563 DOI: 10.1016/j.fgb.2017.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 10/18/2022]
Abstract
The white button mushroom Agaricus bisporus is one of the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. bisporus strains for their potential to convert the components that are poorly utilized by the commercial strain A15. We therefore focused our analysis on the stages where the fungus is producing fruiting bodies. Growth profiling was used to identify A. bisporus strains with different abilities to use plant biomass derived polysaccharides, as well as to transport and metabolize the corresponding monomeric sugars. Six wild-type isolates with diverse growth profiles were compared for mushroom production to A15 strain in semi-commercial cultivation conditions. Transcriptome and proteome analyses of the three most interesting wild-type strains and A15 indicated that the unrelated A. bisporus strains degrade and convert plant biomass polymers in a highly similar manner. This was also supported by the chemical content of the compost during the mushroom production process. Our study therefore reveals a highly conserved physiology for unrelated strains of this species during growth in compost.
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Affiliation(s)
- María Victoria Aguilar Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Aleksandrina Patyshakuliyeva
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics Bijvoet, Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Edita Jurak
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Kristiina Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics Bijvoet, Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet, Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
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24
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Mäkelä MR, Bouzid O, Robl D, Post H, Peng M, Heck A, Altelaar M, de Vries RP. Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis. N Biotechnol 2017; 37:162-171. [PMID: 28188936 DOI: 10.1016/j.nbt.2017.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 11/25/2022]
Abstract
The coprophilic ascomycete fungus Podospora anserina was cultivated on three different plant biomasses, i.e. cotton seed hulls (CSH), soybean hulls (SBH) and acid-pretreated wheat straw (WS) for four days, and the potential of the produced enzyme mixtures was compared in the enzymatic saccharification of the corresponding lignocellulose feedstocks. The enzyme cocktail P. anserina produced after three days of growth on SBH showed superior capacity to release reducing sugars from all tested plant biomass feedstocks compared to the enzyme mixtures from CSH and WS cultures. Detailed proteomics analysis of the culture supernatants revealed that SBH contained the most diverse set of enzymes targeted on plant cell wall polymers and was particularly abundant in xylan, mannan and pectin acting enzymes. The importance of lytic polysaccharide monooxygenases (LPMOs) in plant biomass deconstruction was supported by identification of 20 out of 33 AA9 LPMOs in the SBH cultures. The results highlight the suitability of P. anserina as a source of plant cell wall degrading enzymes for biotechnological applications and the importance of selecting the most optimal substrate for the production of enzyme mixtures.
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Affiliation(s)
- Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, P.O. Box 56, Viikinkaari 9, University of Helsinki, Helsinki, Finland, Finland
| | - Ourdia Bouzid
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Microbiology, Utrecht University, Padualaan 8, 3584 Ch Utrecht, The Netherlands
| | - Diogo Robl
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Brazilian Laboratory of Science and Technology of Bioethanol, Giuseppe Maximo Scolfaro 10.000, Campinas, Brazil
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Albert Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Microbiology, Utrecht University, Padualaan 8, 3584 Ch Utrecht, The Netherlands.
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25
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Abstract
Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems using common culture-dependent techniques restricts access to potentially novel cellulolytic bacteria and beneficial enzymes. The development of molecular-based culture-independent methods such as metagenomics enables researchers to study microbial communities directly from environmental samples, and presents a platform from which enzymes of interest can be sourced. We outline key methodological stages that are required as well as describe specific protocols that are currently used for metagenomic projects dedicated to CAZyme discovery.
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Affiliation(s)
- Benoit J Kunath
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 5003, 1432, Ås, Norway
| | - Andreas Bremges
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- German Center for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Aaron Weimann
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Phillip B Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 5003, 1432, Ås, Norway.
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Mukherjee S, Chandrababunaidu MM, Panda A, Khowala S, Tripathy S. Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. Front Microbiol 2016; 7:596. [PMID: 27242677 PMCID: PMC4865484 DOI: 10.3389/fmicb.2016.00596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/11/2016] [Indexed: 01/24/2023] Open
Abstract
This study catalogs production of industrially important enzymes and changes in transcript expression caused by 2-deoxy D-glucose (2-DG) treatment in Arthrinium malaysianum cultures. Carbon Catabolite Repression (CCR) induced by 2-DG in this species is cAMP independent unlike many other organisms. Higher levels of secreted endoglucanase (EG), β-glucosidase (BGL), β-xylosidase (BXL), and filter paper activity assay (FPase) enzymes under 2-DG treatment can be exploited for commercial purposes. An integrated RNA sequencing and quantitative proteomic analysis was performed to investigate the cellular response to 2-DG in A. malaysianum. Analysis of RNASeq data under 2-DG treated and control condition reveals that 56% of the unigenes do not have any known similarity to proteins in non-redundant database. Gene Ontology IDs were assigned to 36% of the transcripts (13260) and about 5207 (14%) were mapped to Kyoto Encyclopedia of Genes and Genomes pathway (KEGG). About 1711 genes encoding 2691 transcripts were differentially expressed in treated vs. control samples. Out of the 2691 differentially expressed transcripts, only 582 have any known function. The most up regulated genes belonged to Pentose Phosphate Pathways and carbohydrate degradation class as expected. In addition, genes involved in protein folding, binding, catalytic activity, DNA repair, and secondary metabolites were up-regulated under 2-DG treatment. Whereas genes encoding glycosylation pathways, growth, nutrient reservoir activity was repressed. Gene ontology analysis of the differentially expressed genes indicates metabolic process (35%) is the pre-dominant class followed by carbohydrate degradation (11%), protein folding, and trafficking (6.2%) and transport (5.3%) classes. Unlike other organisms, conventional unfolded protein response (UPR) was not activated in either control or treated conditions. Major enzymes secreted by A. malaysianum are those degrading plant polysaccharides, the most dominant ones being β-glucosidase, as demonstrated by the 2D gel analysis. A set of 7 differentially expressed mRNAs were validated by qPCR. Transmission electron microscopy analyses demonstrated that the 2-DG treated cell walls of hyphae showed significant differences in the cell-wall thickness. Overall 2-DG treatment in A. malaysianum induced secretion of large amount of commercially viable enzymes compared to other known species.
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Affiliation(s)
- Soumya Mukherjee
- Drug Development Diagnostic and Biotechnology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Mathu Malar Chandrababunaidu
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Arijit Panda
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Suman Khowala
- Drug Development Diagnostic and Biotechnology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
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27
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Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Pühler A, Fogelqvist J, Varrelmann M, Schlüter A, Dixelius C. Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. BMC Genomics 2016; 17:245. [PMID: 26988094 PMCID: PMC4794925 DOI: 10.1186/s12864-016-2561-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background Sugar beet (Beta vulgaris) is a crop cultivated for its high content in sugar, but it is vulnerable to many soil-borne pathogens. One of them is the basidiomycete Rhizoctonia solani. This fungal species has a compatibility system regulating hyphal fusions (anastomosis). Consequently, R. solani species are categorized in anastomosis groups (AGs). AG2-2IIIB isolates are most aggressive on sugar beet. In the present study, we report on the draft genome of R. solani AG2-2IIIB using the Illumina technology. Genome analysis, interpretation and comparative genomics of five sequenced R. solani isolates were carried out. Results The draft genome of R. solani AG2-2IIIB has an estimated size of 56.02 Mb. In addition, two normalized EST libraries were sequenced. In total 20,790 of 21,980 AG2-2IIIB isotigs (transcript isoforms) were mapped on the genome with more than 95 % sequence identity. The genome of R. solani AG2-2IIIB was predicted to harbor 11,897 genes and 4908 were found to be isolate-specific. R. solani AG2-2IIIB was predicted to contain 1142 putatively secreted proteins and 473 of them were found to be unique for this isolate. The R. solani AG2-2IIIB genome encodes a high number of carbohydrate active enzymes. The highest numbers were observed for the polysaccharide lyases family 1 (PL-1), glycoside hydrolase family 43 (GH-43) and carbohydrate estarase family 12 (CE-12). Transcription analysis of selected genes representing different enzyme clades revealed a mixed pattern of up- and down-regulation six days after infection on sugar beets featuring variable levels of resistance compared to mycelia of the fungus grown in vitro. Conclusions The established R. solani AG2-2IIIB genome and EST sequences provide important information on the gene content, gene structure and transcriptional activity for this sugar beet pathogen. The enriched genomic platform provides an important platform to enhance our understanding of R. solani biology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2561-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany
| | - Louise Andersson
- Syngenta Seeds AB, Säbyholmsvägen 24, 26191, Landskrona, Sweden.,Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | - Georgios Tzelepis
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany
| | - Johan Fogelqvist
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | | | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany.
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden.
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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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29
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Chateigner-Boutin AL, Suliman M, Bouchet B, Alvarado C, Lollier V, Rogniaux H, Guillon F, Larré C. Endomembrane proteomics reveals putative enzymes involved in cell wall metabolism in wheat grain outer layers. J Exp Bot 2015; 66:2649-58. [PMID: 25769308 PMCID: PMC4986875 DOI: 10.1093/jxb/erv075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cereal grain outer layers fulfil essential functions for the developing seed such as supplying energy and providing protection. In the food industry, the grain outer layers called 'the bran' is valuable since it is rich in dietary fibre and other beneficial nutriments. The outer layers comprise several tissues with a high content in cell wall material. The cell wall composition of the grain peripheral tissues was investigated with specific probes at a stage of active cell wall synthesis. Considerable wall diversity between cell types was revealed. To identify the cellular machinery involved in cell wall synthesis, a subcellular proteomic approach was used targeting the Golgi apparatus where most cell wall polysaccharides are synthesized. The tissues were dissected into outer pericarp and intermediate layers where 822 and 1304 proteins were identified respectively. Many carbohydrate-active enzymes were revealed: some in the two peripheral grain fractions, others only in one tissue. Several protein families specific to one fraction and with characterized homologs in other species might be related to the specific detection of a polysaccharide in a particular cell layer. This report provides new information on grain cell walls and its biosynthesis in the valuable outer tissues, which are poorly studied so far. A better understanding of the mechanisms controlling cell wall composition could help to improve several quality traits of cereal products (e.g. dietary fibre content, biomass conversion to biofuel).
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Affiliation(s)
| | - Muhtadi Suliman
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Brigitte Bouchet
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Camille Alvarado
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Virginie Lollier
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Hélène Rogniaux
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Fabienne Guillon
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Colette Larré
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
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30
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Ferrara MC, Cobucci-Ponzano B, Carpentieri A, Henrissat B, Rossi M, Amoresano A, Moracci M. The identification and molecular characterization of the first archaeal bifunctional exo-β-glucosidase/N-acetyl-β-glucosaminidase demonstrate that family GH116 is made of three functionally distinct subfamilies. Biochim Biophys Acta Gen Subj 2013; 1840:367-77. [PMID: 24060745 DOI: 10.1016/j.bbagen.2013.09.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/13/2013] [Accepted: 09/16/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND β-N-acetylhexosaminidases, which are involved in a variety of biological processes including energy metabolism, cell proliferation, signal transduction and in pathogen-related inflammation and autoimmune diseases, are widely distributed in Bacteria and Eukaryotes, but only few examples have been found in Archaea so far. However, N-acetylgluco- and galactosamine are commonly found in the extracellular storage polymers and in the glycans decorating abundantly expressed glycoproteins from different Crenarchaeota Sulfolobus sp., suggesting that β-N-acetylglucosaminidase activities could be involved in the modification/recycling of these cellular components. METHODS A thermophilic β-N-acetylglucosaminidase was purified from cellular extracts of S. solfataricus, strain P2, identified by mass spectrometry, and cloned and expressed in E. coli. Glycosidase assays on different strains of S. solfataricus, steady state kinetic constants, substrate specificity analysis, and the sensitivity to two inhibitors of the recombinant enzyme were also reported. RESULTS A new β-N-acetylglucosaminidase from S. solfataricus was unequivocally identified as the product of gene sso3039. The detailed enzymatic characterization demonstrates that this enzyme is a bifunctional β-glucosidase/β-N-acetylglucosaminidase belonging to family GH116 of the carbohydrate active enzyme (CAZy) classification. CONCLUSIONS This study allowed us to propose that family GH116 is composed of three subfamilies, which show distinct substrate specificities and inhibitor sensitivities. GENERAL SIGNIFICANCE The characterization of SSO3039 allows, for the first time in Archaea, the identification of an enzyme involved in the metabolism β-N-acetylhexosaminide, an essential component of glycoproteins in this domain of life, and substantially increases our knowledge on the functional role and phylogenetic relationships amongst the GH116 CAZy family members.
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Affiliation(s)
- Maria Carmina Ferrara
- Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
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