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Forsberg Z, Tuveng TR, Eijsink VGH. A modular enzyme with combined hemicellulose-removing and LPMO activity increases cellulose accessibility in softwood. FEBS J 2024. [PMID: 39190632 DOI: 10.1111/febs.17250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/05/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024]
Abstract
Because of the association with other complex polysaccharides, extracting and utilizing cellulose from lignocellulosic materials requires the combined action of a broad range of carbohydrate-active enzymes, including multiple glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The interplay between these enzymes and the way in which Nature orchestrates their co-existence and combined action are topics of great scientific and industrial interest. To gain more insight into these issues, we have studied the lignocellulose-degrading abilities of an enzyme from Caldibacillus cellulovorans (CcLPMO10-Man5), comprising an LPMO domain, a GH5 mannanase domain and two family 3 carbohydrate-binding modules (CBM3). Using a natural softwood substrate, we show that this enzyme promotes cellulase activity, i.e., saccharification of cellulose, both by removing mannan covering the cellulose and by oxidatively breaking up the cellulose structure. Synergy with CcLPMO10-Man5 was most pronounced for two tested cellobiohydrolases, whereas effects were smaller for a tested endoglucanase, which is in line with the notion that cellobiohydrolases and LPMOs attack the same crystalline regions of the cellulose, whereas endoglucanases attack semi-crystalline and amorphous regions. Importantly, the LPMO domain of CcLPMO10-Man5 is incapable of accessing the softwood cellulose in absence of the mannanase domain. Considering that LPMOs not bound to a substrate are sensitive to autocatalytic inactivation, this intramolecular synergy provides a perfect rationale for the evolution of modular enzymes such as CcLPMO10-Man5. The intramolecular coupling of the LPMO with a mannanase and two CBMs ensures that the LPMO is directed to areas where mannans are removed and cellulose thus becomes available.
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Affiliation(s)
- Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Tina R Tuveng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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2
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Wang P, Pei X, Zhou W, Zhao Y, Gu P, Li Y, Gao J. Research and application progress of microbial β-mannanases: a mini-review. World J Microbiol Biotechnol 2024; 40:169. [PMID: 38630389 DOI: 10.1007/s11274-024-03985-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Mannan is a predominant constituent of cork hemicellulose and is widely distributed in various plant tissues. β-Mannanase is the principal mannan-degrading enzyme, which breaks down the β-1,4-linked mannosidic bonds in mannans in an endo-acting manner. Microorganisms are a valuable source of β-mannanase, which exhibits catalytic activity in a wide range of pH and temperature, making it highly versatile and applicable in pharmaceuticals, feed, paper pulping, biorefinery, and other industries. Here, the origin, classification, enzymatic properties, molecular modification, immobilization, and practical applications of microbial β-mannanases are reviewed, the future research directions for microbial β-mannanases are also outlined.
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Affiliation(s)
- Ping Wang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China
| | - Xiaohui Pei
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, PR China
| | - Weiqiang Zhou
- Weili Biotechnology (Shandong) Co., Ltd, Taian, 271400, PR China
| | - Yue Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China
| | - Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China
| | - Yumei Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China.
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China.
- Shandong Engineering Research Center of Key Technologies for High-Value and High-Efficiency Full Industry Chain of Lonicera japonica, Linyi, 273399, PR China.
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3
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Soares NR, Huguet-Tapia JC, Guan D, Clark CA, Yang KT, Kluchka OR, Thombal RS, Kartika R, Badger JH, Pettis GS. Comparative genomics of the niche-specific plant pathogen Streptomyces ipomoeae reveal novel genome content and organization. Appl Environ Microbiol 2023; 89:e0030823. [PMID: 38009923 PMCID: PMC10734452 DOI: 10.1128/aem.00308-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/28/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE While most plant-pathogenic Streptomyces species cause scab disease on a variety of plant hosts, Streptomyces ipomoeae is the sole causative agent of soil rot disease of sweet potato and closely related plant species. Here, genome sequencing of virulent and avirulent S. ipomoeae strains coupled with comparative genomic analyses has identified genome content and organization features unique to this streptomycete plant pathogen. The results here will enable future research into the mechanisms used by S. ipomoeae to cause disease and to persist in its niche environment.
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Affiliation(s)
- Natasha R. Soares
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | | | - Dongli Guan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher A. Clark
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Kuei-Ting Yang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Olivia R. Kluchka
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Raju S. Thombal
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Rendy Kartika
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jonathan H. Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gregg S. Pettis
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
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4
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Takasuka TE, Kim H, Deng K, Bianchetti CM, Yamashita K, Beebe ET, Bergeman LF, Vander Meulen KA, Deutsch S, Ralph J, Adams PD, Northen TR, Fox BG. Quantitative Analysis of The High-Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase. Chembiochem 2023; 24:e202300357. [PMID: 37402642 DOI: 10.1002/cbic.202300357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
Kelp is an abundant, farmable biomass-containing laminarin and alginate as major polysaccharides, providing an excellent model substrate to study their deconstruction by simple enzyme mixtures. Our previous study showed strong reactivity of the glycoside hydrolase family 55 during hydrolysis of purified laminarin, raising the question of its reactivity with intact kelp. In this study, we determined that a combination of a single glycoside hydrolase family 55 β-1,3-exoglucanase with a broad-specificity alginate lyase from the polysaccharide lyase family 18 gives efficient hydrolysis of untreated kelp to a mixture of simple sugars, that is, glucose, gentiobiose, mannitol-end glucose, and mannuronic and guluronic acids and their soluble oligomers. Quantitative assignments from nanostructure initiator mass spectrometry (NIMS) and 2D HSQC NMR spectroscopy and analysis of the reaction time-course are provided. The data suggest that binary combinations of enzymes targeted to the unique polysaccharide composition of marine biomass are sufficient to deconstruct kelp into soluble sugars for microbial fermentation.
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Affiliation(s)
- Taichi E Takasuka
- Research Faculty of Agriculture and, Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
- Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hoon Kim
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Present address: U.S. Department of Agriculture, Forest Service, Forest Products Laboratory, 1 Gifford Pinchot Drive, Madison, WI 53726, USA
| | - Kai Deng
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA 94551, USA
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
| | - Christopher M Bianchetti
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kaho Yamashita
- Research Faculty of Agriculture and, Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
| | - Emily T Beebe
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Lai F Bergeman
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Kirk A Vander Meulen
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Samuel Deutsch
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA 94551, USA
| | - John Ralph
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brian G Fox
- Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Kumar V, Fox BG, Takasuka TE. Consolidated bioprocessing of plant biomass to polyhydroxyalkanoate by co-culture of Streptomyces sp. SirexAA-E and Priestia megaterium. BIORESOURCE TECHNOLOGY 2023; 376:128934. [PMID: 36940873 DOI: 10.1016/j.biortech.2023.128934] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Polyhydroxyalkanoate (PHA) production from plant biomass is an ideal way to realize sustainable PHA-based bioplastic. The present study demonstrated consolidated bioconversion of plant biomass to PHA by co-culturing two specialized bacteria, cellulolytic Streptomyces sp. SirexAA-E and PHA producing Priestia megaterium. In monoculture, S. sp. SirexAA-E does not produce PHA, while P. megaterium did not grow on plant polysaccharides. The co-culture showed poly(3-hydroxybutyrate) (PHB) production using purified polysaccharides, including cellulose, xylan, mannan and their combinations, and plant biomass (Miscanthus, corn stalk and corn leaves) as sole carbon sources, confirmed by GC-MS. The co-culture inoculated with 1:4 (v/v) ratio of S. sp. SirexAA-E to P. megaterium produced 40 mg PHB/g Miscanthus using 0.5% biomass loading. Realtime PCR showed ∼85% S. sp. SirexAA-E and ∼15% P. megaterium in the co-culture. Thus, this study provides a concept of proof for one-pot bioconversion of plant biomass into PHB without separate saccharification processes.
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Affiliation(s)
- Vijay Kumar
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Brian G Fox
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan; US-DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan; Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan.
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Martins MP, Morais MAB, Persinoti GF, Galinari RH, Yu L, Yoshimi Y, Passos Nunes FB, Lima TB, Barbieri SF, Silveira JLM, Lombard V, Terrapon N, Dupree P, Henrissat B, Murakami MT. Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:1358-1372. [DOI: 10.1107/s2059798322009561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
Glycoside hydrolase family 5 (GH5) harbors diverse substrate specificities and modes of action, exhibiting notable molecular adaptations to cope with the stereochemical complexity imposed by glycosides and carbohydrates such as cellulose, xyloglucan, mixed-linkage β-glucan, laminarin, (hetero)xylan, (hetero)mannan, galactan, chitosan, N-glycan, rutin and hesperidin. GH5 has been divided into subfamilies, many with higher functional specificity, several of which have not been characterized to date and some that have yet to be discovered with the exploration of sequence/taxonomic diversity. In this work, the current GH5 subfamily inventory is expanded with the discovery of the GH5_57 subfamily by describing an endo-β-mannanase (CapGH5_57) from an uncultured Bacteroidales bacterium recovered from the capybara gut microbiota. Biochemical characterization showed that CapGH5_57 is active on glucomannan, releasing oligosaccharides with a degree of polymerization from 2 to 6, indicating it to be an endo-β-mannanase. The crystal structure, which was solved using single-wavelength anomalous diffraction, revealed a massively redesigned catalytic interface compared with GH5 mannanases. The typical aromatic platforms and the characteristic α-helix-containing β6–α6 loop in the positive-subsite region of GH5_7 mannanases are absent in CapGH5_57, generating a large and open catalytic interface that might favor the binding of branched substrates. Supporting this, CapGH5_57 contains a tryptophan residue adjacent and perpendicular to the cleavage site, indicative of an anchoring site for a substrate with a substitution at the −1 glycosyl moiety. Taken together, these results suggest that despite presenting endo activity on glucomannan, CapGH5_57 may have a new type of substituted heteromannan as its natural substrate. This work demonstrates the still great potential for discoveries regarding the mechanistic and functional diversity of this large and polyspecific GH family by unveiling a novel catalytic interface sculpted to recognize complex heteromannans, which led to the establishment of the GH5_57 subfamily.
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7
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Møller MS. Impact of Modular Architecture on Activity of Glycoside Hydrolase Family 5 Subfamily 8 Mannanases. Molecules 2022; 27:1915. [PMID: 35335278 PMCID: PMC8952944 DOI: 10.3390/molecules27061915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Glycoside hydrolase family 5 subfamily 8 (GH5_8) mannanases belong to Firmicutes, Actinomycetia, and Proteobacteria. The presence or absence of carbohydrate-binding modules (CBMs) present a striking difference. While various GH5_8 mannanases need a CBM for binding galactomannans, removal of the CBM did not affect activity of some, whereas it in other cases reduced the catalytic efficiency due to increased KM. Here, monomodular GH5_8 mannanases from Eubacterium siraeum (EsGH5_8) and Xanthomonas citri pv. aurantifolii (XcGH5_8) were produced and characterized to clarify if GH5_8 mannanases from Firmicutes and Proteobacteria without CBM(s) possess distinct properties. EsGH5_8 showed a remarkably high temperature optimum of 55 °C, while XcGH5_8 had an optimum at 30 °C. Both enzymes were highly active on carob galactomannan and konjac glucomannan. Notably, EsGH5_8 was equally active on both substrates, whereas XcGH5_8 preferred galactomannan. The KM values were comparable with those of catalytic domains of truncated GH5_8s, while the turn-over numbers (kcat) were in the higher end. Notably, XcGH5_8 bound to but did not degrade insoluble ivory nut mannan. The findings support the hypothesis that GH5_8 mannanases with CBMs target insoluble mannans found in plant cell walls and seeds, while monomodular GH5_8 members have soluble mannans and mannooligosaccharides as primary substrates.
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Affiliation(s)
- Marie Sofie Møller
- Applied Molecular Enzyme Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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8
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Sagarika MS, Parameswaran C, Senapati A, Barala J, Mitra D, Prabhukarthikeyan SR, Kumar A, Nayak AK, Panneerselvam P. Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150451. [PMID: 34607097 DOI: 10.1016/j.scitotenv.2021.150451] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.
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Affiliation(s)
- Mahapatra Smruthi Sagarika
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India; Indira Gandhi Agricultural University, Raipur, Chhattisgarh 492012, India
| | | | - Ansuman Senapati
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Jatiprasad Barala
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Debasis Mitra
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | | | - Anjani Kumar
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
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Mannose- and Mannobiose-Specific Responses of the Insect-Associated Cellulolytic Bacterium Streptomyces sp. Strain SirexAA-E. Appl Environ Microbiol 2021; 87:e0271920. [PMID: 33990299 DOI: 10.1128/aem.02719-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The cellulolytic insect symbiont bacterium Streptomyces sp. strain SirexAA-E secretes a suite of carbohydrate-active enzymes (CAZymes), which are involved in the degradation of various polysaccharides in the plant cell wall, in response to the available carbon sources. Here, we examined a poorly understood response of this bacterium to mannan, one of the major plant cell wall components. SirexAA-E grew well on mannose, carboxymethyl cellulose (CMC), and locust bean gum (LBG) as sole carbon sources in the culture medium. The secreted proteins from each culture supernatant were tested for their polysaccharide-degrading ability, and the composition of secreted CAZymes in each sample was determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results indicated that mannose, LBG, and CMC induced the secretion of mannan and cellulose-degrading enzymes. Interestingly, two α-1,2-mannosidases were abundantly secreted during growth on mannose and LBG. Using genomic analysis, we found a unique 12-bp palindromic sequence motif at 4 locations in the SirexAA-E genome, two of which were found upstream of the above-mentioned α-1,2-mannosidase genes, along with a newly identified mannose and mannobiose-responsive transcriptional regulator, SsManR. Furthermore, the previously reported cellobiose-responsive repressor, SsCebR, was determined to also use mannobiose as an effector ligand. To test whether mannobiose induces the sets of genes under the control of the two regulators, SirexAA-E was grown on mannobiose, and the secretome composition was analyzed. As hypothesized, the composition of the mannobiose secretome combined sets of CAZymes found in both LBG and CMC secretomes, and thus they are likely under the regulation of both SsManR and SsCebR. IMPORTANCE Streptomyces sp. SirexAA-E, a microbial symbiont of biomass-harvesting insects, secretes a suite of polysaccharide-degrading enzymes dependent on the available carbon sources. However, the response of this bacterium to mannan has not been documented. In this study, we investigated the response of this bacterium to mannose, mannobiose, and galactomannan (LBG). By combining biochemical, proteomic, and genomic approaches, we discovered a novel mannose and mannobiose responsive transcriptional regulator, SsManR, which selectively regulates three α-1,2-mannosidase-coding genes. We also demonstrated that the previously described cellobiose responsive regulator, SsCebR, could use mannobiose as an effector ligand. Overall, our findings suggest that the Streptomyces sp. SirexAA-E responds to mannose and mannooligosaccharides through two different transcriptional repressors that regulate the secretion of the plant cell wall-degrading enzymes to extract carbon sources in the host environment.
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10
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Liu J, Sun D, Zhu J, Liu C, Liu W. Carbohydrate-binding modules targeting branched polysaccharides: overcoming side-chain recalcitrance in a non-catalytic approach. BIORESOUR BIOPROCESS 2021; 8:28. [PMID: 38650221 PMCID: PMC10992016 DOI: 10.1186/s40643-021-00381-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/07/2021] [Indexed: 12/25/2022] Open
Abstract
Extensive decoration of backbones is a major factor resulting in resistance of enzymatic conversion in hemicellulose and other branched polysaccharides. Employing debranching enzymes is the main strategy to overcome this kind of recalcitrance at present. A carbohydrate-binding module (CBM) is a contiguous amino acid sequence that can promote the binding of enzymes to various carbohydrates, thereby facilitating enzymatic hydrolysis. According to previous studies, CBMs can be classified into four types based on their preference in ligand type, where Type III and IV CBMs prefer to branched polysaccharides than the linear and thus are able to specifically enhance the hydrolysis of substrates containing side chains. With a role in dominating the hydrolysis of branched substrates, Type III and IV CBMs could represent a non-catalytic approach in overcoming side-chain recalcitrance.
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Affiliation(s)
- Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No. 101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No. 101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No. 101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No. 101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China.
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No. 101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China.
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11
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da Silva VM, Cabral AD, Sperança MA, Squina FM, Muniz JRC, Martin L, Nicolet Y, Garcia W. High-resolution structure of a modular hyperthermostable endo-β-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140437. [PMID: 32325255 DOI: 10.1016/j.bbapap.2020.140437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/20/2020] [Accepted: 04/18/2020] [Indexed: 11/16/2022]
Abstract
The endo-β-1,4-mannanase from the hyperthermostable bacterium Thermotoga petrophila (TpMan) is an enzyme that catalyzes the hydrolysis of mannan and heteromannan polysaccharides. Of the three domains that comprise TpMan, the N-terminal GH5 catalytic domain and the C-terminal carbohydrate-binding domain are connected through a central ancillary domain of unknown structure and function. In this study, we report the partial crystal structure of the TpMan at 1.45 Å resolution, so far, the first modular hyperthermostable endo-β-1,4-mannanase structure determined. The structure exhibits two domains, a (β/α)8-barrel GH5 catalytic domain connected via a linker to the central domain with an immunoglobulin-like β-sandwich fold formed of seven β-strands. Functional analysis showed that whereas the immunoglobulin-like domain does not have the carbohydrate-binding function, it stacks on the GH5 catalytic domain acting as a thermostabilizing domain and allowing operation at hyperthermophilic conditions. The carbohydrate-binding domain is absent in the crystal structure most likely due to its high flexibility around the immunoglobulin-like domain which may act also as a pivot. These results represent new structural and functional information useful on biotechnological applications for biofuel and food industries.
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Affiliation(s)
- Viviam M da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil; Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Aline D Cabral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Marcia A Sperança
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - João Renato C Muniz
- São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil.
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Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization. Sci Rep 2016; 6:36100. [PMID: 27808246 PMCID: PMC5093618 DOI: 10.1038/srep36100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/10/2016] [Indexed: 11/09/2022] Open
Abstract
The bacterium Microbacterium aurum strain B8.A degrades granular starches, using the multi-domain MaAmyA α-amylase to initiate granule degradation through pore formation. This paper reports the characterization of the M. aurum B8.A MaAmyB enzyme, a second starch-acting enzyme with multiple FNIII and CBM25 domains. MaAmyB was characterized as an α-glucan 1,4-α-maltohexaosidase with the ability to subsequently hydrolyze maltohexaose to maltose through the release of glucose. MaAmyB also displays exo-activity with a double blocked PNPG7 substrate, releasing PNP. In M. aurum B8.A, MaAmyB may contribute to degradation of starch granules by rapidly hydrolyzing the helical and linear starch chains that become exposed after pore formation by MaAmyA. Bioinformatics analysis showed that MaAmyB represents a novel GH13 subfamily, designated GH13_42, currently with 165 members, all in Gram-positive soil dwelling bacteria, mostly Streptomyces. All members have an unusually large catalytic domain (AB-regions), due to three insertions compared to established α-amylases, and an aberrant C-region, which has only 30% identity to established GH13 C-regions. Most GH13_42 members have three N-terminal domains (2 CBM25 and 1 FNIII). This is unusual as starch binding domains are commonly found at the C-termini of α-amylases. The evolution of the multi-domain M. aurum B8.A MaAmyA and MaAmyB enzymes is discussed.
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Kumagai Y, Uraji M, Wan K, Okuyama M, Kimura A, Hatanaka T. Molecular insights into the mechanism of thermal stability of actinomycete mannanase. FEBS Lett 2016; 590:2862-9. [DOI: 10.1002/1873-3468.12322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Yuya Kumagai
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries; Research Institute for Biological Sciences (RIBS); Okayama Japan
- Research Faculty of Agriculture; Hokkaido University; Sapporo Japan
| | - Misugi Uraji
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries; Research Institute for Biological Sciences (RIBS); Okayama Japan
| | - Kun Wan
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries; Research Institute for Biological Sciences (RIBS); Okayama Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture; Hokkaido University; Sapporo Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture; Hokkaido University; Sapporo Japan
| | - Tadashi Hatanaka
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries; Research Institute for Biological Sciences (RIBS); Okayama Japan
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14
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Kumagai Y, Yamashita K, Tagami T, Uraji M, Wan K, Okuyama M, Yao M, Kimura A, Hatanaka T. The loop structure of Actinomycete glycoside hydrolase family 5 mannanases governs substrate recognition. FEBS J 2015; 282:4001-14. [PMID: 26257335 DOI: 10.1111/febs.13401] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/23/2015] [Accepted: 08/05/2015] [Indexed: 02/01/2023]
Abstract
Endo-β-1,4-mannanases from Streptomyces thermolilacinus (StMan) and Thermobifida fusca (TfMan) demonstrated different substrate specificities. StMan hydrolyzed galactosylmannooligosaccharide (GGM5; 6(III) ,6(IV) -α-d-galactosyl mannopentaose) to GGM3 and M2, whereas TfMan hydrolyzed GGM5 to GGM4 and M1. To determine the region involved in the substrate specificity, we constructed chimeric enzymes of StMan and TfMan and evaluated their substrate specificities. Moreover, the crystal structure of the catalytic domain of StMan (StMandC) and the complex structure of the inactive mutant StE273AdC with M6 were solved at resolutions of 1.60 and 1.50 Å, respectively. Structural comparisons of StMandC and the catalytic domain of TfMan lead to the identification of a subsite around -1 in StMandC that could accommodate a galactose branch. These findings demonstrate that the two loops (loop7 and loop8) are responsible for substrate recognition in GH5 actinomycete mannanases. In particular, Trp281 in loop7 of StMan, which is located in a narrow and deep cleft, plays an important role in its affinity toward linear substrates. Asp310 in loop8 of StMan specifically bound to the galactosyl unit in the -1 subsite.
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Affiliation(s)
- Yuya Kumagai
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences (RIBS), Okayama, Japan.,Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Keitaro Yamashita
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takayoshi Tagami
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Misugi Uraji
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences (RIBS), Okayama, Japan
| | - Kun Wan
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences (RIBS), Okayama, Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tadashi Hatanaka
- Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences (RIBS), Okayama, Japan
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15
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Bianchetti CM, Takasuka TE, Deutsch S, Udell HS, Yik EJ, Bergeman LF, Fox BG. Active site and laminarin binding in glycoside hydrolase family 55. J Biol Chem 2015; 290:11819-32. [PMID: 25752603 DOI: 10.1074/jbc.m114.623579] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 11/06/2022] Open
Abstract
The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.
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Affiliation(s)
- Christopher M Bianchetti
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, the Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, Wisconsin 54901
| | - Taichi E Takasuka
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, the Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Sam Deutsch
- the Joint Genome Institute, Walnut Creek, California 94598, and
| | - Hannah S Udell
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Eric J Yik
- the Department of Chemistry and Biochemistry, California State University-Fullerton, Fullerton, California 92831
| | - Lai F Bergeman
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Brian G Fox
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706,
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16
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Kim KH, Ramadhar TR, Beemelmanns C, Cao S, Poulsen M, Currie CR, Clardy J. Natalamycin A, an Ansamycin from a Termite-Associated Streptomyces sp. Chem Sci 2014; 5:4333-4338. [PMID: 25386334 PMCID: PMC4224317 DOI: 10.1039/c4sc01136h] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We report a preliminary functional and complete structural characterization of a highly unusual geldanamycin analog, natalamycin A, that was isolated from Streptomyces strain M56 recovered from a South African nest of Macrotermes natalensis termites. Bioassay-guided fractionation based on antifungal activity led to the isolation of natalamycin A, and a combination of NMR spectroscopy and X-ray crystallographic analysis, including highly-accurate quantum-chemical NMR calculations on the largest and most conformationally-flexible system to date, revealed natalamycin A's three-dimensional solid- and solution-state structure. This structure along with the structures of related compounds isolated from the same source suggest a geldanamycin-like biosynthetic pathway with unusual post-PKS modifications.
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Affiliation(s)
- Ki Hyun Kim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts, 02115, United States of America
| | - Timothy R. Ramadhar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts, 02115, United States of America
| | - Christine Beemelmanns
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts, 02115, United States of America
| | - Shugeng Cao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts, 02115, United States of America
| | - Michael Poulsen
- Department of Bacteriology, University of Wisconsin-Madison, 6145 Microbial Science Building, 1550 Linden Drive, Madison, Wisconsin, 53706, United States of America
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, 6145 Microbial Science Building, 1550 Linden Drive, Madison, Wisconsin, 53706, United States of America
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts, 02115, United States of America
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