1
|
Hernández-Benítez LJ, Ramírez-Rodríguez MA, Hernández-Santoyo A, Rodríguez-Romero A. A trimeric glycosylated GH45 cellulase from the red abalone (Haliotis rufescens) exhibits endo and exoactivity. PLoS One 2024; 19:e0301604. [PMID: 38635649 PMCID: PMC11025796 DOI: 10.1371/journal.pone.0301604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
The red abalone (Haliotis rufescens) represents North America's most important aquaculture species. Its hepatopancreas is rich in cellulases and other polysaccharide-degrading enzymes, which provide it the remarkable ability to digest cellulose-rich macroalgae; nevertheless, its cellulolytic systems are poorly explored. This manuscript describes some functional and structural properties of an endogenous trimeric glycosylated endoglucanase from H. rufescens. The purified enzyme showed a molecular mass of 23.4 kDa determined by MALDI-TOF mass spectrometry, which behaved as a homotrimer in gel filtration chromatography and zymograms. According to the periodic acid-Schiff reagent staining, detecting sugar moieties in SDS-PAGE gel confirmed that abalone cellulase is a glycoprotein. Hydrolysis of cello-oligosaccharides and p-nitrophenyl-β-D-glucopyranosides confirmed its endo/exoactivity. A maximum enzyme activity toward 0.5% (w/v) carboxymethylcellulose of 53.9 ± 1.0 U/mg was achieved at 45°C and pH 6.0. We elucidated the abalone cellulase primary structure using proteases and mass spectrometry methods. Based on these results and using a bioinformatic approach, we identified the gene encoding this enzyme and deduced its full-length amino acid sequence; the mature protein comprised 177 residues with a calculated molecular mass of 19.1 kDa and, according to sequence similarity, it was classified into the glycosyl-hydrolase family 45 subfamily B. An AlphaFold theoretical model and docking simulations with cellopentaose confirmed that abalone cellulase is a β-sheet rich protein, as also observed by circular dichroism experiments, with conserved catalytic residues: Asp26, Asn109, and Asp134. Interestingly, the AlphaFold-Multimer analysis indicated a trimeric assembly for abalone cellulase, which supported our experimental findings. The discovery and characterization of these enzymes may contribute to developing efficient cellulose bioconversion processes for biofuels and sustainable bioproducts.
Collapse
|
2
|
Chen X, Cheng W, Li S, Tang X, Wei Z. The "quality" and "quantity" of microbial species drive the degradation of cellulose during composting. BIORESOURCE TECHNOLOGY 2021; 320:124425. [PMID: 33242687 DOI: 10.1016/j.biortech.2020.124425] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/10/2020] [Accepted: 11/14/2020] [Indexed: 06/11/2023]
Abstract
The aim of this study was to explore the contribution of microbial community to cellulose degradation during cellulosic wastes composting. Three raw materials with different cellulose content were employed, including rice straws (RS), leaves (L) and mushroom dregs (MD). The cellulose degraded by 92.09%, 56.68% and 40.03% during RS, L and MD composting, respectively, which could be explained by cellulases activity. Besides, each cellulase were only linked to a specific group of bacteria, thus cellulose degradation needed the cooperation of various microorganisms. Ultimately, structural equation models verified that the richness and evenness of microbial community were the primary driving factors of cellulose degradation. The richness symbolized microbial functionality, which was equivalent to the "quality" of microbial species. The evenness symbolized the scope of function, which was equivalent to the "quantity". Therefore, the "quality" and "quantity" of microbial species drove cellulose degradation during RS, L and MD composting.
Collapse
Affiliation(s)
- Xiaomeng Chen
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China; College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Wanting Cheng
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Shenzhou Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiaofei Tang
- Heilongjiang Province Environmental Science Research Institute, Harbin 150056, China
| | - Zimin Wei
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China; College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| |
Collapse
|
3
|
Salem H, Kirsch R, Pauchet Y, Berasategui A, Fukumori K, Moriyama M, Cripps M, Windsor D, Fukatsu T, Gerardo NM. Symbiont Digestive Range Reflects Host Plant Breadth in Herbivorous Beetles. Curr Biol 2020; 30:2875-2886.e4. [PMID: 32502409 DOI: 10.1016/j.cub.2020.05.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/05/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Numerous adaptations are gained in light of a symbiotic lifestyle. Here, we investigated the obligate partnership between tortoise leaf beetles (Chrysomelidae: Cassidinae) and their pectinolytic Stammera symbionts to detail how changes to the bacterium's streamlined metabolic range can shape the digestive physiology and ecological opportunity of its herbivorous host. Comparative genomics of 13 Stammera strains revealed high functional conservation, highlighted by the universal presence of polygalacturonase, a primary pectinase targeting nature's most abundant pectic class, homogalacturonan (HG). Despite this conservation, we unexpectedly discovered a disparate distribution for rhamnogalacturonan lyase, a secondary pectinase hydrolyzing the pectic heteropolymer, rhamnogalacturonan I (RG-I). Consistent with the annotation of rhamnogalacturonan lyase in Stammera, cassidines are able to depolymerize RG-I relative to beetles whose symbionts lack the gene. Given the omnipresence of HG and RG-I in foliage, Stammera that encode pectinases targeting both substrates allow their hosts to overcome a greater diversity of plant cell wall polysaccharides and maximize access to the nutritionally rich cytosol. Possibly facilitated by their symbionts' expanded digestive range, cassidines additionally endowed with rhamnogalacturonan lyase appear to utilize a broader diversity of angiosperms than those beetles whose symbionts solely supplement polygalacturonase. Our findings highlight how symbiont metabolic diversity, in concert with host adaptations, may serve as a potential source of evolutionary innovations for herbivorous lineages.
Collapse
Affiliation(s)
- Hassan Salem
- Department of Biology, Emory University, Atlanta, GA 30322, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Mutualisms Research Group, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - Kayoko Fukumori
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Minoru Moriyama
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Michael Cripps
- AgResearch, Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Donald Windsor
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | | |
Collapse
|
4
|
Busch A, Danchin EGJ, Pauchet Y. Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in Phytophaga beetles. BMC Evol Biol 2019; 19:100. [PMID: 31077129 PMCID: PMC6509783 DOI: 10.1186/s12862-019-1429-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cellulose, a major polysaccharide of the plant cell wall, consists of β-1,4-linked glucose moieties forming a molecular network recalcitrant to enzymatic breakdown. Although cellulose is potentially a rich source of energy, the ability to degrade it is rare in animals and was believed to be present only in cellulolytic microbes. Recently, it has become clear that some animals encode endogenous cellulases belonging to several glycoside hydrolase families (GHs), including GH45. GH45s are distributed patchily among the Metazoa and, in insects, are encoded only by the genomes of Phytophaga beetles. This study aims to understand both the enzymatic functions and the evolutionary history of GH45s in these beetles. RESULTS To this end, we biochemically assessed the enzymatic activities of 37 GH45s derived from five species of Phytophaga beetles and discovered that beetle-derived GH45s degrade three different substrates: amorphous cellulose, xyloglucan and glucomannan. Our phylogenetic and gene structure analyses indicate that at least one gene encoding a putative cellulolytic GH45 was present in the last common ancestor of the Phytophaga, and that GH45 xyloglucanases evolved several times independently in these beetles. The most closely related clade to Phytophaga GH45s was composed of fungal sequences, suggesting this GH family was acquired by horizontal gene transfer from fungi. Besides the insects, other arthropod GH45s do not share a common origin and appear to have emerged at least three times independently. CONCLUSION The rise of functional innovation from gene duplication events has been a fundamental process in the evolution of GH45s in Phytophaga beetles. Both, enzymatic activity and ancestral origin suggest that GH45s were likely an essential prerequisite for the adaptation allowing Phytophaga beetles to feed on plants.
Collapse
Affiliation(s)
- André Busch
- Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
| | | | - Yannick Pauchet
- Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany.
| |
Collapse
|
5
|
Tsuji A, Yuasa K, Asada C. Cellulose-binding activity of a 21-kDa endo-ß-1,4-glucanase lacking cellulose-binding domain and its synergy with other cellulases in the digestive fluid of Aplysia kurodai. PLoS One 2018; 13:e0205915. [PMID: 30412581 PMCID: PMC6226162 DOI: 10.1371/journal.pone.0205915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/03/2018] [Indexed: 12/05/2022] Open
Abstract
Endo-ß-1,4-glucanase AkEG21 belonging to glycosyl hydrolase family 45 (GHF45) is the most abundant cellulase in the digestive fluid of sea hare (Aplysia kurodai). The specific activity of this 21-kDa enzyme is considerably lower than those of other endo ß-1,4-glucanases in the digestive fluid of A. kurodai, therefore its role in whole cellulose hydrolysis by sea hare is still uncertain. Although AkEG21 has a catalytic domain without a cellulose binding domain, it demonstrated stable binding to cellulose fibers, similar to that of fungal cellobiohydrolase (CBH) 1 and CBH 2, which is strongly inhibited by cellohexaose, suggesting the involvement of the catalytic site in cellulose binding. Cellulose-bound AkEG21 hydrolyzed cellulose to cellobiose, cellotriose and cellotetraose, but could not digest an external substrate, azo-carboxymethyl cellulose. Cellulose hydrolysis was considerably stimulated by the synergistic action of cellulose-bound AkEG21 and AkEG45, another ß-1,4-endoglucanase present in the digestive fluid of sea hare; however no synergy in carboxymethylcellulose hydrolysis was observed. When AkEG21 was removed from the digestive fluid by immunoprecipitation, the cellulose hydrolyzing activity of the fluid was significantly reduced, indicating a critical role of AkEG21 in cellulose hydrolysis by A. kurodai. These findings suggest that AkEG21 is a processive endoglucanase functionally equivalent to the CBH, which provides a CBH-independent mechanism for the mollusk to digest seaweed cellulose to glucose.
Collapse
Affiliation(s)
- Akihiko Tsuji
- Department of Biomolecular Function and Technology, Graduate School of Bioscience & Bioindustry, Tokushima University, Minamijosanjima, Tokushima, Japan
- * E-mail:
| | - Keizo Yuasa
- Department of Biomolecular Function and Technology, Graduate School of Bioscience & Bioindustry, Tokushima University, Minamijosanjima, Tokushima, Japan
| | - Chikako Asada
- Department of Bioresource Chemistry and Technology, Graduate School of Bioscience & Bioindustry, Tokushima University, Minamijosanjima, Tokushima, Japan
| |
Collapse
|
6
|
Luo C, Li Y, Liao H, Yang Y. De novo transcriptome assembly of the bamboo snout beetle Cyrtotrachelus buqueti reveals ability to degrade lignocellulose of bamboo feedstock. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:292. [PMID: 30386429 PMCID: PMC6204003 DOI: 10.1186/s13068-018-1291-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/15/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND The bamboo weevil Cyrtotrachelus buqueti, which is considered a pest species, damages bamboo shoots via its piercing-sucking mode of feeding. C. buqueti is well known for its ability to transform bamboo shoot biomass into nutrients and energy for growth, development and reproduction with high specificity and efficacy of bioconversion. Woody bamboo is a perennial grass that is a potential feedstock for lignocellulosic biomass because of its high growth rate and lignocellulose content. To verify our hypothesis that C. buqueti efficiently degrades bamboo lignocellulose, we assessed the bamboo lignocellulose-degrading ability of this insect through RNA sequencing for identifying a potential route for utilisation of bamboo biomass. RESULTS Analysis of carbohydrate-active enzyme (CAZyme) family genes in the developmental transcriptome of C. buqueti revealed 1082 unigenes, including 55 glycoside hydrolases (GH) families containing 309 GHs, 51 glycosyltransferases (GT) families containing 329 GTs, 8 carbohydrate esterases (CE) families containing 174 CEs, 6 polysaccharide lyases (PL) families containing 11 PLs, 8 auxiliary activities (AA) families containing 131 enzymes with AAs and 17 carbohydrate-binding modules (CBM) families containing 128 CBMs. We used weighted gene co-expression network analysis to analyse developmental RNA sequencing data, and 19 unique modules were identified in the analysis. Of these modules, the expression of MEyellow module genes was unique and the module included numerous CAZyme family genes. CAZyme genes in this module were divided into two groups depending on whether gene expression was higher in the adult/larval stages or in the egg/pupal stages. Enzyme assays revealed that cellulase activity was highest in the midgut whereas lignin-degrading enzyme activity was highest in the hindgut, consistent with findings from intestinal gene expression studies. We also analysed the expression of CAZyme genes in the transcriptome of C. buqueti from two cities and found that several genes were also assigned to CAZyme families. The insect had genes and enzymes associated with lignocellulose degradation, the expression of which differed with developmental stage and intestinal region. CONCLUSION Cyrtotrachelus buqueti exhibits lignocellulose degradation-related enzymes and genes, most notably CAZyme family genes. CAZyme family genes showed differences in expression at different developmental stages, with adults being more effective at cellulose degradation and larvae at lignin degradation, as well as at different regions of the intestine, with the midgut being more cellulolytic than the hindgut. This degradative system could be utilised for the bioconversion of bamboo lignocellulosic biomass.
Collapse
Affiliation(s)
- Chaobing Luo
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
| | - Yuanqiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
- College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Hong Liao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
| | - Yaojun Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
| |
Collapse
|
7
|
Nguyen STC, Freund HL, Kasanjian J, Berlemont R. Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. Appl Microbiol Biotechnol 2018; 102:1629-1637. [PMID: 29359269 DOI: 10.1007/s00253-018-8778-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Abstract
The enzymatic deconstruction of structural polysaccharides, which relies on the production of specific glycoside hydrolases (GHs), is an essential process across environments. Over the past few decades, researchers studying the diversity and evolution of these enzymes have isolated and biochemically characterized thousands of these proteins. The carbohydrate-active enzymes database (CAZy) lists these proteins and provides some metadata. Here, the sequences and metadata of characterized sequences derived from GH families associated with the deconstruction of cellulose, xylan, and chitin were collected and discussed. First, although few polyspecific enzymes are identified, characterized GH families are mostly monospecific. Next, the taxonomic distribution of characterized GH mirrors the distribution of identified sequences in sequenced genomes. This provides a rationale for connecting the identification of GH sequences to specific reactions or lineages. Finally, we tested the annotation of the characterized GHs using HMM scan and the protein families database (Pfam). The vast majority of GHs targeting cellulose, xylan, and chitin can be identified using this publicly accessible approach.
Collapse
Affiliation(s)
- Stanley T C Nguyen
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Hannah L Freund
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Joshua Kasanjian
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Renaud Berlemont
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA.
| |
Collapse
|
8
|
|
9
|
High-level expression and purification of a molluskan endoglucanase from Ampullaria crossean in Pichia pastoris. Protein Expr Purif 2017; 139:8-13. [DOI: 10.1016/j.pep.2017.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 06/29/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022]
|
10
|
Kimura S, Nakayama K, Wada M, Kim UJ, Azumi K, Ojima T, Nozawa A, Kitamura SI, Hirose E. Cellulose is not degraded in the tunic of the edible ascidian Halocynthia roretzi contracting soft tunic syndrome. DISEASES OF AQUATIC ORGANISMS 2015; 116:143-148. [PMID: 26480917 DOI: 10.3354/dao02913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Soft tunic syndrome is a fatal disease in the edible ascidian Halocynthia roretzi, causing serious damage to ascidian aquaculture in Korea and Japan. In diseased individuals, the tunic, an integumentary extracellular matrix of ascidians, softens and eventually tears. This is an infectious disease caused by the kinetoplastid flagellate Azumiobodo hoyamushi. However, the mechanism of tunic softening remains unknown. Because cellulose fibrils are the main component of the tunic, we compared the contents and structures of cellulose in healthy and diseased tunics by means of biochemical quantification and X-ray diffractometry. Unexpectedly, the cellulose contents and structures of cellulose microfibrils were almost the same regardless of the presence or absence of the disease. Therefore, it is unlikely that thinning of the microfibrils occurred in the softened tunic, because digestion should have resulted in decreases in crystallinity index and crystallite size. Moreover, cellulase was not detected in pure cultures of A. hoyamushi in biochemical and expressed sequence tag analyses. These results indicate that cellulose degradation does not occur in the softened tunic.
Collapse
Affiliation(s)
- Satoshi Kimura
- Department of Biomaterial Science, Graduate School of Agricultural and Life Science, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|