1
|
Hoque E, Fritscher J. Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment? Crit Rev Microbiol 2023:1-24. [PMID: 37452612 DOI: 10.1080/1040841x.2023.2224425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 07/18/2023]
Abstract
Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.
Collapse
Affiliation(s)
- Enamul Hoque
- Department of Biotechnology, University of Science and Technology, Foy's Lake, Chittagong, Bangladesh
- International Virtual Institute for Advanced Science and Technology (IVAST), Section Microbial Technology, Munich, Germany
- Department of Environmental Science, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Fritscher
- Department of Biotechnology, University of Science and Technology, Foy's Lake, Chittagong, Bangladesh
- International Virtual Institute for Advanced Science and Technology (IVAST), Section Microbial Technology, Munich, Germany
- Department of Environmental Science, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| |
Collapse
|
2
|
Enzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery Innovation. Microbiol Mol Biol Rev 2022; 86:e0004122. [PMID: 35852448 PMCID: PMC9769567 DOI: 10.1128/mmbr.00041-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Lignocellulosic biorefineries require innovative solutions to realize their full potential, and the discovery of novel lignocellulose-active enzymes could improve biorefinery deconstruction processes. Enzymatic deconstruction of plant cell walls is challenging, as noncarbohydrate linkages in hemicellulosic sidechains and lignin protect labile carbohydrates from hydrolysis. Highly specialized microbes that degrade plant biomass are attractive sources of enzymes for improving lignocellulose deconstruction, and the anaerobic gut fungi (Neocallimastigomycetes) stand out as having great potential for harboring novel lignocellulose-active enzymes. We discuss the known aspects of Neocallimastigomycetes lignocellulose deconstruction, including their extensive carbohydrate-active enzyme content, proficiency at deconstructing complex lignocellulose, unique physiology, synergistic enzyme complexes, and sizeable uncharacterized gene content. Progress describing Neocallimastigomycetes and their enzymes has been rapid in recent years, and it will only continue to expand. In particular, direct manipulation of anaerobic fungal genomes, effective heterologous expression of anaerobic fungal enzymes, and the ability to directly relate chemical changes in lignocellulose to fungal gene regulation will accelerate the discovery and subsequent deployment of Neocallimastigomycetes lignocellulose-active enzymes.
Collapse
|
3
|
Huang HC, Qi LH, Chen YC, Tsai LC. Crystal structures of the GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo and endo activity and its complex with cellobiose. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:1138-1147. [PMID: 31793907 DOI: 10.1107/s2059798319013597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/04/2019] [Indexed: 11/10/2022]
Abstract
The catalytic domain (residues 128-449) of the Orpinomyces sp. Y102 CelC7 enzyme (Orp CelC7) exhibits cellobiohydrolase and cellotriohydrolase activities. Crystal structures of Orp CelC7 and its cellobiose-bound complex have been solved at resolutions of 1.80 and 2.78 Å, respectively. Cellobiose occupies subsites +1 and +2 within the active site of Orp CelC7 and forms hydrogen bonds to two key residues: Asp248 and Asp409. Furthermore, its substrate-binding sites have both tunnel-like and open-cleft conformations, suggesting that the glycoside hydrolase family 6 (GH6) Orp CelC7 enzyme may perform enzymatic hydrolysis in the same way as endoglucanases and cellobiohydrolases. LC-MS/MS analysis revealed cellobiose (major) and cellotriose (minor) to be the respective products of endo and exo activity of the GH6 Orp CelC7.
Collapse
Affiliation(s)
- Hsiao Chuan Huang
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
| | - Liu Hong Qi
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
| | - Yo Chia Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Li Chu Tsai
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
| |
Collapse
|
4
|
A biochemical comparison of fungal GH6 cellobiohydrolases. Biochem J 2019; 476:2157-2172. [DOI: 10.1042/bcj20190185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 02/02/2023]
Abstract
AbstractCellobiohydrolases (CBHs) from glycoside hydrolase family 6 (GH6) make up an important part of the secretome in many cellulolytic fungi. They are also of technical interest, particularly because they are part of the enzyme cocktails that are used for the industrial breakdown of lignocellulosic biomass. Nevertheless, functional studies of GH6 CBHs are scarce and focused on a few model enzymes. To elucidate functional breadth among GH6 CBHs, we conducted a comparative biochemical study of seven GH6 CBHs originating from fungi living in different habitats, in addition to one enzyme variant. The enzyme sequences were investigated by phylogenetic analyses to ensure that they were not closely related phylogenetically. The selected enzymes were all heterologously expressed in Aspergillus oryzae, purified and thoroughly characterized biochemically. This approach allowed direct comparisons of functional data, and the results revealed substantial variability. For example, the adsorption capacity on cellulose spanned two orders of magnitude and kinetic parameters, derived from two independent steady-state methods also varied significantly. While the different functional parameters covered wide ranges, they were not independent since they changed in parallel between two poles. One pole was characterized by strong substrate interactions, high adsorption capacity and low turnover number while the other showed weak substrate interactions, poor adsorption and high turnover. The investigated enzymes essentially defined a continuum between these two opposites, and this scaling of functional parameters raises interesting questions regarding functional plasticity and evolution of GH6 CBHs.
Collapse
|
5
|
Escuder-Rodríguez JJ, DeCastro ME, Cerdán ME, Rodríguez-Belmonte E, Becerra M, González-Siso MI. Cellulases from Thermophiles Found by Metagenomics. Microorganisms 2018; 6:microorganisms6030066. [PMID: 29996513 PMCID: PMC6165527 DOI: 10.3390/microorganisms6030066] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 01/05/2023] Open
Abstract
Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a prerequisite for their implementation, these enzymes need to be able to operate in the conditions the industrial process requires. Thus, cellulases retrieved from extremophiles, and more specifically those of thermophiles, are likely to be more appropriate for industrial needs in which high temperatures are involved. Metagenomics, the study of genes and gene products from the whole community genomic DNA present in an environmental sample, is a powerful tool for bioprospecting in search of novel enzymes. In this review, we describe the cellulolytic systems, we summarize their biotechnological applications, and we discuss the strategies adopted in the field of metagenomics for the discovery of new cellulases, focusing on those of thermophilic microorganisms.
Collapse
Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| |
Collapse
|
6
|
Seppälä S, Wilken SE, Knop D, Solomon KV, O’Malley MA. The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown. Metab Eng 2017; 44:45-59. [DOI: 10.1016/j.ymben.2017.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/16/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022]
|
7
|
Morrison JM, Elshahed MS, Youssef NH. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci Rep 2016; 6:29217. [PMID: 27381262 PMCID: PMC4933900 DOI: 10.1038/srep29217] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023] Open
Abstract
The anaerobic fungus Orpinomyces strain C1A is capable of growth on various types of lignocellulosic substrates, and harbors an impressive reservoir of carbohydrate active enzymes (CAZymes). Using a minimum enzyme cocktail strategy, we constituted a four-component lignocellulolytic cocktail derived from highly transcribed C1A, and evaluated its efficacy against pretreated corn stover and switchgrass. Hydrolysis yields ranged between 65–77.4%, depending on the lignocellulosic substrate and pretreatment applied. Addition of a highly expressed anaerobic fungal swollenin improved hydrolysis yields by up to 7%. Compared to the commercial cocktail CTec2, these anaerobic fungal cocktails provided comparable or slightly lower hydrolysis yields. Further, the differences in efficacy between commercial and anaerobic cocktails were often only realized after extended (168 hr) incubations. Under certain conditions, the hydrolysis yields of the anaerobic fungal cocktail was slightly superior to that realized by CTec2. We attribute the observed high hydrolysis yields to the high specific activity and affinity of the individual enzymes of the cocktail, as well as the high level of synergy and multi-functionality observed in multiple components. Collectively, this effort provides a novel platform for constructing highly effective enzymes for biofuel production and represents the first lignocellulolytic enzyme cocktail created from anaerobic fungal enzymes.
Collapse
Affiliation(s)
- Jessica M Morrison
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
8
|
Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| |
Collapse
|
9
|
Chen YC, Chen WT, Liu JC, Tsai LC, Cheng HL. A highly active beta-glucanase from a new strain of rumen fungus Orpinomyces sp.Y102 exhibits cellobiohydrolase and cellotriohydrolase activities. BIORESOURCE TECHNOLOGY 2014; 170:513-521. [PMID: 25164344 DOI: 10.1016/j.biortech.2014.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/31/2014] [Accepted: 08/01/2014] [Indexed: 06/03/2023]
Abstract
A new strain of rumen fungus was isolated from Bos taurus, identified and designated Orpinomyces sp.Y102. A clone, celC7, isolated from the cDNA library of Orpinomyces sp.Y102, was predicted to encode a protein containing a signal peptide (Residues 1-17), an N-terminal dockerin-containing domain, and a C-terminal cellobiohydrolase catalytic domain of glycoside hydrolase family 6. CelC7 was insoluble when expressed in Escherichia coli. Deletion of 17 or 105 residues from the N-terminus significantly improved its solubility. The resulting enzymes, CelC7(-17) and CelC7(-105), were highly active to β-glucan substrates and were stable between pH 5.0 and 11.0. CelC7(-105) worked as an exocellulase releasing cellobiose and cellotriose from acid-swollen Avicel and cellooligosaccharides, and displayed a Vmax of 6321.64μmole/min/mg and a Km of 2.18mg/ml to barley β-glucan. Further, the crude extract of CelC7(-105) facilitated ethanol fermentation from cellulose. Thus, CelC7(-105) is a good candidate for industrial applications such as biofuel production.
Collapse
Affiliation(s)
- Yo-Chia Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, 1, Shuehfu Rd., Neipu, Pingtung 91201, Taiwan, ROC
| | - Wan-Ting Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, 1, Shuehfu Rd., Neipu, Pingtung 91201, Taiwan, ROC
| | - Jeng-Chen Liu
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, 1, Shuehfu Rd., Neipu, Pingtung 91201, Taiwan, ROC
| | - Li-Chu Tsai
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, 1, Sec. 3, Chung-Hsiao E. Rd., Taipei 10608, Taiwan, ROC
| | - Hsueh-Ling Cheng
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, 1, Shuehfu Rd., Neipu, Pingtung 91201, Taiwan, ROC.
| |
Collapse
|
10
|
Blackman LM, Cullerne DP, Hardham AR. Bioinformatic characterisation of genes encoding cell wall degrading enzymes in the Phytophthora parasitica genome. BMC Genomics 2014; 15:785. [PMID: 25214042 PMCID: PMC4176579 DOI: 10.1186/1471-2164-15-785] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 09/03/2014] [Indexed: 12/13/2022] Open
Abstract
Background A critical aspect of plant infection by the majority of pathogens is penetration of the plant cell wall. This process requires the production and secretion of a broad spectrum of pathogen enzymes that target and degrade the many complex polysaccharides in the plant cell wall. As a necessary framework for a study of the expression of cell wall degrading enzymes (CWDEs) produced by the broad host range phytopathogen, Phytophthora parasitica, we have conducted an in-depth bioinformatics analysis of the entire complement of genes encoding CWDEs in this pathogen’s genome. Results Our bioinformatic analysis indicates that 431 (2%) of the 20,825 predicted proteins encoded by the P. parasitica genome, are carbohydrate-active enzymes (CAZymes) involved in the degradation of cell wall polysaccharides. Of the 431 proteins, 337 contain classical N-terminal secretion signals and 67 are predicted to be targeted to the non-classical secretion pathway. Identification of CAZyme catalytic activity based on primary protein sequence is difficult, nevertheless, detailed comparisons with previously characterized enzymes has allowed us to determine likely enzyme activities and targeted substrates for many of the P. parasitica CWDEs. Some proteins (12%) contain more than one CAZyme module but, in most cases, multiple modules are from the same CAZyme family. Only 12 P. parasitica CWDEs contain both catalytically-active (glycosyl hydrolase) and non-catalytic (carbohydrate binding) modules, a situation that contrasts with that in fungal phytopathogens. Other striking differences between the complements of CWDEs in P. parasitica and fungal phytopathogens are seen in the CAZyme families that target cellulose, pectins or β-1,3-glucans (e.g. callose). About 25% of P. parasitica CAZymes are solely directed towards pectin degradation, with the majority coming from pectin lyase or carbohydrate esterase families. Fungal phytopathogens typically contain less than half the numbers of these CAZymes. The P. parasitica genome, like that of other Oomycetes, is rich in CAZymes that target β-1,3-glucans. Conclusions This detailed analysis of the full complement of P. parasitica cell wall degrading enzymes provides a framework for an in-depth study of patterns of expression of these pathogen genes during plant infection and the induction or repression of expression by selected substrates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-785) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Leila M Blackman
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT 0200, Australia.
| | | | | |
Collapse
|
11
|
Carbohydrate-binding modules of fungal cellulases: occurrence in nature, function, and relevance in industrial biomass conversion. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:103-65. [PMID: 24767427 DOI: 10.1016/b978-0-12-800260-5.00004-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this review, the present knowledge on the occurrence of cellulases, with a special emphasis on the presence of carbohydrate-binding modules (CBMs) in various fungal strains, has been summarized. The importance of efficient fungal cellulases is growing due to their potential uses in biorefinery processes where lignocellulosic biomasses are converted to platform sugars and further to biofuels and chemicals. Most secreted cellulases studied in detail have a bimodular structure containing an active core domain attached to a CBM. CBMs are traditionally been considered as essential parts in cellulases, especially in cellobiohydrolases. However, presently available genome data indicate that many cellulases lack the binding domains in cellulose-degrading organisms. Recent data also demonstrate that CBMs are not necessary for the action of cellulases and they solely increase the concentration of enzymes on the substrate surfaces. On the other hand, in practical industrial processes where high substrate concentrations with low amounts of water are employed, the enzymes have been shown to act equally efficiently with and without CBM. Furthermore, available kinetic data show that enzymes without CBMs can desorb more readily from the often lignaceous substrates, that is, they are not stuck on the substrates and are thus available for new actions. In this review, the available data on the natural habitats of different wood-degrading organisms (with emphasis on the amount of water present during wood degradation) and occurrence of cellulose-binding domains in their genome have been assessed in order to identify evolutionary advantages for the development of CBM-less cellulases in nature.
Collapse
|
12
|
Haitjema CH, Solomon KV, Henske JK, Theodorou MK, O'Malley MA. Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production. Biotechnol Bioeng 2014; 111:1471-82. [PMID: 24788404 DOI: 10.1002/bit.25264] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 12/12/2022]
Abstract
Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this review briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. We also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.
Collapse
Affiliation(s)
- Charles H Haitjema
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106
| | | | | | | | | |
Collapse
|
13
|
Wang HC, Chen YC, Huang CT, Hseu RS. Cloning and characterization of a thermostable and pH-stable cellobiohydrolase from Neocallimastix patriciarum J11. Protein Expr Purif 2013; 90:153-9. [PMID: 23770555 DOI: 10.1016/j.pep.2013.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/02/2013] [Accepted: 06/05/2013] [Indexed: 11/28/2022]
Abstract
An 1888-bp cDNA designated celA, isolated from a cDNA library of Neocallimastix patriciarum J11 was cloned. The celA had an open reading frame of 1530 bp encoding J11 CelA of 510 amino acids. The primary structure analysis of J11 CelA revealed a complete cellulose-binding domain at the N-terminal, followed by an Asn, Ala, Gly, Gln and Pro-rich linker and ending with a C-terminal glycosyl hydrolase family 6 catalytic domain. The mature J11 CelA was overexpressed in Escherichia coli and purified to homogeneity. This enzyme had high specific activities towards barley β-glucan and lichenan, low toward carboxymethyl cellulose (CMC), Avicel, and H3PO4-swollen Avicel (PSA). The product of Avicel hydrolysis was cellobiose indicating that J11 CelA is a typical cellobiohydrolase. The recombinant J11 CelA had an optimal pH of 6.0 and was stable over a wide range of pH (5.2-11.3). The enzyme showed an optimal temperature of 50°C and was still maintained approximately 50% of the maximum activity in response to the treatment at 70°C for 1h. Cobalt and Fe(3+) at 1 mM greatly activated the enzyme activity. As a thermostable and pH stable enzyme with crystalline cellulose-degrading activity, J11 CelA is a potential candidate for the bioethanol industry.
Collapse
Affiliation(s)
- Hui-Chang Wang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | | | | | | |
Collapse
|
14
|
|
15
|
Punt PJ, Levasseur A, Visser H, Wery J, Record E. Fungal protein production: design and production of chimeric proteins. Annu Rev Microbiol 2012; 65:57-69. [PMID: 21639784 DOI: 10.1146/annurev.micro.112408.134009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For more than a century, filamentous fungi have been used for the production of a wide variety of endogenous enzymes of industrial interest. More recently, with the use of genetic engineering tools developed for these organisms, this use has expanded for the production of nonnative heterologous proteins. In this review, an overview is given of examples describing the production of a special class of these proteins, namely chimeric proteins. The production of two types of chimeric proteins have been explored: (a) proteins grafted for a specific substrate-binding domain and (b) fusion proteins containing two separate enzymatic activities. Various application areas for the use of these chimeric proteins are described.
Collapse
Affiliation(s)
- Peter J Punt
- TNO Microbiology and Systems Biology, 3700 AJ, Zeist, The Netherlands.
| | | | | | | | | |
Collapse
|
16
|
Jin X, Meng N, Xia LM. Expression of an endo-β-1,4-glucanase gene from orpinomyces PC-2 in Pichia pastoris. Int J Mol Sci 2011; 12:3366-80. [PMID: 21686190 PMCID: PMC3116196 DOI: 10.3390/ijms12053366] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 05/03/2011] [Accepted: 05/23/2011] [Indexed: 12/03/2022] Open
Abstract
The endo-β-1,4-glucanase gene celE from the anaerobic fungus Orpinomyces PC-2 was placed under the control of an alcohol oxidase promoter (AOX1) in the plasmid pPIC9K, and integrated into the genome of a methylotrophic yeast P. pastoris GS115 by electroporation. The strain with highest endo-β-1,4-glucanase activity was selected and designed as P. pastoris egE, and cultivated in shaking flasks. The culture supernatant was assayed by SDS-polyacrylamide gel electrophoresis and showed a single band at about 52 kDa. Furthermore, the recombinant P. pastoris egE was proved to possess the ability to utilize sodium carboxymethyl cellulose as a carbon source. The recombinant endoglucanase produced by P. pastoris showed maximum activity at pH 6.0 and temperature 45 °C, indicating it was a mesophilic neutral endo-β-1,4-glucanase, suitable for denim biofinishing/washing. Further research was carried out in suitable fermentation medium in shaking flasks. The most favorable methanol addition concentration was discussed and given as 1.0%. After methanol induction for 96 h, the endo-β-1,4-glucanase activity reached 72.5 IU mL−1. This is the first report on expression and characterization of endo-β-1,4-glucanase from Orpinomyces in P. pastoris. The endo-β-1,4-glucanase secreted by recombinant P. pastoris represents an attractive potential for both academic research and textile industry application.
Collapse
Affiliation(s)
- Xin Jin
- Department of Chemical Engineering and Bioengineering, Zhejiang University, Hangzhou 310027, China; E-Mails: (X.J.); (N.M.)
| | | | | |
Collapse
|
17
|
Chu CY, Tseng CW, Yueh PY, Duan CH, Liu JR. Molecular cloning and characterization of a β-glucanase from Piromyces rhizinflatus. J Biosci Bioeng 2011; 111:541-6. [DOI: 10.1016/j.jbiosc.2011.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 10/18/2022]
|
18
|
Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS. Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME JOURNAL 2010; 4:1225-35. [PMID: 20410935 DOI: 10.1038/ismej.2010.49] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phylogenetic diversity and community structure of members of the gut anaerobic fungi (AF) (phylum Neocallimastigomycota) were investigated in 30 different herbivore species that belong to 10 different mammalian and reptilian families using the internal transcribed spacer region-1 (ITS-1) ribosomal RNA (rRNA) region as a phylogenetic marker. A total of 267 287 sequences representing all known anaerobic fungal genera were obtained in this study. Sequences affiliated with the genus Piromyces were the most abundant, being encountered in 28 different samples, and representing 36% of the sequences obtained. On the other hand, sequences affiliated with the genera Cyllamyces and Orpinomyces were the least abundant, being encountered in 2, and 8 samples, and representing 0.7%, and 1.1% of the total sequences obtained, respectively. Further, 38.3% of the sequences obtained did not cluster with previously identified genera and formed eight phylogenetically distinct novel anaerobic fungal lineages. Some of these novel lineages were widely distributed (for example NG1 and NG3), whereas others were animal specific, being encountered in only one or two animals (for example NG4, NG6, NG7, and NG8). The impact of various physiological and environmental factors on the diversity and community structure of AF was examined. The results suggest that animal host phylogeny exerts the most significant role on shaping anaerobic fungal diversity and community composition. These results greatly expand the documented global phylogenetic diversity of members of this poorly studied group of fungi that has an important function in initiating plant fiber degradation during fermentative digestion in ruminant and non-ruminant herbivores.
Collapse
Affiliation(s)
- Audra S Liggenstoffer
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | | | | |
Collapse
|
19
|
Maki M, Leung KT, Qin W. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int J Biol Sci 2009; 5:500-16. [PMID: 19680472 PMCID: PMC2726447 DOI: 10.7150/ijbs.5.500] [Citation(s) in RCA: 261] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/21/2009] [Indexed: 11/05/2022] Open
Abstract
Lignocellulosic biomass is a renewable and abundant resource with great potential for bioconversion to value-added bioproducts. However, the biorefining process remains economically unfeasible due to a lack of biocatalysts that can overcome costly hurdles such as cooling from high temperature, pumping of oxygen/stirring, and, neutralization from acidic or basic pH. The extreme environmental resistance of bacteria permits screening and isolation of novel cellulases to help overcome these challenges. Rapid, efficient cellulase screening techniques, using cellulase assays and metagenomic libraries, are a must. Rare cellulases with activities on soluble and crystalline cellulose have been isolated from strains of Paenibacillus and Bacillus and shown to have high thermostability and/or activity over a wide pH spectrum. While novel cellulases from strains like Cellulomonas flavigena and Terendinibacter turnerae, produce multifunctional cellulases with broader substrate utilization. These enzymes offer a framework for enhancement of cellulases including: specific activity, thermalstability, or end-product inhibition. In addition, anaerobic bacteria like the clostridia offer potential due to species capable of producing compound multienzyme complexes called cellulosomes. Cellulosomes provide synergy and close proximity of enzymes to substrate, increasing activity towards crystalline cellulose. This has lead to the construction of designer cellulosomes enhanced for specific substrate activity. Furthermore, cellulosome-producing Clostridium thermocellum and its ability to ferment sugars to ethanol; its amenability to co-culture and, recent advances in genetic engineering, offer a promising future in biofuels. The exploitation of bacteria in the search for improved enzymes or strategies provides a means to upgrade feasibility for lignocellulosic biomass conversion, ultimately providing means to a 'greener' technology.
Collapse
Affiliation(s)
- Miranda Maki
- Biorefining Research Initiative, Lakehead University, Thunder Bay, Ontario, Canada
| | | | | |
Collapse
|
20
|
Peer A, Smith SP, Bayer EA, Lamed R, Borovok I. Noncellulosomal cohesin- and dockerin-like modules in the three domains of life. FEMS Microbiol Lett 2008; 291:1-16. [PMID: 19025568 DOI: 10.1111/j.1574-6968.2008.01420.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The high-affinity cohesin-dockerin interaction was originally discovered as modular components, which mediate the assembly of the various subunits of the multienzyme cellulosome complex that characterizes some cellulolytic bacteria. Until recently, the presence of cohesins and dockerins within a bacterial proteome was considered a definitive signature of a cellulosome-producing bacterium. Widespread genome sequencing has since revealed a wealth of putative cohesin- and dockerin-containing proteins in Bacteria, Archaea, and in primitive eukaryotes. The newly identified modules appear to serve diverse functions that are clearly distinct from the classical cellulosome archetype, and the vast majority of parent proteins are not predicted glycoside hydrolases. In most cases, only a few such genes have been identified in a given microorganism, which encode proteins containing but a single cohesin and/or dockerin. In some cases, one or the other module appears to be missing from a given species, and in other cases both modules occur within the same protein. This review provides a bioinformatics-based survey of the current status of cohesin- and dockerin-like sequences in species from the Bacteria, Archaea, and Eukarya. Surprisingly, many identified modules and their parent proteins are clearly unrelated to cellulosomes. The cellulosome paradigm may thus be the exception rather than the rule for bacterial, archaeal, and eukaryotic employment of cohesin and dockerin modules.
Collapse
Affiliation(s)
- Ayelet Peer
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | | | | | | | | |
Collapse
|
21
|
Ljungdahl LG. The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use. Ann N Y Acad Sci 2008; 1125:308-21. [PMID: 18378601 DOI: 10.1196/annals.1419.030] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Anaerobic fungi, first described in 1975 by Orpin, live in close contact with bacteria and other microorganisms in the rumen and caecum of herbivorous animals, where they digest ingested plant food. Seventeen distinct anaerobic fungi belonging to five different genera have been described. They have been found in at least 50 different herbivorous animals. Anaerobic fungi do not possess mitochondria, but instead have hydrogenosomes, which form hydrogen and carbon dioxide from pyruvate and malate during fermentation of carbohydrates. In addition, they are very oxygen- and temperature-sensitive, and their DNA has an unusually high AT content of from 72 to 87 mol%. My initial reason for studying anaerobic fungi was because they solubilize lignocellulose and produce all enzymes needed to efficiently hydrolyze cellulose and hemicelluloses. Although some of these enzymes are found free in the medium, most of them are associated with cellulosomal and polycellulosomal complexes, in which the enzymes are attached through fungal dockerins to scaffolding proteins; this is similar to what has been found for cellulosomes from anaerobic bacteria. Although cellulosomes from anaerobic fungi share many properties with cellulosomes of anaerobic cellulolytic bacteria and have comparable structures, their structures differ in their amino acid sequences. I discuss some features of the cellulosome of the anaerobic fungus Orpinomyces sp. PC-2 and some possible uses of its enzymes in industrial settings.
Collapse
Affiliation(s)
- Lars G Ljungdahl
- Department of Biochemistry and Molecular Biology, Fred C. Davison Life Sciences Complex, University of Georgia, Athens, GA 30602-7229, USA.
| |
Collapse
|
22
|
Carboxymethylcellulase production by the anaerobic rumen fungusNeocallimastix sp. GMLF7. ANN MICROBIOL 2008. [DOI: 10.1007/bf03179454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
23
|
Nagy T, Tunnicliffe RB, Higgins LD, Walters C, Gilbert HJ, Williamson MP. Characterization of a double dockerin from the cellulosome of the anaerobic fungus Piromyces equi. J Mol Biol 2007; 373:612-22. [PMID: 17869267 DOI: 10.1016/j.jmb.2007.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
The assembly into supramolecular complexes of proteins having complementary activities is central to cellular function. One such complex of considerable biological and industrial significance is the plant cell wall-degrading apparatus of anaerobic microorganisms, termed the cellulosome. A central feature of bacterial cellulosomes is a large non-catalytic protein, the scaffoldin, which contains multiple cohesin domains. An array of digestive enzymes is incorporated into the cellulosome through the interaction of the dockerin domains, present in the catalytic subunits, with the cohesin domains that are present in the scaffoldin. By contrast, in anaerobic fungi, such as Piromyces equi, the dockerins of cellulosomal enzymes are often present in tandem copies; however, the identity of the cognate cohesin domains in these organisms is unclear, hindering further biotechnological development of the fungal cellulosome. Here, we characterise the solution structure and function of a double-dockerin construct from the P. equi endoglucanase Cel45A. We show that the two domains are connected by a flexible linker that is short enough to keep the binding sites of the two domains on adjacent surfaces, and allows the double-dockerin construct to bind more tightly to cellulosomes than a single domain and with greater coverage. The double dockerin binds to the GH3 beta-glucosidase component of the fungal cellulosome, which is thereby identified as a potential scaffoldin.
Collapse
Affiliation(s)
- Tibor Nagy
- Institute for Cell and Molecular Biosciences, The University of Newcastle upon Tyne, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | | | | | | | | | | |
Collapse
|
24
|
Tsai CF, Qiu X, Liu JH. A comparative analysis of two cDNA clones of the cellulase gene family from anaerobic fungus Piromyces rhizinflata. Anaerobe 2007; 9:131-40. [PMID: 16887700 DOI: 10.1016/s1075-9964(03)00087-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2003] [Revised: 05/12/2003] [Accepted: 05/30/2003] [Indexed: 11/28/2022]
Abstract
Cellulase family and some other glycosyl hydrolases of anaerobic fungi inhabiting the digestive tract of ruminants are believed to form an enzyme complex called cellulosome. Study of the individual component of cellulosome may shed light on understanding the organization of this complex and its functional mechanism. We have analysed the primary sequences of two cellulase clones, cel5B and cel6A, isolated from the cDNA library of ruminal fungus, Piromyces rhizinflata strain 2301. The deduced amino acid sequences of the catalytic domain of Cel5B, encoded by cel5B, showed homology with the subfamily 4 of the family 5 (subfamily 5(4)) of glycosyl hydrolases, while cel6A encoded Cel6A belonged to family 6 of glycosyl hydrolases. Phylogenetic tree analysis suggested that the genes of subfamily 5(4) glycosyl hydrolases of P. rhizinflata might have been acquired from rumen bacteria. Cel5B and Cel6A were modular enzymes consisting of a catalytic domain and dockerin domain(s), but not a cellulose binding domain. The occurrence of dockerin domains indicated that both enzymes were cellulosome components. The catalytic domain of the Cel5B (Cel5B') and Cel6A (Cel6A') recombinant proteins were purified. The optimal activity conditions with carboxymethyl cellulose (CMC) as the substrate were pH 6.0 and 50 degrees C for Cel5B', and pH 6.0 and 37-45 degrees C for Cel6A'. Both Cel5B' and Cel6A' exhibited activity against CMC, barley beta-glucan, Lichenan, and oat spelt xylan. Cel5B' could also hydrolyse p-nitrophenyl-beta-d-cellobioside, Avicel and filter paper while Cel6A' did not show any activity on these substrates. It is apparent that Cel6A' acted as an endoglucanase and Cel5B' possessed both endoglucanase and exoglucanase activities. No synergic effect was observed for these recombinant enzymes in vitro on Avicel and CMC.
Collapse
Affiliation(s)
- Cheng-Fang Tsai
- Institute of BioAgricultural Sciences, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | | | | |
Collapse
|
25
|
. YRAF, . EREH, . KMG, . WAL. Application of Factorial Designs for Optimization of Avicelase Production by a Thermophilic Geobacillus Isolate. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/jm.2007.13.23] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
26
|
Hughes SR, Riedmuller SB, Mertens JA, Li XL, Bischoff KM, Qureshi N, Cotta MA, Farrelly PJ. High-throughput screening of cellulase F mutants from multiplexed plasmid sets using an automated plate assay on a functional proteomic robotic workcell. Proteome Sci 2006; 4:10. [PMID: 16670026 PMCID: PMC1479318 DOI: 10.1186/1477-5956-4-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 05/02/2006] [Indexed: 11/23/2022] Open
Abstract
Background The field of plasmid-based functional proteomics requires the rapid assay of proteins expressed from plasmid libraries. Automation is essential since large sets of mutant open reading frames are being cloned for evaluation. To date no integrated automated platform is available to carry out the entire process including production of plasmid libraries, expression of cloned genes, and functional testing of expressed proteins. Results We used a functional proteomic assay in a multiplexed setting on an integrated plasmid-based robotic workcell for high-throughput screening of mutants of cellulase F, an endoglucanase from the anaerobic fungus Orpinomyces PC-2. This allowed us to identify plasmids containing optimized clones expressing mutants with improved activity at lower pH. A plasmid library of mutagenized clones of the celF gene with targeted variations in the last four codons was constructed by site-directed PCR mutagenesis and transformed into Escherichia coli. A robotic picker integrated into the workcell was used to inoculate medium in a 96-well deep well plate, combining the transformants into a multiplexed set in each well, and the plate was incubated on the workcell. Plasmids were prepared from the multiplexed culture on the liquid handler component of the workcell and used for in vitro transcription/translation. The multiplexed expressed recombinant proteins were screened for improved activity and stability in an azo-carboxymethylcellulose plate assay. The multiplexed wells containing mutants with improved activity were identified and linked back to the corresponding multiplexed cultures stored in glycerol. Spread plates were prepared from the glycerol stocks and the workcell was used to pick single colonies from the spread plates, prepare plasmid, produce recombinant protein, and assay for activity. The screening assay and subsequent deconvolution of the multiplexed wells resulted in identification of improved CelF mutants and corresponding optimized clones in expression-ready plasmids. Conclusion The multiplex method using an integrated automated platform for high-throughput screening in a functional proteomic assay allows rapid identification of plasmids containing optimized clones ready for use in subsequent applications including transformations to produce improved strains or cell lines.
Collapse
Affiliation(s)
- Stephen R Hughes
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Bioproducts and Biocatalysis (BBC) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | | | - Jeffrey A Mertens
- USDA, ARS, NCAUR, Fermentation Biotechnology (FBT) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Xin-Liang Li
- USDA, ARS, NCAUR, Fermentation Biotechnology (FBT) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Kenneth M Bischoff
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Bioproducts and Biocatalysis (BBC) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Nasib Qureshi
- USDA, ARS, NCAUR, Fermentation Biotechnology (FBT) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Michael A Cotta
- USDA, ARS, NCAUR, Fermentation Biotechnology (FBT) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Philip J Farrelly
- Hudson Control Group, Inc., 10 Stern Avenue, Springfield, NJ 07081, USA
| |
Collapse
|
27
|
Ximenes EA, Chen H, Kataeva IA, Cotta MA, Felix CR, Ljungdahl LG, Li XL. A mannanase, ManA, of the polycentric anaerobic fungus Orpinomyces sp. strain PC-2 has carbohydrate binding and docking modules. Can J Microbiol 2006; 51:559-68. [PMID: 16175204 PMCID: PMC6448567 DOI: 10.1139/w05-033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The anaerobic fungus Orpinomyces sp. strain PC-2 produces a broad spectrum of glycoside hydrolases, most of which are components of a high molecular mass cellulosomal complex. Here we report about a cDNA (manA) having 1924 bp isolated from the fungus and found to encode a polypeptide of 579 amino acid residues. Analysis of the deduced sequence revealed that it had a mannanase catalytic module, a family 1 carbohydrate-binding module, and a noncatalytic docking module. The catalytic module was homologous to aerobic fungal mannanases belonging to family 5 glycoside hydrolases, but unrelated to the previously isolated mannanases (family 26) of the anaerobic fungus Piromyces. No mannanase activity could be detected in Escherichia coli harboring a manA-containing plasmid. The manA was expressed in Saccharomyces cerevisiae and ManA was secreted into the culture medium in multiple forms. The purified extracellular heterologous mannanase hydrolyzed several types of mannan but lacked activity against cellulose, chitin, or beta-glucan. The enzyme had high specific activity toward locust bean mannan and an extremely broad pH profile. It was stable for several hours at 50 degrees C, but was rapidly inactivated at 60 degrees C. The carbohydrate-binding module of the Man A produced separately in E. coli bound preferably to insoluble lignocellulosic substrates, suggesting that it might play an important role in the complex enzyme system of the fungus for lignocellulose degradation.
Collapse
Affiliation(s)
- Eduardo A. Ximenes
- Laboratorio De Enzimologia, Departmento De Biologia Celular, Universidade De Brasilia, Asa Norte, Brasilia-DF-Brazil 70910-900, Brazil
| | - Huizhong Chen
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079-9502, USA
| | - Irina A. Kataeva
- Department of Biochemistry and Molecular Biology and Center for Biological Resource Recovery, The University of Georgia, Athens, GA 30602-7229, USA
| | - Michael A. Cotta
- Fermentation Biotechnology Research Unit, National Center for Agricultural Utilization Research, USDA/ARS, 1815 N. University Street, Peoria, IL 61604, USA
| | - Carlos R. Felix
- Laboratorio De Enzimologia, Departmento De Biologia Celular, Universidade De Brasilia, Asa Norte, Brasilia-DF-Brazil 70910-900, Brazil
| | - Lars G. Ljungdahl
- Department of Biochemistry and Molecular Biology and Center for Biological Resource Recovery, The University of Georgia, Athens, GA 30602-7229, USA
| | | |
Collapse
|
28
|
Mertz B, Kuczenski RS, Larsen RT, Hill AD, Reilly PJ. Phylogenetic analysis of family 6 glycoside hydrolases. Biopolymers 2005; 79:197-206. [PMID: 16086389 DOI: 10.1002/bip.20347] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Multiple sequence alignment separates members of glycoside hydrolase Family 6 into eight subfamilies: one of mainly actinobacterial endoglucanases (EGs), one of ascomycotal EGs, one of chytridiomycotal EGs and cellobiohydrolases (CBHs), one of actinobacterial and proteobacterial CBHs, one of chytridiomycotal CBHs, two of ascomycotal CBHs, and one of basidiomycotal CBHs. Each also has some proteins of unknown function. Multiple sequence alignment also extends to all of Family 6 the observation that lengths of loops that form the active-site tunnel in CBHs vary among subfamilies, and along with loop conformations, determine enzyme function.
Collapse
Affiliation(s)
- Blake Mertz
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | | | | | | | | |
Collapse
|
29
|
Huang YH, Huang CT, Hseu RS. Effects of dockerin domains onNeocallimastix frontalisxylanases. FEMS Microbiol Lett 2005; 243:455-60. [PMID: 15686849 DOI: 10.1016/j.femsle.2005.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Revised: 12/20/2004] [Accepted: 01/06/2005] [Indexed: 11/24/2022] Open
Abstract
Two xylanase genes were cloned from the anaerobic fungus Neocallimastix frontalis. Xyn11A had a modular structure of two catalytic domains and two dockerin domains, while Xyn11B had one catalytic domain and two dockerin domains. The characteristics of the xylanases with and without dockerin domains were investigated. The deletion of dockerin domains had little influence on the optimal pH of xylanases, while it significantly affected the optimal temperatures. The optimal temperatures increased from 55 to 60 degrees C for Xyn11A and 60 to 65 degrees C for Xyn11B after the deletion of dockerin domains. The increase of optimal temperatures was attributed to the lower stability of the second structure in full length xylanase than that in the truncated one as evidenced by the circular dichroism spectroscopy. The specific activity of Xyn11A and Xyn11B increased about 64% and 330%, respectively, after the deletion of the dockerin domains. The removal of dockerin domains appeared to increase the overall efficiency of Xyn11A' (1.2-) and Xyn11B' (2.9-) fold with oat spelts xylan as reflected by the values of k(cat)/K(m). The results suggest that the dockerin domain might play an important role in the characteristics of xylanases from anaerobic fungi.
Collapse
Affiliation(s)
- Ya-Hui Huang
- Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 106, Taiwan, ROC
| | | | | |
Collapse
|
30
|
Li XL, Ljungdahl LG, Ximenes EA, Chen H, Felix CR, Cotta MA, Dien BS. Properties of a recombinant beta-glucosidase from polycentric anaerobic fungus Orpinomyces PC-2 and its application for cellulose hydrolysis. Appl Biochem Biotechnol 2004; 113-116:233-50. [PMID: 15054209 PMCID: PMC5890932 DOI: 10.1385/abab:113:1-3:233] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A beta-glucosidase (BglA, EC 3.2.1.21) gene from the polycentric anaerobic fungus Orpinomyces PC-2 was cloned and sequenced. The enzyme containing 657 amino acid residues was homologous to certain animal, plant, and bacterial beta-glucosidases but lacked significant similarity to those from aerobic fungi. Neither cellulose- nor protein-binding domains were found in BglA. When expressed in Saccharomyces cerevisiae, the enzyme was secreted in two forms with masses of about 110 kDa and also found in two forms associated with the yeast cells. Km and Vmax values of the secreted BglA were 0.762 mM and 8.20 micromol/(min x mg), respectively, with p-nitrophenyl-beta-D-glucopyranoside (pNPG) as the substrate and 0.310 mM and 6.45 micromol/(min.mg), respectively, for the hydrolysis of cellobiose. Glucose competitively inhibited the hydrolysis of pNPG with a Ki of 3.6 mM. Beta-glucosidase significantly enhanced the conversion of cellulosic materials into glucose by Trichoderma reesei cellulase preparations, demonstrating its potential for use in biofuel and feedstock chemical production.
Collapse
Affiliation(s)
- Xin-Liang Li
- Fermentation Biotechnology Research Unit, National Center for Agricultural Utilization Research, USDA/ARS,1815 N. University Street, Peoria, IL 61604-3902, USA.
| | | | | | | | | | | | | |
Collapse
|
31
|
Harhangi HR, Akhmanova A, Steenbakkers PJM, Jetten MSM, van der Drift C, Op den Camp HJM. Genomic DNA analysis of genes encoding (hemi-)cellulolytic enzymes of the anaerobic fungus Piromyces sp. E2. Gene 2003; 314:73-80. [PMID: 14527719 DOI: 10.1016/s0378-1119(03)00705-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Anaerobic fungi contain more than one copy of genes encoding (hemi-)cellulases in their genome. The arrangement of these genes on the chromosomes was not known. A genomic DNA (gDNA) library of Piromyces sp. E2 was screened with different probes specific for (hemi-)cellulolytic enzymes. This screening resulted in three gDNA clones with genes encoding glycoside hydrolase enzymes of families 1 (beta-glucosidase), 6 (exoglucanase) and 26 (mannanase). Each clone contained two or more genes of the same family. Comparison of the gene copies on a clone revealed that they were highly homologous, and in addition, 54-75% of the substitutions was synonymous. One of the mannanase genes contained an intron. PCR with selected primers resulted in a gDNA clone with a new representative (cel9B) of glycoside hydrolase family 9 (endoglucanase). Comparison with cel9A revealed that cel9B had 67% homology on the nucleotide level. Furthermore, three introns were present. All results of this paper taken together provided evidence for duplications of (hemi-)cellulolytic genes, which resulted in clusters of almost identical genes arranged head-to-tail on the genome. In contrast to other eukaryotes, this phenomenon appears frequently in anaerobic fungi.
Collapse
Affiliation(s)
- Harry R Harhangi
- Department of Microbiology, Faculty of Science, University of Nijmegen, Toernooiveld 1, NL-6525 ED, Nijmegen, The Netherlands
| | | | | | | | | | | |
Collapse
|
32
|
Harhangi HR, Freelove ACJ, Ubhayasekera W, van Dinther M, Steenbakkers PJM, Akhmanova A, van der Drift C, Jetten MSM, Mowbray SL, Gilbert HJ, Op den Camp HJM. Cel6A, a major exoglucanase from the cellulosome of the anaerobic fungi Piromyces sp. E2 and Piromyces equi. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1628:30-9. [PMID: 12850270 DOI: 10.1016/s0167-4781(03)00112-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Anaerobic fungi possess high cellulolytic activities, which are organised in high molecular mass (HMM) complexes. Besides catalytic modules, the cellulolytic enzyme components of these complexes contain non-catalytic modules, known as dockerins, that play a key role in complex assembly. Screening of a genomic and a cDNA library of two Piromyces species resulted in the isolation of two clones containing inserts of 5.5 kb (Piromyces sp. E2) and 1.5 kb (Piromyces equi). Both clones contained the complete coding region of a glycoside hydrolase (GH) from family 6, consisting of a 20 amino acid signal peptide, a 76 (sp. E2)/81 (P. equi) amino acid stretch comprising two fungal non-catalytic docking domains (NCDDs), a 24 (sp. E2)/16 (P. equi) amino acid linker, and a 369 amino acid catalytic module. Homology modelling of the catalytic module strongly suggests that the Piromyces enzymes will be processive cellobiohydrolases. The catalytic residues and all nearby residues are conserved. The reaction is thus expected to proceed via a classical single-displacement (inverting) mechanism that is characteristic of this family of GHs. The enzyme, defined as Cel6A, encoded by the full-length Piromyces E2 sequence was expressed in Escherichia coli. The recombinant protein expressed had a molecular mass of 55 kDa and showed activity against Avicel, supporting the observed relationship of the sequence to those of known cellobiohydrolases. Affinity-purified cellulosomes of Piromyces sp. E2 were analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and sodium dodecyl sulfate-polyacrylamide gel (SDS-PAGE) electrophoresis. A major band was detected with the molecular weight of Cel6A. A tryptic fingerprint of this protein confirmed its identity.
Collapse
Affiliation(s)
- Harry R Harhangi
- Department of Microbiology, Faculty of Science, University of Nijmegen, Toernooiveld 1, NL-6525 ED, Nijmegen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Steenbakkers PJM, Harhangi HR, Bosscher MW, van der Hooft MMC, Keltjens JT, van der Drift C, Vogels GD, op den Camp HJM. beta-Glucosidase in cellulosome of the anaerobic fungus Piromyces sp. strain E2 is a family 3 glycoside hydrolase. Biochem J 2003; 370:963-70. [PMID: 12485115 PMCID: PMC1223235 DOI: 10.1042/bj20021767] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2002] [Revised: 12/13/2002] [Accepted: 12/16/2002] [Indexed: 11/17/2022]
Abstract
The cellulosomes of anaerobic fungi convert crystalline cellulose solely into glucose, in contrast with bacterial cellulosomes which produce cellobiose. Previously, a beta-glucosidase was identified in the cellulosome of Piromyces sp. strain E2 by zymogram analysis, which represented approx. 25% of the extracellular beta-glucosidase activity. To identify the component in the fungal cellulosome responsible for the beta-glucosidase activity, immunoscreening with anti-cellulosome antibodies was used to isolate the corresponding gene. A 2737 bp immunoclone was isolated from a cDNA library. The clone encoded an extracellular protein containing a eukaryotic family 3 glycoside hydrolase domain homologue and was therefore named cel3A. The C-terminal end of the encoded Cel3A protein consisted of an auxiliary domain and three fungal dockerins, typical for cellulosome components. The Cel3A catalytic domain was expressed in Escherichia coli BL21 and purified. Biochemical analyses of the recombinant protein showed that the Cel3A catalytic domain was specific for beta-glucosidic bonds and functioned as an exoglucohydrolase on soluble substrates as well as cellulose. Comparison of the apparent K (m) and K (i) values of heterologous Cel3A and the fungal cellulosome for p -nitrophenyl-beta-D-glucopyranoside and D-glucono-1,5-delta-lactone respectively indicated that cel3A encodes the beta-glucosidase activity of the Piromyces sp. strain E2 cellulosome.
Collapse
Affiliation(s)
- Peter J M Steenbakkers
- Department of Microbiology, Faculty of Science, University of Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Rincon MT, Ding SY, McCrae SI, Martin JC, Aurilia V, Lamed R, Shoham Y, Bayer EA, Flint HJ. Novel organization and divergent dockerin specificities in the cellulosome system of Ruminococcus flavefaciens. J Bacteriol 2003; 185:703-13. [PMID: 12533446 PMCID: PMC142803 DOI: 10.1128/jb.185.3.703-713.2003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2002] [Accepted: 09/30/2002] [Indexed: 11/20/2022] Open
Abstract
The DNA sequence coding for putative cellulosomal scaffolding protein ScaA from the rumen cellulolytic anaerobe Ruminococcus flavefaciens 17 was completed. The mature protein exhibits a calculated molecular mass of 90,198 Da and comprises three cohesin domains, a C-terminal dockerin, and a unique N-terminal X domain of unknown function. A novel feature of ScaA is the absence of an identifiable cellulose-binding module. Nevertheless, native ScaA was detected among proteins that attach to cellulose and appeared as a glycosylated band migrating at around 130 kDa. The ScaA dockerin was previously shown to interact with the cohesin-containing putative surface-anchoring protein ScaB. Here, six of the seven cohesins from ScaB were overexpressed as histidine-tagged products in E. coli; despite their considerable sequence differences, each ScaB cohesin specifically recognized the native 130-kDa ScaA protein. The binding specificities of dockerins found in R. flavefaciens plant cell wall-degrading enzymes were examined next. The dockerin sequences of the enzymes EndA, EndB, XynB, and XynD are all closely related but differ from those of XynE and CesA. A recombinant ScaA cohesin bound selectively to dockerin-containing fragments of EndB, but not to those of XynE or CesA. Furthermore, dockerin-containing EndB and XynB, but not XynE or CesA, constructs bound specifically to native ScaA. XynE- and CesA-derived probes did however bind a number of alternative R. flavefaciens bands, including an approximately 110-kDa supernatant protein expressed selectively in cultures grown on xylan. Our findings indicate that in addition to the ScaA dockerin-ScaB cohesin interaction, at least two distinct dockerin-binding specificities are involved in the novel organization of plant cell wall-degrading enzymes in this species and suggest that different scaffoldins and perhaps multiple enzyme complexes may exist in R. flavefaciens.
Collapse
Affiliation(s)
- Marco T Rincon
- Gut Microbiology Group, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Steenbakkers PJM, Ubhayasekera W, Goossen HJAM, van Lierop EMHM, van der Drift C, Vogels GD, Mowbray SL, Op den Camp HJM. An intron-containing glycoside hydrolase family 9 cellulase gene encodes the dominant 90 kDa component of the cellulosome of the anaerobic fungus Piromyces sp. strain E2. Biochem J 2002; 365:193-204. [PMID: 12071852 PMCID: PMC1222669 DOI: 10.1042/bj20011866] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The cellulosome produced by Piromyces sp. strain E2 during growth on filter paper was purified by using an optimized cellulose-affinity method consisting of steps of EDTA washing of the cellulose-bound protein followed by elution with water. Three dominant proteins were identified in the cellulosome preparation, with molecular masses of 55, 80 and 90 kDa. Treatment of cellulose-bound cellulosome with a number of denaturing agents was also tested. Incubation with 0.5% (w/v) SDS or 8 M urea released most cellulosomal proteins, while leaving the greater fraction of the 80, 90 and 170 kDa components. To investigate the major 90 kDa cellulosome protein further, the corresponding gene, cel9A, was isolated, using immunoscreening and N-terminal sequencing. Inspection of the cel9A genomic organization revealed the presence of four introns, allowing the construction of a consensus for introns in anaerobic fungi. The 2800 bp cDNA clone contained an open reading frame of 2334 bp encoding a 757-residue extracellular protein. Cel9A includes a 445-residue glycoside hydrolase family 9 catalytic domain, and so is the first fungal representative of this large family. Both modelling of the catalytic domain as well as the activity measured with low level expression in Escherichia coli indicated that Cel9A is an endoglucanase. The catalytic domain is succeeded by a putative beta-sheet module of 160 amino acids with unknown function, followed by a threonine-rich linker and three fungal docking domains. Homology modelling of the Cel9A dockerins suggested that the cysteine residues present are all involved in disulphide bridges. The results presented here are used to discuss evolution of glycoside hydrolase family 9 enzymes.
Collapse
Affiliation(s)
- Peter J M Steenbakkers
- Department of Microbiology, Faculty of Science, University of Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Steenbakkers PJ, Li XL, Ximenes EA, Arts JG, Chen H, Ljungdahl LG, Op Den Camp HJ. Noncatalytic docking domains of cellulosomes of anaerobic fungi. J Bacteriol 2001; 183:5325-33. [PMID: 11514516 PMCID: PMC95415 DOI: 10.1128/jb.183.18.5325-5333.2001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A method is presented for the specific isolation of genes encoding cellulosome components from anaerobic fungi. The catalytic components of the cellulosome of anaerobic fungi typically contain, besides the catalytic domain, mostly two copies of a 40-amino-acid cysteine-rich, noncatalytic docking domain (NCDD) interspaced by short linkers. Degenerate primers were designed to anneal to the highly conserved region within the NCDDs of the monocentric fungus Piromyces sp. strain E2 and the polycentric fungus Orpinomyces sp. strain PC-2. Through PCR using cDNA from Orpinomyces sp. and genomic DNA from Piromyces sp. as templates, respectively, 9 and 19 PCR products were isolated encoding novel NCDD linker sequences. Screening of an Orpinomyces sp. cDNA library with four of these PCR products resulted in the isolation of new genes encoding cellulosome components. An alignment of the partial NCDD sequence information obtained and an alignment of database-accessible NCDD sequences, focusing on the number and position of cysteine residues, indicated the presence of three structural subfamilies within fungal NCDDs. Furthermore, evidence is presented that the NCDDs in CelC from the polycentric fungus Orpinomyces sp. strain PC-2 specifically recognize four proteins in a cellulosome preparation, indicating the presence of multiple scaffoldins.
Collapse
Affiliation(s)
- P J Steenbakkers
- Department of Microbiology, Faculty of Science, University of Nijmegen, NL-6525 ED Nijmegen, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
37
|
Mechaly A, Fierobe HP, Belaich A, Belaich JP, Lamed R, Shoham Y, Bayer EA. Cohesin-dockerin interaction in cellulosome assembly: a single hydroxyl group of a dockerin domain distinguishes between nonrecognition and high affinity recognition. J Biol Chem 2001; 276:9883-8. [PMID: 11148206 DOI: 10.1074/jbc.m009237200] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The assembly of enzyme components into the cellulosome complex is dictated by the cohesin-dockerin interaction. In a recent article (Mechaly, A., Yaron, S., Lamed, R., Fierobe, H.-P., Belaich, A., Belaich, J.-P., Shoham, Y., and Bayer, E. A. (2000) Proteins 39, 170-177), we provided experimental evidence that four previously predicted dockerin residues play a decisive role in the specificity of this high affinity interaction, although additional residues were also implicated. In the present communication, we examine further the contributing factors for the recognition of a dockerin by a cohesin domain between the respective cellulosomal systems of Clostridium thermocellum and Clostridium cellulolyticum. In this context, the four confirmed residues were analyzed for their individual effect on selectivity. In addition, other dockerin residues were discerned that could conceivably contribute to the interaction, and the suspected residues were similarly modified by site-directed mutagenesis. The results indicate that mutation of a single residue from threonine to leucine at a given position of the C. thermocellum dockerin differentiates between its nonrecognition and high affinity recognition (K(a) approximately 10(9) m(-1)) by a cohesin from C. cellulolyticum. This suggests that the presence or absence of a single decisive hydroxyl group is critical to the observed biorecognition. This study further implicates additional residues as secondary determinants in the specificity of interaction, because interconversion of selected residues reduced intraspecies self-recognition by at least three orders of magnitude. Nevertheless, as the latter mutageneses served to reduce but not annul the cohesin-dockerin interaction within this species, it follows that other subtle alterations play a comparatively minor role in the recognition between these two modules.
Collapse
Affiliation(s)
- A Mechaly
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | | | | | |
Collapse
|
38
|
Rosewich UL, Kistler HC. Role of Horizontal Gene Transfer in the Evolution of Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2000; 38:325-363. [PMID: 11701846 DOI: 10.1146/annurev.phyto.38.1.325] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Although evidence for horizontal gene transfer (HGT) in eukaryotes remains largely anecdotal, literature on HGT in fungi suggests that it may have been more important in the evolution of fungi than in other eukaryotes. Still, HGT in fungi has not been widely accepted because the mechanisms by which it may occur are unknown, because it is usually not directly observed but rather implied as an outcome, and because there are often equally plausible alternative explanations. Despite these reservations, HGT has been justifiably invoked for a variety of sequences including plasmids, introns, transposons, genes, gene clusters, and even whole chromosomes. In some instances HGT has also been confirmed under experimental conditions. It is this ability to address the phenomenon in an experimental setting that makes fungi well suited as model systems in which to study the mechanisms and consequences of HGT in eukaryotic organisms.
Collapse
Affiliation(s)
- U Liane Rosewich
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, 1551 Lindig Street, St. Paul, Minnesota 55108; e-mail: ,
| | - H Corby Kistler
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, 1551 Lindig Street, St. Paul, Minnesota 55108; e-mail: ,
| |
Collapse
|
39
|
Eberhardt RY, Gilbert HJ, Hazlewood GP. Primary sequence and enzymic properties of two modular endoglucanases, Cel5A and Cel45A, from the anaerobic fungus Piromyces equi. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 8):1999-2008. [PMID: 10931904 DOI: 10.1099/00221287-146-8-1999] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two endoglucanase cDNAs, designated cel5A and cel45A, were isolated from a cDNA library of the anaerobic fungus Piromyces equi. Sequence analysis revealed that cel5A has an open reading frame of 5142 bp and encodes a 1714 amino acid modular enzyme, Cel5A, with a molecular mass of 194847 Da. Cel5A consists of four catalytic domains homologous to family-5 glycosyl hydrolases, two C-terminal dockerins and one N-terminal dockerin. This is the first report of a complete gene containing tandem repeats of family-5 catalytic domains. The cDNA cel45A has an open reading frame of 1233 bp and encodes a 410 amino acid modular enzyme, Cel45A, with a molecular mass of 44380 Da. The catalytic domain, located at the C terminus, is homologous to the family-45 glycosyl hydrolases. Cel45A is the first family-45 enzyme to be described in an anaerobe. The presence of dockerins at the N and C termini of Cel5A and at the N terminus of Cel45A implies that both enzymes are part of the high-molecular-mass cellulose-degrading complex produced by Piromyces equi. The catalytic domain nearest the C terminus of Cel5A and the catalytic domain of Cel45A were hyperexpressed as thioredoxin fusion proteins, Trx-Cel5A' and Trx-Cel45A', and subjected to biochemical analysis. Trx-Cel5A' has a broad substrate range, showing activity against carboxymethylcellulose, acid-swollen cellulose, barley beta-glucan, lichenin, carob galactomannan, p-nitrophenyl beta-D-cellobiopyranoside and xylan. Trx-Cel45A' is active against carboxymethylcellulose, acid-swollen cellulose and the mixed linkage glucans, barley beta-glucan and lichenin.
Collapse
Affiliation(s)
- Ruth Y Eberhardt
- Laboratory of Molecular Enzymology, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK1
| | - Harry J Gilbert
- Department of Biological and Nutritional Sciences, The University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, UK2
| | - Geoffrey P Hazlewood
- Laboratory of Molecular Enzymology, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK1
| |
Collapse
|
40
|
Davies GJ, Brzozowski AM, Dauter M, Varrot A, Schülein M. Structure and function of Humicola insolens family 6 cellulases: structure of the endoglucanase, Cel6B, at 1.6 A resolution. Biochem J 2000; 348 Pt 1:201-7. [PMID: 10794732 PMCID: PMC1221054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Cellulases are traditionally classified as either endoglucanases or cellobiohydrolases on the basis of their respective catalytic activities on crystalline cellulose, which is generally hydrolysed more efficiently only by the cellobiohydrolases. On the basis of the Trichoderma reesei cellobiohydrolase II structure, it was proposed that the active-site tunnel of cellobiohydrolases permitted the processive hydrolysis of cellulose, whereas the corresponding endoglucanases would display open active-site clefts [Rouvinen, Bergfors, Teeri, Knowles and Jones (1990) Science 249, 380-386]. Glycoside hydrolase family 6 contains both cellobiohydrolases and endoglucanases. The structure of the catalytic core of the family 6 endoglucanase Cel6B from Humicola insolens has been solved by molecular replacement with the known T. reesei cellobiohydrolase II as the search model. Strangely, at the sequence level, this enzyme exhibits the highest sequence similarity to family 6 cellobiohydrolases and displays just one of the loop deletions traditionally associated with endoglucanases in this family. However, this enzyme shows no activity on crystalline substrates but a high activity on soluble substrates, which is typical of an endoglucanase. The three-dimensional structure reveals that the deletion of just a single loop of the active site, coupled with the resultant conformational change in a second 'cellobiohydrolase-specific' loop, peels open the active-site tunnel to reveal a substrate-binding groove.
Collapse
Affiliation(s)
- G J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K.
| | | | | | | | | |
Collapse
|
41
|
Blum DL, Kataeva IA, Li XL, Ljungdahl LG. Feruloyl esterase activity of the Clostridium thermocellum cellulosome can be attributed to previously unknown domains of XynY and XynZ. J Bacteriol 2000; 182:1346-51. [PMID: 10671457 PMCID: PMC94422 DOI: 10.1128/jb.182.5.1346-1351.2000] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cellulosome of Clostridium thermocellum is a multiprotein complex with endo- and exocellulase, xylanase, beta-glucanase, and acetyl xylan esterase activities. XynY and XynZ, components of the cellulosome, are composed of several domains including xylanase domains and domains of unknown function (UDs). Database searches revealed that the C- and N-terminal UDs of XynY and XynZ, respectively, have sequence homology with the sequence of a feruloyl esterase of strain PC-2 of the anaerobic fungus Orpinomyces. Purified cellulosomes from C. thermocellum were found to hydrolyze FAXX (O-(5-O-[(E)-feruloyl]-alpha-L-arabinofuranosyl)-(1-->3)-O-beta-D- xyl opyranosyl-(1-->4)-D-xylopyranose) and FAX(3) (5-O-[(E)-feruloyl]-[O-beta-D-xylopyranosyl-(1-->2)]-O-alpha-L- arabinofuranosyl-[1-->3])-O-beta-D-xylopyranosyl-(1-->4)-D-xylopyranose) , yielding ferulic acid as a product, indicating that they have feruloyl esterase activity. Nucleotide sequences corresponding to the UDs of XynY and XynZ were cloned into Escherichia coli, and the expressed proteins hydrolyzed FAXX and FAX(3). The recombinant feruloyl esterase domain of XynZ alone (FAE(XynZ)) and with the adjacent cellulose binding domain (FAE-CBD(XynZ)) were characterized. FAE-CBD(XynZ) had a molecular mass of 45 kDa that corresponded to the expected product of the 1,203-bp gene. K(m) and V(max) values for FAX(3) were 5 mM and 12.5 U/mg, respectively, at pH 6.0 and 60 degrees C. PAX(3), a substrate similar to FAX(3) but with a p-coumaroyl group instead of a feruloyl moiety was hydrolyzed at a rate 10 times slower. The recombinant enzyme was active between pH 3 to 10 with an optimum between pH 4 to 7 and at temperatures up to 70 degrees C. Treatment of Coastal Bermuda grass with the enzyme released mainly ferulic acid and a lower amount of p-coumaric acid. FAE(XynZ) had similar properties. Removal of the 40 C-terminal amino acids, residues 247 to 286, of FAE(XynZ) resulted in protein without activity. Feruloyl esterases are believed to aid in a release of lignin from hemicellulose and may be involved in lignin solubilization. The presence of feruloyl esterase in the C. thermocellum cellulosome together with its other hydrolytic activities demonstrates a powerful enzymatic potential of this organelle in plant cell wall decomposition.
Collapse
Affiliation(s)
- D L Blum
- Department of Biochemistry and Molecular Biology and the Center for Biological Resource Recovery, The University of Georgia, Athens, Georgia 30602, USA
| | | | | | | |
Collapse
|
42
|
Kataeva I, Li XL, Chen H, Choi SK, Ljungdahl LG. Cloning and sequence analysis of a new cellulase gene encoding CelK, a major cellulosome component of Clostridium thermocellum: evidence for gene duplication and recombination. J Bacteriol 1999; 181:5288-95. [PMID: 10464199 PMCID: PMC94034 DOI: 10.1128/jb.181.17.5288-5295.1999] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cellulolytic and hemicellulolytic complex of Clostridium thermocellum, termed cellulosome, consists of up to 26 polypeptides, of which at least 17 have been sequenced. They include 12 cellulases, 3 xylanases, 1 lichenase, and CipA, a scaffolding polypeptide. We report here a new cellulase gene, celK, coding for CelK, a 98-kDa major component of the cellulosome. The gene has an open reading frame (ORF) of 2,685 nucleotides coding for a polypeptide of 895 amino acid residues with a calculated mass of 100,552 Da. A signal peptide of 27 amino acid residues is cut off during secretion, resulting in a mature enzyme of 97,572 Da. The nucleotide sequence is highly similar to that of cbhA (V. V. Zverlov et al., J. Bacteriol. 180:3091-3099, 1998), having an ORF of 3,690 bp coding for the 1,230-amino-acid-residue CbhA of the same bacterium. Homologous regions of the two genes are 86.5 and 84.3% identical without deletion or insertion on the nucleotide and amino acid levels, respectively. Both have domain structures consisting of a signal peptide, a family IV cellulose binding domain (CBD), a family 9 glycosyl hydrolase domain, and a dockerin domain. A striking distinction between the two polypeptides is that there is a 330-amino-acid insertion in CbhA between the catalytic domain and the dockerin domain containing a fibronectin type 3-like domain and family III CBD. This insertion, missing in CelK, is responsible for the size difference between CelK and CbhA. Upstream and downstream flanking sequences of the two genes show no homology. The data indicate that celK and cbhA in the genome of C. thermocellum have evolved through gene duplication and recombination of domain coding sequences. celK without a dockerin domain was expressed in Escherichia coli and purified. The enzyme had pH and temperature optima at 6.0 and 65 degrees C, respectively. It hydrolyzed p-nitrophenyl-beta-D-cellobioside with a Km and a Vmax of 1.67 microM and 15.1 U/mg, respectively. Cellobiose was a strong inhibitor of CelK activity, with a Ki of 0.29 mM. The enzyme was thermostable, after 200 h of incubation at 60 degrees C, 97% of the original activity remained. Properties of the enzyme indicated that it is a cellobiohydrolase.
Collapse
Affiliation(s)
- I Kataeva
- Center for Biological Resource Recovery and Department of Biochemistry & Molecular Biology, The University of Georgia, Athens, Georgia 30602-7229, USA
| | | | | | | | | |
Collapse
|
43
|
Blum DL, Li XL, Chen H, Ljungdahl LG. Characterization of an acetyl xylan esterase from the anaerobic fungus Orpinomyces sp. strain PC-2. Appl Environ Microbiol 1999; 65:3990-5. [PMID: 10473406 PMCID: PMC99731 DOI: 10.1128/aem.65.9.3990-3995.1999] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 1,067-bp cDNA, designated axeA, coding for an acetyl xylan esterase (AxeA) was cloned from the anaerobic rumen fungus Orpinomyces sp. strain PC-2. The gene had an open reading frame of 939 bp encoding a polypeptide of 313 amino acid residues with a calculated mass of 34,845 Da. An active esterase using the original start codon of the cDNA was synthesized in Escherichia coli. Two active forms of the esterase were purified from recombinant E. coli cultures. The size difference of 8 amino acids was a result of cleavages at two different sites within the signal peptide. The enzyme released acetate from several acetylated substrates, including acetylated xylan. The activity toward acetylated xylan was tripled in the presence of recombinant xylanase A from the same fungus. Using p-nitrophenyl acetate as a substrate, the enzyme had a K(m) of 0.9 mM and a V(max) of 785 micromol min(-1) mg(-1). It had temperature and pH optima of 30 degrees C and 9.0, respectively. AxeA had 56% amino acid identity with BnaA, an acetyl xylan esterase of Neocallimastix patriciarum, but the Orpinomyces AxeA was devoid of a noncatalytic repeated peptide domain (NCRPD) found at the carboxy terminus of the Neocallimastix BnaA. The NCRPD found in many glycosyl hydrolases and esterases of anaerobic fungi has been postulated to function as a docking domain for cellulase-hemicellulase complexes, similar to the dockerin of the cellulosome of Clostridium thermocellum. The difference in domain structures indicated that the two highly similar esterases of Orpinomyces and Neocallimastix may be differently located, the former being a free enzyme and the latter being a component of a cellulase-hemicellulase complex. Sequence data indicate that AxeA and BnaA might represent a new family of hydrolases.
Collapse
Affiliation(s)
- D L Blum
- Department of Biochemistry and Molecular Biology and the Center for Biological Resource Recovery, The University of Georgia, Athens, Georgia 30602, USA
| | | | | | | |
Collapse
|
44
|
Shoham Y, Lamed R, Bayer EA. The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides. Trends Microbiol 1999; 7:275-81. [PMID: 10390637 DOI: 10.1016/s0966-842x(99)01533-4] [Citation(s) in RCA: 239] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The cellulosome is an extracellular supramolecular machine that can efficiently degrade crystalline cellulosic substrates and associated plant cell wall polysaccharides. The cellulosome arrangement can also promote adhesion to the insoluble substrate, thus providing individual microbial cells with a direct competitive advantage in the utilization of the soluble hydrolysis products.
Collapse
Affiliation(s)
- Y Shoham
- Dept of Food Engineering and Biotechnology, Technion-Israel Institute of Technology, Haifa 32000, Israel.
| | | | | |
Collapse
|
45
|
Abstract
The structural complexity and rigidity of cellulosic substrates have given rise to a phenomenal diversity of degradative enzymes--the cellulases. Cellulolytic microorganisms produce a wide variety of different catalytic and noncatalytic enzyme modules, which form the cellulases and act synergistically on their substrate. In some microbes, several types of cellulases are organized into an elaborate multifunctional supramolecular complex, known as the cellulosome. A combination of molecular genetic, biochemical, chemical, crystallographic and microscopic techniques are paving the way for new insights into both the structure of cellulose and the mechanisms of its hydrolysis.
Collapse
Affiliation(s)
- E A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
| | | | | | | |
Collapse
|
46
|
Chen H, Li XL, Blum DL, Ljungdahl LG. Two genes of the anaerobic fungus Orpinomyces sp. strain PC-2 encoding cellulases with endoglucanase activities may have arisen by gene duplication. FEMS Microbiol Lett 1998; 159:63-8. [PMID: 9485595 DOI: 10.1111/j.1574-6968.1998.tb12842.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A cDNA designated celE cloned from Orpinomyces PC-2 consisted of an open reading frame encoding a polypeptide (CelE) of 477 amino acids. CelE was highly homologous to CelBs of Orpinomyces (72.3% identity) and neocallimastix (67.9% identity) and like them it had a non-catalytic repeated peptide domain (NCRPD) at the C-terminal end. The catalytic domain of CelE was homologous to glycosyl hydrolases of Family 5, found in several anaerobic bacteria. The gene of celE was devoid of introns. The recombinant proteins CelE and CelB of Orpinomyces PC-2 randomly hydrolyzed carboxymethylcellulose and cello-oligosaccharides in the pattern of endoglucanases. The results indicated that a gene of bacterial origin was duplicated to form celE and celB of Orpinomyces PC-2.
Collapse
Affiliation(s)
- H Chen
- Center for Biological Resource Recovery, University of Georgia, Athens 30602-7229, USA
| | | | | | | |
Collapse
|