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Zhang Z, Xing J, Li X, Lu X, Liu G, Qu Y, Zhao J. Review of research progress on the production of cellulase from filamentous fungi. Int J Biol Macromol 2024; 277:134539. [PMID: 39122065 DOI: 10.1016/j.ijbiomac.2024.134539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Cellulases have been widely used in many fields such as animal feed, textile, food, lignocellulose bioconversion, etc. Efficient and low-cost production of cellulases is very important for its industrial application, especially in bioconversion of lignocellulosic biomass. Filamentous fungi are currently widely used in industrial cellulase production due to their ability to secrete large amounts of active free cellulases extracellularly. This review comprehensively summarized the research progress on cellulases from filamentous fungi in recent years, including filamentous fungi used for cellulase production and its modification strategies, enzyme compositions, characterization methods and application of fungal cellulase systems, and the production of fungal cellulase includes production processes, factors affecting cellulase production such as inducers, fermentation medium, process parameters and their control strategies. Also, the future perspectives and research topics in fungal cellulase production are presented in the end of the review. The review helps to deepen the understanding of the current status of fungal cellulases, thereby promoting the production technology progress and industrial application of filamentous fungal cellulase.
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Affiliation(s)
- Zheng Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jing Xing
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xianqin Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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Haddad Momeni M, Zitting A, Jäämuru V, Turunen R, Penttilä P, Buchko GW, Hiltunen S, Maiorova N, Koivula A, Sapkota J, Marjamaa K, Master ER. Insights into the action of phylogenetically diverse microbial expansins on the structure of cellulose microfibrils. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:56. [PMID: 38654330 DOI: 10.1186/s13068-024-02500-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Microbial expansins (EXLXs) are non-lytic proteins homologous to plant expansins involved in plant cell wall formation. Due to their non-lytic cell wall loosening properties and potential to disaggregate cellulosic structures, there is considerable interest in exploring the ability of microbial expansins (EXLX) to assist the processing of cellulosic biomass for broader biotechnological applications. Herein, EXLXs with different modular structure and from diverse phylogenetic origin were compared in terms of ability to bind cellulosic, xylosic, and chitinous substrates, to structurally modify cellulosic fibrils, and to boost enzymatic deconstruction of hardwood pulp. RESULTS Five heterogeneously produced EXLXs (Clavibacter michiganensis; CmiEXLX2, Dickeya aquatica; DaqEXLX1, Xanthomonas sacchari; XsaEXLX1, Nothophytophthora sp.; NspEXLX1 and Phytophthora cactorum; PcaEXLX1) were shown to bind xylan and hardwood pulp at pH 5.5 and CmiEXLX2 (harboring a family-2 carbohydrate-binding module) also bound well to crystalline cellulose. Small-angle X-ray scattering revealed a 20-25% increase in interfibrillar distance between neighboring cellulose microfibrils following treatment with CmiEXLX2, DaqEXLX1, or NspEXLX1. Correspondingly, combining xylanase with CmiEXLX2 and DaqEXLX1 increased product yield from hardwood pulp by ~ 25%, while supplementing the TrAA9A LPMO from Trichoderma reesei with CmiEXLX2, DaqEXLX1, and NspEXLX1 increased total product yield by over 35%. CONCLUSION This direct comparison of diverse EXLXs revealed consistent impacts on interfibrillar spacing of cellulose microfibers and performance of carbohydrate-active enzymes predicted to act on fiber surfaces. These findings uncover new possibilities to employ EXLXs in the creation of value-added materials from cellulosic biomass.
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Affiliation(s)
- Majid Haddad Momeni
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
| | - Aleksi Zitting
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Vilma Jäämuru
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Rosaliina Turunen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Paavo Penttilä
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Salla Hiltunen
- NE Research Center, UPM Pulp Research and Innovations, 53200, Lappeenranta, Finland
| | - Natalia Maiorova
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Espoo, Finland
| | - Janak Sapkota
- NE Research Center, UPM Pulp Research and Innovations, 53200, Lappeenranta, Finland
| | - Kaisa Marjamaa
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Espoo, Finland
| | - Emma R Master
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
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Contreras-Cornejo HA, Schmoll M, Esquivel-Ayala BA, González-Esquivel CE, Rocha-Ramírez V, Larsen J. Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystems. Microbiol Res 2024; 281:127621. [PMID: 38295679 DOI: 10.1016/j.micres.2024.127621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/26/2023] [Accepted: 01/13/2024] [Indexed: 02/16/2024]
Abstract
Trichoderma spp. are free-living fungi present in virtually all terrestrial ecosystems. These soil fungi can stimulate plant growth and increase plant nutrient acquisition of macro- and micronutrients and water uptake. Generally, plant growth promotion by Trichoderma is a consequence of the activity of potent fungal signaling metabolites diffused in soil with hormone-like activity, including indolic compounds as indole-3-acetic acid (IAA) produced at concentrations ranging from 14 to 234 μg l-1, and volatile organic compounds such as sesquiterpene isoprenoids (C15), 6-pentyl-2H-pyran-2-one (6-PP) and ethylene (ET) produced at levels from 10 to 120 ng over a period of six days, which in turn, might impact plant endogenous signaling mechanisms orchestrated by plant hormones. Plant growth stimulation occurs without the need of physical contact between both organisms and/or during root colonization. When associated with plants Trichoderma may cause significant biochemical changes in plant content of carbohydrates, amino acids, organic acids and lipids, as detected in Arabidopsis thaliana, maize (Zea mays), tomato (Lycopersicon esculentum) and barley (Hordeum vulgare), which may improve the plant health status during the complete life cycle. Trichoderma-induced plant beneficial effects such as mechanisms of defense and growth are likely to be inherited to the next generations. Depending on the environmental conditions perceived by the fungus during its interaction with plants, Trichoderma can reprogram and/or activate molecular mechanisms commonly modulated by IAA, ET and abscisic acid (ABA) to induce an adaptative physiological response to abiotic stress, including drought, salinity, or environmental pollution. This review, provides a state of the art overview focused on the canonical mechanisms of these beneficial fungi involved in plant growth promotion traits under different environmental scenarios and shows new insights on Trichoderma metabolites from different chemical classes that can modulate specific plant growth aspects. Also, we suggest new research directions on Trichoderma spp. and their secondary metabolites with biological activity on plant growth.
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Affiliation(s)
- Hexon Angel Contreras-Cornejo
- Laboratorio Nacional de Innovación Ecotecnológica para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Mexico; IIES-UNAM, Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico.
| | - Monika Schmoll
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Centre of Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Blanca Alicia Esquivel-Ayala
- Laboratorio de Entomología, Facultad de Biología, Edificio B4, Universidad Michoacana de San Nicolás de Hidalgo, Gral. Francisco J. Múgica S/N, Ciudad Universitaria, CP 58030 Morelia, Michoacán, Mexico
| | - Carlos E González-Esquivel
- Laboratorio Nacional de Innovación Ecotecnológica para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Mexico; IIES-UNAM, Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - Victor Rocha-Ramírez
- Laboratorio Nacional de Innovación Ecotecnológica para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Mexico; IIES-UNAM, Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - John Larsen
- Laboratorio Nacional de Innovación Ecotecnológica para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Mexico; IIES-UNAM, Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico
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Dahiya D, Koitto T, Kutvonen K, Wang Y, Haddad Momeni M, de Ruijter S, Master ER. Fungal loosenin-like proteins boost the cellulolytic enzyme conversion of pretreated wood fiber and cellulosic pulps. BIORESOURCE TECHNOLOGY 2024; 394:130188. [PMID: 38104665 DOI: 10.1016/j.biortech.2023.130188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
Microbial expansin-related proteins, including loosenins, can disrupt cellulose networks and increase enzyme accessibility to cellulosic substrates. Herein, four loosenins from Phanerochaete carnosa (PcaLOOLs), and a PcaLOOL fused to a family 63 carbohydrate-binding module, were compared for ability to boost the cellulolytic deconstruction of steam pretreated softwood (SSW) and kraft pulps from softwood (ND-BSKP) and hardwood (ND-BHKP). Amending the Cellic® CTec-2 cellulase cocktail with PcaLOOLs increased reducing products from SSW by up to 40 %, corresponding to 28 % higher glucose yield. Amending Cellic® CTec-2 with PcaLOOLs also increased the release of glucose from ND-BSKP and ND-BHKP by 82 % and 28 %, respectively. Xylose release from ND-BSKP and ND-BHKP increased by 47 % and 57 %, respectively, highlighting the potential of PcaLOOLs to enhance hemicellulose recovery. Scanning electron microscopy and fiber image analysis revealed fibrillation and curlation of ND-BSKP after PcaLOOL treatment, consistent with increasing enzyme accessibility to targeted substrates.
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Affiliation(s)
- Deepika Dahiya
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Taru Koitto
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Kim Kutvonen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Yan Wang
- Biorefining Business Development & Production, St1 Oy, Firdonkatu 2, 00520 Helsinki, Finland
| | - Majid Haddad Momeni
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Siiri de Ruijter
- Biorefining Business Development & Production, St1 Oy, Firdonkatu 2, 00520 Helsinki, Finland
| | - Emma R Master
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland; Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, M5S 3E5 Toronto, Ontario, Canada.
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Haque MA, Barman DN, Rahman A, Hossain MS, Ghosh S, Nahar MA, Nahar MNEN, Saha JK, Cho KM, Yun HD. Molecular Cloning, In Silico Analysis, and Characterization of a Novel Cellulose Microfibril Swelling Gene Isolated from Bacillus sp. Strain AY8. Microorganisms 2023; 11:2857. [PMID: 38138001 PMCID: PMC10745351 DOI: 10.3390/microorganisms11122857] [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: 10/16/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
A novel cellulose microfibril swelling (Cms) gene of Bacillus sp. AY8 was successfully cloned and sequenced using a set of primers designed based on the conserved region of the gene from the genomic database. The molecular cloning of the Cms gene revealed that the gene consisted of 679 bp sequences encoding 225 amino acids. Further in silico analysis unveiled that the Cms gene contained the NlpC/P60 conserved region that exhibited a homology of 98% with the NlpC/P60 family proteins found in both the strains, Burkholderialata sp. and Burkholderia vietnamiensis. The recombinant Cms enzyme had a significant impact on the reduction of crystallinity indices (CrI) of various substrates including a 3%, a 3.97%, a 4.66%, and a substantial 14.07% for filter paper, defatted cotton fiber, avicel, and alpha cellulose, respectively. Additionally, notable changes in the spectral features were observed among the substrates treated with recombinant Cms enzymes compared to the untreated control. Specifically, there was a decrease in band intensities within the spectral regions of 3000-3450 cm-1, 2900 cm-1, 1429 cm-1, and 1371 cm-1 for the treated filter paper, cotton fiber, avicel, and alpha cellulose, respectively. Furthermore, the recombinant Cms enzyme exhibited a maximum cellulose swelling activity at a pH of 7.0 along with a temperature of 40 °C. The molecular docking data revealed that ligand molecules, such as cellobiose, dextrin, maltose 1-phosphate, and feruloyated xyloglucan, effectively bonded to the active site of the Cms enzyme. The molecular dynamics simulations of the Cms enzyme displayed stable interactions with cellobiose and dextrin molecules up to 100 ns. It is noteworthy to mention that the conserved region of the Cms enzyme did not match with those of the bioadditives like expansins and swollenin proteins. This study is the initial report of a bacterial cellulose microfibril swellase enzyme, which could potentially serve as an additive to enhance biofuel production by releasing fermentable sugars from cellulose.
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Affiliation(s)
- Md. Azizul Haque
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh; (M.S.H.); (M.A.N.); (M.N.-E.-N.N.)
| | - Dhirendra Nath Barman
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh;
| | - Aminur Rahman
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Md. Shohorab Hossain
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh; (M.S.H.); (M.A.N.); (M.N.-E.-N.N.)
- Department of Biochemistry and Molecular Biology, Trust University, Barisal 8200, Bangladesh
| | - Sibdas Ghosh
- Department of Biological Sciences, College of Arts and Sciences, Carlow University, 3333 Fifth Avenue, Pittsburgh, PA 15213, USA;
| | - Most. Aynun Nahar
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh; (M.S.H.); (M.A.N.); (M.N.-E.-N.N.)
| | - Mst. Nur-E-Nazmun Nahar
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh; (M.S.H.); (M.A.N.); (M.N.-E.-N.N.)
| | - Joyanta K. Saha
- Department of Chemistry, Jagannath University, Dhaka 1100, Bangladesh;
| | - Kye Man Cho
- Department of GreenBio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Han Dae Yun
- Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju 52725, Republic of Korea
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Li G, Yuan Y, Jin B, Zhang Z, Murtaza B, Zhao H, Li X, Wang L, Xu Y. Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides. Front Microbiol 2023; 14:1205767. [PMID: 37608941 PMCID: PMC10440823 DOI: 10.3389/fmicb.2023.1205767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.
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Affiliation(s)
- Gen Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yue Yuan
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Bowen Jin
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhiqiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Hong Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
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Yang T, Li X, Xu N, Guo Y, Liu G, Zhao J. Preparation of cellulose nanocrystals from commercial dissolving pulp using an engineered cellulase system. BIORESOUR BIOPROCESS 2023; 10:42. [PMID: 38647579 PMCID: PMC10992297 DOI: 10.1186/s40643-023-00658-z] [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: 01/19/2023] [Accepted: 06/21/2023] [Indexed: 04/25/2024] Open
Abstract
There is increasing attention to the production of cellulose nanocrystals (CNCs) from lignocellulosic biomass by enzymatic hydrolysis with cellulase. In this study, the feasibility of the application of a cellulase system from engineered strain Penicillium oxalicum cEES in the production of CNCs was assessed. Using commercial eucalyptus dissolving pulp (EDP) as substrate, the CNCs were successfully obtained by enzymatic hydrolysis with the cellulase cEES, and the total yields of CNCs reached 15.7% through three-step enzymatic hydrolysis of total 72 h (24 h for each step). The prepared CNCs were characterized and found that their crystallinity and thermal stability were higher than that of EDP. In the later stage of enzymatic hydrolysis, the process efficiency of enzymatic preparation of CNCs greatly decreased because of the high crystallinity of cellulosic substrate, and a simple homogenization treatment can promote the enzymatic hydrolysis, as well as produce fusiform CNCs with more uniform size and more fermentable sugar that could be further converted into fuels and bulk chemicals through fermentation. This study provides a feasible enzymatic preparation process for CNCs with engineered cellulase and commercial cellulosic materials.
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Affiliation(s)
- Tiantian Yang
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China.
| | - Nuo Xu
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China
| | - Yingjie Guo
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China.
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8
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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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9
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Dutta P, Mahanta M, Singh SB, Thakuria D, Deb L, Kumari A, Upamanya GK, Boruah S, Dey U, Mishra AK, Vanlaltani L, VijayReddy D, Heisnam P, Pandey AK. Molecular interaction between plants and Trichoderma species against soil-borne plant pathogens. FRONTIERS IN PLANT SCIENCE 2023; 14:1145715. [PMID: 37255560 PMCID: PMC10225716 DOI: 10.3389/fpls.2023.1145715] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/05/2023] [Indexed: 06/01/2023]
Abstract
Trichoderma spp. (Hypocreales) are used worldwide as a lucrative biocontrol agent. The interactions of Trichoderma spp. with host plants and pathogens at a molecular level are important in understanding the various mechanisms adopted by the fungus to attain a close relationship with their plant host through superior antifungal/antimicrobial activity. When working in synchrony, mycoparasitism, antibiosis, competition, and the induction of a systemic acquired resistance (SAR)-like response are considered key factors in deciding the biocontrol potential of Trichoderma. Sucrose-rich root exudates of the host plant attract Trichoderma. The soluble secretome of Trichoderma plays a significant role in attachment to and penetration and colonization of plant roots, as well as modulating the mycoparasitic and antibiosis activity of Trichoderma. This review aims to gather information on how Trichoderma interacts with host plants and its role as a biocontrol agent of soil-borne phytopathogens, and to give a comprehensive account of the diverse molecular aspects of this interaction.
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Affiliation(s)
- Pranab Dutta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Madhusmita Mahanta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | | | - Dwipendra Thakuria
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Imphal, India
| | - Lipa Deb
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Arti Kumari
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Gunadhya K. Upamanya
- Sarat Chandra Singha (SCS) College of Agriculture, Assam Agricultural University (Jorhat), Dhubri, Assam, India
| | - Sarodee Boruah
- Krishi Vigyan Kendra (KVK)-Tinsukia, Assam Agricultural University (Jorhat), Tinsukia, Assam, India
| | - Utpal Dey
- Krishi Vigyan Kendra (KVK)-Sepahijala, Central Agricultural University (Imphal), Tripura, Sepahijala, India
| | - A. K. Mishra
- Department of Plant Pathology, Dr Rajendra Prasad Central Agricultural University, Bihar, Samastipur, India
| | - Lydia Vanlaltani
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Dumpapenchala VijayReddy
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Meghalaya, Imphal, India
| | - Punabati Heisnam
- Department of Agronomy, Central Agricultural University (Imphal), Pasighat, India
| | - Abhay K. Pandey
- Department of Mycology and Microbiology, Tea Research Association, North Bengal Regional, R & D Center, Jalpaiguri, West Bengal, India
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10
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Li N, Li J, Chen Y, Shen Y, Wei D, Wang W. Mechanism of Zn 2+ regulation of cellulase production in Trichoderma reesei Rut-C30. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:73. [PMID: 37118821 PMCID: PMC10148476 DOI: 10.1186/s13068-023-02323-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND Trichoderma reesei Rut-C30 is a hypercellulolytic mutant strain that degrades abundant sources of lignocellulosic plant biomass, yielding renewable biofuels. Although Zn2+ is an activator of enzymes in almost all organisms, its effects on cellulase activity in T. reesei have yet to be reported. RESULTS Although high concentrations of Zn2+ severely suppressed the extension of T. reesei mycelia, the application of 1-4 mM Zn2+ enhanced cellulase and xylanase production in the high-yielding cellulase-producing Rut-C30 strain of T. reesei. Expression of the major cellulase, xylanase, and two essential transcription activator genes (xyr1 and ace3) increased in response to Zn2+ stimulation. Transcriptome analysis revealed that the mRNA levels of plc-e encoding phospholipase C, which is involved in the calcium signaling pathway, were enhanced by Zn2+ application. The disruption of plc-e abolished the cellulase-positive influence of Zn2+ in the early phase of induction, indicating that plc-e is involved in Zn2+-induced cellulase production. Furthermore, treatment with LaCl3 (a plasma membrane Ca2+ channel blocker) and deletion of crz1 (calcineurin-responsive zinc finger transcription factor 1) indicated that calcium signaling is partially involved in this process. Moreover, we identified the zinc-responsive transcription factor zafA, the transcriptional levels of which declined in response to Zn2+ stress. Deletion of zafA indicates that this factor plays a prominent role in mediating the Zn2+-induced excessive production of cellulase. CONCLUSIONS For the first time, we have demonstrated that Zn2+ is toxic to T. reesei, although promotes a marked increase in cellulase production. This positive influence of Zn2+ is facilitated by the plc-e gene and zafA transcription factor. These findings provide insights into the role of Zn2+ in T. reesei and the mechanisms underlying signal transduction in cellulase synthesis.
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Affiliation(s)
- Ni Li
- The State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, P. O. Box 311, Shanghai, 200237, China
| | - Jing Li
- The State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, P. O. Box 311, Shanghai, 200237, China
| | - Yumeng Chen
- The State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, P. O. Box 311, Shanghai, 200237, China
| | - Yaling Shen
- The State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, P. O. Box 311, Shanghai, 200237, China
| | - Dongzhi Wei
- The State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, P. O. Box 311, Shanghai, 200237, China
| | - Wei Wang
- The State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, P. O. Box 311, Shanghai, 200237, China.
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11
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Monschein M, Ioannou E, Koitto T, Al Amin LAKM, Varis JJ, Wagner ER, Mikkonen KS, Cosgrove DJ, Master ER. Loosenin-Like Proteins from Phanerochaete carnosa Impact Both Cellulose and Chitin Fiber Networks. Appl Environ Microbiol 2023; 89:e0186322. [PMID: 36645281 PMCID: PMC9888185 DOI: 10.1128/aem.01863-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/19/2022] [Indexed: 01/17/2023] Open
Abstract
Microbial expansin-related proteins are ubiquitous across bacterial and fungal organisms and reportedly play a role in the modification and deconstruction of cell wall polysaccharides, including lignocellulose. So far, very few microbial expansin-related proteins, including loosenins and loosenin-like (LOOL) proteins, have been functionally characterized. Herein, four LOOLs encoded by Phanerochaete carnosa and belonging to different subfamilies (i.e., PcaLOOL7 and PcaLOOL9 from subfamily A and PcaLOOL2 and PcaLOOL12 from subfamily B) were recombinantly produced and the purified proteins were characterized using diverse cellulose and chitin substrates. The purified PcaLOOLs weakened cellulose filter paper and cellulose nanofibril networks (CNF); however, none significantly boosted cellulase activity on the selected cellulose substrates (Avicel and Whatman paper). Although fusing the family 63 carbohydrate-binding module (CBM63) of BsEXLX1 encoded by Bacillus subtilis to PcaLOOLs increased their binding to cellulose, the CBM63 fusion appeared to reduce the cellulose filter paper weakening observed using wild-type proteins. Binding of PcaLOOLs to alpha-chitin was considerably higher than that to cellulose (Avicel) and was pH dependent, with the highest binding at pH 5.0. Amendment of certain PcaLOOLs in fungal liquid cultivations also impacted the density of the cultivated mycelia. The present study reveals the potential of fungal expansin-related proteins to impact both cellulose and chitin networks and points to a possible biological role in fungal cell wall processing. IMPORTANCE The present study deepens investigations of microbial expansin-related proteins and their applied significance by (i) reporting a detailed comparison of diverse loosenins encoded by the same organism, (ii) considering both cellulosic and chitin-containing materials as targeted substrates, and (iii) investigating the impact of the C-terminal carbohydrate binding module (CBM) present in other expansin-related proteins on loosenin function. By revealing the potential of fungal loosenins to impact both cellulose and chitin-containing networks, our study reveals a possible biological and applied role of loosenins in fungal cell wall processing.
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Affiliation(s)
- Mareike Monschein
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Eleni Ioannou
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Taru Koitto
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | | | - Jutta J. Varis
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Edward R. Wagner
- Department of Biology, Pennsylvania State University, University Park, State College, Pennsylvania, USA
- Center for Lignocellulose Structure and Formation, Pennsylvania State University, University Park, State College, Pennsylvania, USA
| | - Kirsi S. Mikkonen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Daniel J. Cosgrove
- Department of Biology, Pennsylvania State University, University Park, State College, Pennsylvania, USA
- Center for Lignocellulose Structure and Formation, Pennsylvania State University, University Park, State College, Pennsylvania, USA
| | - Emma R. Master
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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12
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Monschein M, Jurak E, Paasela T, Koitto T, Lambauer V, Pavicic M, Enjalbert T, Dumon C, Master ER. PACER: a novel 3D plant cell wall model for the analysis of non-catalytic and enzymatic responses. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:30. [PMID: 35296345 PMCID: PMC8928621 DOI: 10.1186/s13068-022-02128-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/05/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Substrate accessibility remains a key limitation to the efficient enzymatic deconstruction of lignocellulosic biomass. Limited substrate accessibility is often addressed by increasing enzyme loading, which increases process and product costs. Alternatively, considerable efforts are underway world-wide to identify amorphogenesis-inducing proteins and protein domains that increase the accessibility of carbohydrate-active enzymes to targeted lignocellulose components.
Results
We established a three-dimensional assay, PACER (plant cell wall model for the analysis of non-catalytic and enzymatic responses), that enables analysis of enzyme migration through defined lignocellulose composites. A cellulose/azo-xylan composite was made to demonstrate the PACER concept and then used to test the migration and activity of multiple xylanolytic enzymes. In addition to non-catalytic domains of xylanases, the potential of loosenin-like proteins to boost xylanase migration through cellulose/azo-xylan composites was observed.
Conclusions
The PACER assay is inexpensive and parallelizable, suitable for screening proteins for ability to increase enzyme accessibility to lignocellulose substrates. Using the PACER assay, we visualized the impact of xylan-binding modules and loosenin-like proteins on xylanase mobility and access to targeted substrates. Given the flexibility to use different composite materials, the PACER assay presents a versatile platform to study impacts of lignocellulose components on enzyme access to targeted substrates.
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13
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Christopher M, Sreeja-Raju A, Sankar M, Gokhale DV, Pandey A, Sukumaran RK. Lignocellulose degradation by Penicillium janthinellum enzymes is influenced by its variable secretome and a unique set of feedstock characteristics. BIORESOURCE TECHNOLOGY 2022; 365:128129. [PMID: 36252760 DOI: 10.1016/j.biortech.2022.128129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Substrate characteristics and proteins that affect lignocellulose-hydrolysis by the hypercellulolytic fungus Penicillium janthinellum NCIM 1366 (PJ-1366) were investigated. The hydrolysis rate of PJ-1366 enzymes was very high, with upto 75 % of the reaction being completed in initial 4 h. Comparison of the hydrolytic efficiencies on differently pretreated biomass indicated that the greatest (negative) effect was imparted by lignin, suggesting that improving ligninase activity of the PJ-1366 enzymes may help to improve hydrolysis. Larger pore sizes and higher crystallinity of substrates, which favor enzyme penetration and processive hydrolysis, positively influenced hydrolysis efficiency. For alkali-pretreated substrates, 16 FPU/g of PJ-1366 cellulases released the sugar-equivalent of using 10 FPU/g of a commercial biomass hydrolyzing enzyme. By correlation analysis, 41 proteins, including 20 CAZymes were identified, whose abundance in the secretome positively correlated with the cellulase activities of the culture filtrate. These proteins may be considered as the primary drivers of FPase/CMCase/pNPGase/xylanase activity in PJ-1366.
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Affiliation(s)
- Meera Christopher
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Athiraraj Sreeja-Raju
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Meena Sankar
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Ashok Pandey
- Centre for Innovation & Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226 001, Uttar Pradesh, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun 248 007, Uttarakhand, India; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
| | - Rajeev K Sukumaran
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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14
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Antoszewski M, Mierek-Adamska A, Dąbrowska GB. The Importance of Microorganisms for Sustainable Agriculture-A Review. Metabolites 2022; 12:1100. [PMID: 36422239 PMCID: PMC9694901 DOI: 10.3390/metabo12111100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
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Affiliation(s)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
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15
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Schalamun M, Schmoll M. Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1002161. [PMID: 37746224 PMCID: PMC10512326 DOI: 10.3389/ffunb.2022.1002161] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/25/2022] [Indexed: 09/26/2023]
Abstract
The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.
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Affiliation(s)
- Miriam Schalamun
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Monika Schmoll
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
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16
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Poveda J, Díaz-González S, Díaz-Urbano M, Velasco P, Sacristán S. Fungal endophytes of Brassicaceae: Molecular interactions and crop benefits. FRONTIERS IN PLANT SCIENCE 2022; 13:932288. [PMID: 35991403 PMCID: PMC9390090 DOI: 10.3389/fpls.2022.932288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Brassicaceae family includes an important group of plants of great scientific interest, e.g., the model plant Arabidopsis thaliana, and of economic interest, such as crops of the genus Brassica (Brassica oleracea, Brassica napus, Brassica rapa, etc.). This group of plants is characterized by the synthesis and accumulation in their tissues of secondary metabolites called glucosinolates (GSLs), sulfur-containing compounds mainly involved in plant defense against pathogens and pests. Brassicaceae plants are among the 30% of plant species that cannot establish optimal associations with mycorrhizal hosts (together with other plant families such as Proteaceae, Chenopodiaceae, and Caryophyllaceae), and GSLs could be involved in this evolutionary process of non-interaction. However, this group of plants can establish beneficial interactions with endophytic fungi, which requires a reduction of defensive responses by the host plant and/or an evasion, tolerance, or suppression of plant defenses by the fungus. Although much remains to be known about the mechanisms involved in the Brassicaceae-endophyte fungal interaction, several cases have been described, in which the fungi need to interfere with the GSL synthesis and hydrolysis in the host plant, or even directly degrade GSLs before they are hydrolyzed to antifungal isothiocyanates. Once the Brassicaceae-endophyte fungus symbiosis is formed, the host plant can obtain important benefits from an agricultural point of view, such as plant growth promotion and increase in yield and quality, increased tolerance to abiotic stresses, and direct and indirect control of plant pests and diseases. This review compiles the studies on the interaction between endophytic fungi and Brassicaceae plants, discussing the mechanisms involved in the success of the symbiosis, together with the benefits obtained by these plants. Due to their unique characteristics, the family Brassicaceae can be seen as a fruitful source of novel beneficial endophytes with applications to crops, as well as to generate new models of study that allow us to better understand the interactions of these amazing fungi with plants.
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Affiliation(s)
- Jorge Poveda
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Sandra Díaz-González
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - María Díaz-Urbano
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG), Spanish National Research Council (CSIC), Pontevedra, Spain
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG), Spanish National Research Council (CSIC), Pontevedra, Spain
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
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17
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Aspergillus Hydrophobins: Physicochemical Properties, Biochemical Properties, and Functions in Solid Polymer Degradation. Microorganisms 2022; 10:microorganisms10081498. [PMID: 35893556 PMCID: PMC9394342 DOI: 10.3390/microorganisms10081498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 01/27/2023] Open
Abstract
Hydrophobins are small amphipathic proteins conserved in filamentous fungi. In this review, the properties and functions of Aspergillus hydrophobins are comprehensively discussed on the basis of recent findings. Multiple Aspergillus hydrophobins have been identified and categorized in conventional class I and two non-conventional classes. Some Aspergillus hydrophobins can be purified in a water phase without organic solvents. Class I hydrophobins of Aspergilli self-assemble to form amphipathic membranes. At the air–liquid interface, RolA of Aspergillus oryzae self-assembles via four stages, and its self-assembled films consist of two layers, a rodlet membrane facing air and rod-like structures facing liquid. The self-assembly depends mainly on hydrophobin conformation and solution pH. Cys4–Cys5 and Cys7–Cys8 loops, disulfide bonds, and conserved Cys residues of RodA-like hydrophobins are necessary for self-assembly at the interface and for adsorption to solid surfaces. AfRodA helps Aspergillus fumigatus to evade recognition by the host immune system. RodA-like hydrophobins recruit cutinases to promote the hydrolysis of aliphatic polyesters. This mechanism appears to be conserved in Aspergillus and other filamentous fungi, and may be beneficial for their growth. Aspergilli produce various small secreted proteins (SSPs) including hydrophobins, hydrophobic surface–binding proteins, and effector proteins. Aspergilli may use a wide variety of SSPs to decompose solid polymers.
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18
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Abbas A, Mubeen M, Zheng H, Sohail MA, Shakeel Q, Solanki MK, Iftikhar Y, Sharma S, Kashyap BK, Hussain S, del Carmen Zuñiga Romano M, Moya-Elizondo EA, Zhou L. Trichoderma spp. Genes Involved in the Biocontrol Activity Against Rhizoctonia solani. Front Microbiol 2022; 13:884469. [PMID: 35694310 PMCID: PMC9174946 DOI: 10.3389/fmicb.2022.884469] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/27/2022] [Indexed: 11/15/2022] Open
Abstract
Rhizoctonia solani is a pathogen that causes considerable harm to plants worldwide. In the absence of hosts, R. solani survives in the soil by forming sclerotia, and management methods, such as cultivar breeding, crop rotations, and fungicide sprays, are insufficient and/or inefficient in controlling R. solani. One of the most challenging problems facing agriculture in the twenty-first century besides with the impact of global warming. Environmentally friendly techniques of crop production and improved agricultural practices are essential for long-term food security. Trichoderma spp. could serve as an excellent example of a model fungus to enhance crop productivity in a sustainable way. Among biocontrol mechanisms, mycoparasitism, competition, and antibiosis are the fundamental mechanisms by which Trichoderma spp. defend against R. solani, thereby preventing or obstructing its proliferation. Additionally, Trichoderma spp. induce a mixed induced systemic resistance (ISR) or systemic acquired resistance (SAR) in plants against R. solani, known as Trichoderma-ISR. Stimulation of every biocontrol mechanism involves Trichoderma spp. genes responsible for encoding secondary metabolites, siderophores, signaling molecules, enzymes for cell wall degradation, and plant growth regulators. Rhizoctonia solani biological control through genes of Trichoderma spp. is summarized in this paper. It also gives information on the Trichoderma-ISR in plants against R. solani. Nonetheless, fast-paced current research on Trichoderma spp. is required to properly utilize their true potential against diseases caused by R. solani.
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Affiliation(s)
- Aqleem Abbas
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mustansar Mubeen
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Hongxia Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qaiser Shakeel
- Department of Plant Pathology, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Yasir Iftikhar
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
- *Correspondence: Yasir Iftikhar,
| | - Sagar Sharma
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Brijendra Kumar Kashyap
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, India
| | - Sarfaraz Hussain
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | | | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Lei Zhou,
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Pan L, Harper K, Queiroz O, Copani G, Cappellozza BI. Effects of a Bacillus-based direct-fed microbial on in vitro nutrient digestibility of forage and high-starch concentrate substrates. Transl Anim Sci 2022; 6:txac067. [PMID: 35702175 PMCID: PMC9186312 DOI: 10.1093/tas/txac067] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Two experiments evaluated the effects of a Bacillus-based direct-fed microbial (DFM) on in vitro dry matter (DM) and neutral detergent fiber (NDF; experiment 1) and starch (experiment 2) digestibility of a variety of ruminant feedstuffs. In experiment 1, 10 forage sources were evaluated: ryegrass, alfalfa hay, leucaena, corn silage, spinifex, buffel grass, flinders grass, Mitchell grass, Rhodes grass hay, and Queensland bluegrass. Experimental treatments were control (forages with no probiotic inoculation; CON) and forage sources inoculated with a mixture containing Bacillus licheniformis and Bacillus subtilis (3.2 × 109 CFU per g; DFM). In vitro DM and NDF digestibility were evaluated at 24- and 48-h post-treatment inoculation. Treatment × hour interactions were noted for IVDMD (in vitro dry matter digestibility) and IVNDFD (in vitro neutral detergent fibre digestibility) (P ≤ 0.05). More specifically, DFM inoculation increased (P ≤ 0.03) IVDMD at 24 h in four forages and increased 48-h IVDMD (P ≤ 0.02) in alfalfa hay, ryegrass, leucaena, and Mitchell grass hay, but opposite results were observed for Queensland bluegrass (P < 0.01). A 24- and 48-h IVNDFD increased following DFM inoculation (P ≤ 0.02) in five forage sources, but reduced for Queensland bluegrass (P < 0.01). When the forages were classified according to their quality, main treatment effects were detected for IVDMD (P ≤ 0.02) and IVNDFD (P < 0.01). In experiment 2, five common cereal grains were evaluated—high-density barley (82 g/100 mL), low-density barley (69 g/100 mL), corn, sorghum, and wheat—under the same treatments as in experiment 1. In vitro starch digestibility (IVSD) was evaluated at 6- and 12-h following treatment inoculation. Treatment × hour interactions were observed for starch digestibility in three out of five concentrate sources (P ≤ 0.001). Inoculation of DFM yielded greater 24-h starch digestibility for high-, low-density barley, and wheat (P ≤ 0.02), but also greater at 48 h in wheat (P < 0.0001). Moreover, mean starch digestibility improved for corn and sorghum inoculated with DFM (P < 0.01). Using a Bacillus-based DFM (B. licheniformis and B. subtilis) improved the mean in vitro DM and NDF digestibility of different forage sources of varying qualities (based on crude protein content). Similarly, IVSD was also greater following DFM inoculation, highlighting the potential of this probiotic to improve nutrient digestibility and utilization in the beef and dairy cattle herd.
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Affiliation(s)
- Liyi Pan
- University of Queensland, School of Agriculture and Food Sciences, Gatton, Australia
| | - Karen Harper
- University of Queensland, School of Agriculture and Food Sciences, Gatton, Australia
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20
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Raheja Y, Singh V, Kaur B, Basotra N, Di Falco M, Tsang A, Singh Chadha B. Combination of system biology and classical approaches for developing biorefinery relevant lignocellulolytic Rasamsonia emersonii strain. BIORESOURCE TECHNOLOGY 2022; 351:127039. [PMID: 35318142 DOI: 10.1016/j.biortech.2022.127039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The objective of this study was to develop thermophilic fungus Rasamsonia emersonii using integrated system biology tools (genomics, proteomics and transcriptional analysis) in combination with classical strain breeding approaches. Developed hyper cellulolytic mutant strain M36 showed endoglucanase (476.35 U/ml), β-glucosidase (70.54 U/ml), cellobiohydrolase (15.17 U/ml), FPase (4.89 U/ml) and xylanase (485.21 U/ml) on cellulose/gram flour based production medium. Comparison of the expression profile at proteome and transcriptional level of the developed strain and wild type parent gave detailed insight into the up-regulation of different CAZymes including glycosyl hydrolases (GH5, GH6, GH7, GH3, GH10) and auxiliary enzymes (lytic polysaccharide monooxygenase, swollenin) at system level. Furthermore, the potential of lignocellulolytic enzyme produced by the developed strain and custom designed cocktail spiked with heterologously expressed lytic polysaccharide monooxygenase from Mycothermus thermophiloides were analyzed for the hydrolysis of biorefinery relevant unwashed pretreated rice straw slurry (PRAJ and IOCL) @17% substrate loading rate.
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Affiliation(s)
- Yashika Raheja
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Varinder Singh
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Baljit Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Neha Basotra
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Marcos Di Falco
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Adrian Tsang
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
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Yuan Y, Chen C, Wang X, Shen S, Guo X, Chen X, Yang F, Li X. A novel accessory protein ArCel5 from cellulose-gelatinizing fungus Arthrobotrys sp. CX1. BIORESOUR BIOPROCESS 2022; 9:27. [PMID: 38647580 PMCID: PMC10991334 DOI: 10.1186/s40643-022-00519-1] [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: 01/14/2022] [Accepted: 03/06/2022] [Indexed: 11/10/2022] Open
Abstract
Improved understanding of cellulose swelling mechanism is beneficial for increasing the hydrolysis efficiency of cellulosic substrates. Here, we report a family 5 glycoside hydrolase ArCel5 isolated from the cellulose-gelatinizing fungus Arthrobotrys sp. CX1. ArCel5 exhibited low specific hydrolysis activity and high cellulose swelling capability, which suggested that this protein might function as an accessory protein. Homology modeling glycosylation detection revealed that ArCel5 is a multi-domain protein including a family 1 carbohydrate-binding module, a glycosylation linker, and a catalytic domain. The adsorption capacity, structural changes and hydrature index of filter paper treated by different ArCel5 mutants demonstrated that CBM1 and linker played an essential role in recognizing, binding and decrystallizing cellulosic substrates, which further encouraged the synergistic action between ArCel5 and cellulases. Notably, glycosylation modification further strengthened the function of the linker region. Overall, our study provides insight into the cellulose decrystallization mechanism by a novel accessory protein ArCel5 that will benefit future applications.
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Affiliation(s)
- Yue Yuan
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Chunshu Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xueyan Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Shaonian Shen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xiaoyu Guo
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China.
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China.
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22
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Xing M, Wang Y, Zhao Y, Chi Z, Chi Z, Liu G. C-Terminal Bacterial Immunoglobulin-like Domain of κ-Carrageenase Serves as a Multifunctional Module to Promote κ-Carrageenan Hydrolysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1212-1222. [PMID: 35057622 DOI: 10.1021/acs.jafc.1c07233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
κ-Carrageenase is an important component for κ-carrageenan oligosaccharide production. Generally, noncatalytic domains are appended to carbohydrate-active domains and potentiate catalytic activity. However, studies devoted to κ-carrageenase are relatively few. Here, a C-terminal bacterial immunoglobulin-like domain (Big_2) was identified in κ-carrageenase (PpCgk) from Pseudoalteromonas porphyrae. Biochemical characterization of native PpCgk and its two truncations, PpCgkCD (catalytic domain) and PpBig_2 (Big_2 domain), revealed that the specific activity, catalytic efficiency (kcat/Km(app)), specific κ-carrageenan-binding capacity, and thermostability of PpCgk were significantly higher than those of PpCgkCD, suggesting that the noncatalytic PpBig_2 domain is a multifunctional module and essential for maintaining the activity and thermostability of PpCgk. Furthermore, it was found that the mode of action of PpCgk was more processive on both the dissolved and gelled substrates than that of PpCgkCD, indicating that PpBig_2 contributes to the processivity of PpCgk. Interestingly, PpBig_2 can be used as an independent module to enhance the hydrolysis of κ-carrageenan through its disruptive function. In addition, sequence analysis suggests that Big_2 domains are highly conserved in bacterial κ-carrageenases, implying the universality of their noncatalytic functions. These findings reveal the multifunctional role of the noncatalytic PpBig_2 and will guide future functional analyses and biotechnology applications of Big_2 domains.
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Affiliation(s)
- Mengdan Xing
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Yan Wang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yujuan Zhao
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Zhe Chi
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Zhenming Chi
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Guanglei Liu
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
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23
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Olowe OM, Nicola L, Asemoloye MD, Akanmu AO, Babalola OO. Trichoderma: Potential bio-resource for the management of tomato root rot diseases in Africa. Microbiol Res 2022; 257:126978. [DOI: 10.1016/j.micres.2022.126978] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
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24
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Amengual NG, Csarman F, Wohlschlager L, Ludwig R. Expression and characterization of a family 45 glycosyl hydrolase from Fomitopsis pinicola and comparison to Phanerochaete chrysosporium Cel45A. Enzyme Microb Technol 2022; 156:110000. [PMID: 35123123 PMCID: PMC7613719 DOI: 10.1016/j.enzmictec.2022.110000] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/03/2022]
Abstract
To efficiently decompose biomass, fungi have developed various enzymatic and non-enzymatic strategies and are a source of versatile biocatalysts. The endoglucanases in glycosyl hydrolase CAZy family 45 (GH45) are known for their small size, a high thermostability and a broad substrate specificity that has been employed in textile and detergent industries. Here we report the heterologous expression and characterisation of an GH45 endoglucanase from the brown rot Fomitopsis pinicola and its direct comparison to an already characterised GH45 from the white rot Phanerochaete chrysosporium. Both enzymes were recombinantly expressed in Pichia pastoris and purified by two chromatographic steps. The biochemical characterisation highlighted the acidophilic character, with an optimal pH of 4, and a preference for amorphous substrates as carboxymethyl cellulose (CMC) and substrates containing β-1,4-glucans rather than the previously reported β-1,3/1,4-glucans lichenan and β-glucan. The dominating products from β-1,4-glucans were C3-C6 oligosaccharides, whereas from β-1,3/1,4-glucans glucose was the main reaction product. From the characterisation no differences between the brown rot and the white rot GH45 was evident.
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Affiliation(s)
- Neus Gacias Amengual
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Florian Csarman
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Lena Wohlschlager
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
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Zhang W, Guo J, Wu X, Ren Y, Li C, Meng X, Liu W. Reformulating the Hydrolytic Enzyme Cocktail of Trichoderma reesei by Combining XYR1 Overexpression and Elimination of Four Major Cellulases to Improve Saccharification of Corn Fiber. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:211-222. [PMID: 34935374 DOI: 10.1021/acs.jafc.1c05946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The industrial fungus Trichoderma reesei has an outstanding capability of secreting an enzyme cocktail comprising multiple plant biomass-degrading enzymes. Herein, the overexpression of XYR1, the master transactivator controlling (hemi)cellulase gene expression, was performed in T. reesei lacking four main cellulase-encoding genes. The resultant strain Δ4celOExyr1 was able to produce a dramatically different profile of secretory proteins on soluble glucose or lactose compared with that of the wild-type T. reesei. The Δ4celOExyr1 secretome included cellulases EGIII and BGLI as well as several hemicellulases and nonhydrolytic cellulose degradation-associated proteins that are not preferentially induced in the wild-type T. reesei strain. Δ4celOExyr1 produced a significant amount of α-arabinofuranosidase I on lactose, and the crude enzyme cocktail of Δ4celOExyr1 not only released a considerable quantity of glucose but also exhibited remarkable performance in the hydrolytic release of xylose, arabinose, and mannose from un-pretreated corn fiber. These results showed that the engineered T. reesei strain holds great potential for improving the saccharification efficiency of the hemicellulosic constituents within corn fiber.
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Affiliation(s)
- Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Junqi Guo
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xiaoxiao Wu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Yajing Ren
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Chunyan Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
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26
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Filiatrault-Chastel C, Heiss-Blanquet S, Margeot A, Berrin JG. From fungal secretomes to enzymes cocktails: The path forward to bioeconomy. Biotechnol Adv 2021; 52:107833. [PMID: 34481893 DOI: 10.1016/j.biotechadv.2021.107833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.
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Affiliation(s)
- Camille Filiatrault-Chastel
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France; IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Senta Heiss-Blanquet
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France.
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27
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Defining the Frontiers of Synergism between Cellulolytic Enzymes for Improved Hydrolysis of Lignocellulosic Feedstocks. Catalysts 2021. [DOI: 10.3390/catal11111343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lignocellulose has economic potential as a bio-resource for the production of value-added products (VAPs) and biofuels. The commercialization of biofuels and VAPs requires efficient enzyme cocktail activities that can lower their costs. However, the basis of the synergism between enzymes that compose cellulolytic enzyme cocktails for depolymerizing lignocellulose is not understood. This review aims to address the degree of synergism (DS) thresholds between the cellulolytic enzymes and how this can be used in the formulation of effective cellulolytic enzyme cocktails. DS is a powerful tool that distinguishes between enzymes’ synergism and anti-synergism during the hydrolysis of biomass. It has been established that cellulases, or cellulases and lytic polysaccharide monooxygenases (LPMOs), always synergize during cellulose hydrolysis. However, recent evidence suggests that this is not always the case, as synergism depends on the specific mechanism of action of each enzyme in the combination. Additionally, expansins, nonenzymatic proteins responsible for loosening cell wall fibers, seem to also synergize with cellulases during biomass depolymerization. This review highlighted the following four key factors linked to DS: (1) a DS threshold at which the enzymes synergize and produce a higher product yield than their theoretical sum, (2) a DS threshold at which the enzymes display synergism, but not a higher product yield, (3) a DS threshold at which enzymes do not synergize, and (4) a DS threshold that displays anti-synergy. This review deconvolutes the DS concept for cellulolytic enzymes, to postulate an experimental design approach for achieving higher synergism and cellulose conversion yields.
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28
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Morales-Quintana L, Barrera A, Hereme R, Jara K, Rivera-Mora C, Valenzuela-Riffo F, Gundel PE, Pollmann S, Ramos P. Molecular and structural characterization of expansins modulated by fungal endophytes in the Antarctic Colobanthus quitensis (Kunth) Bartl. Exposed to drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:465-476. [PMID: 34717178 DOI: 10.1016/j.plaphy.2021.10.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/19/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Expansins are proteins involved in cell wall metabolism that play an important role in plant growth, development, fruit ripening and abiotic stress tolerance. In the present study, we analyzed putative expansins that respond to drought stress. Five expansin genes were identified in cDNA libraries isolated from Colobanthus quitensis gown either with or without endophytic fungi under hydric stress. A differential transcript abundance was observed by qPCR analysis upon drought stress. To compare these expansin genes, and to suggest a possible mechanism of action at the molecular level, the structural model of the deduced proteins was obtained by comparative modeling methodology. The structures showed two domains and an open groove on the surface of the proteins was observed in the five structural models. The proteins were evaluated in terms of their protein-ligand interactions using four different ligands. The results suggested differences in their mode of protein-ligand interaction, in particular concerning the residues involved in the protein-ligand interaction. The presented evidence supports the participation of some members of the expansin multiprotein family in the response to drought stress in C. quitensis and suggest that the response is modulated by endophytic fungi.
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Affiliation(s)
- Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédica, Facultad Ciencias de la Salud, Universidad Autónoma de Chile, Talca, 3467987, Chile
| | - Andrea Barrera
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Rasme Hereme
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Karla Jara
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | | | | | - Pedro E Gundel
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; IFEVA (Facultad de Agronomía, Universidad de Buenos Aires - CONICET), Argentina
| | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Spain
| | - Patricio Ramos
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, Chile; Centro de Biotecnología de los Recursos Naturales (CenBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile.
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Pang AP, Zhang F, Hu X, Luo Y, Wang H, Durrani S, Wu FG, Li BZ, Zhou Z, Lu Z, Lin F. Glutamine involvement in nitrogen regulation of cellulase production in fungi. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:199. [PMID: 34645509 PMCID: PMC8513308 DOI: 10.1186/s13068-021-02046-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/23/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Cellulase synthesized by fungi can environment-friendly and sustainably degrades cellulose to fermentable sugars for producing cellulosic biofuels, biobased medicine and fine chemicals. Great efforts have been made to study the regulation mechanism of cellulase biosynthesis in fungi with the focus on the carbon sources, while little attention has been paid to the impact and regulation mechanism of nitrogen sources on cellulase production. RESULTS Glutamine displayed the strongest inhibition effect on cellulase biosynthesis in Trichoderma reesei, followed by yeast extract, urea, tryptone, ammonium sulfate and L-glutamate. Cellulase production, cell growth and sporulation in T. reesei RUT-C30 grown on cellulose were all inhibited with the addition of glutamine (a preferred nitrogen source) with no change for mycelium morphology. This inhibition effect was attributed to both L-glutamine itself and the nitrogen excess induced by its presence. In agreement with the reduced cellulase production, the mRNA levels of 44 genes related to the cellulase production were decreased severely in the presence of glutamine. The transcriptional levels of genes involved in other nitrogen transport, ribosomal biogenesis and glutamine biosynthesis were decreased notably by glutamine, while the expression of genes relevant to glutamate biosynthesis, amino acid catabolism, and glutamine catabolism were increased noticeably. Moreover, the transcriptional level of cellulose signaling related proteins ooc1 and ooc2, and the cellular receptor of rapamycin trFKBP12 was increased remarkably, whose deletion exacerbated the cellulase depression influence of glutamine. CONCLUSION Glutamine may well be the metabolite effector in nitrogen repression of cellulase synthesis, like the role of glucose plays in carbon catabolite repression. Glutamine under excess nitrogen condition repressed cellulase biosynthesis significantly as well as cell growth and sporulation in T. reesei RUT-C30. More importantly, the presence of glutamine notably impacted the transport and metabolism of nitrogen. Genes ooc1, ooc2, and trFKBP12 are associated with the cellulase repression impact of glutamine. These findings advance our understanding of nitrogen regulation of cellulase production in filamentous fungi, which would aid in the rational design of strains and fermentation strategies for cellulase production in industry.
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Affiliation(s)
- Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yongsheng Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zhihua Zhou
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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Effects on Capsicum annuum Plants Colonized with Trichoderma atroviride P. Karst Strains Genetically Modified in Taswo1, a Gene Coding for a Protein with Expansin-like Activity. PLANTS 2021; 10:plants10091919. [PMID: 34579451 PMCID: PMC8468806 DOI: 10.3390/plants10091919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 12/01/2022]
Abstract
Here, we analyzed the effects on Capsicum annuum plants of Trichoderma atroviride P. Karst strains altered in the expression of SWOLLENIN (SWO1), a protein with amorphogenic activity on plant cell wall components. Strains of T. atroviride that overexpressed the Taswo1 gene were constructed as well as deletion mutants. A novel, cheap and accurate method for assessing root colonization was developed. Colonization assays showed that the Taswo1 overexpressing strains invaded the host root better than the WT, resulting in a stronger plant growth-promoting effect. The expression of plant defense marker genes for both the systemic acquired resistance and induced systemic resistance pathways was enhanced in plants inoculated with Taswo1 overexpressing strains, while inoculation with deletion mutant strains resulted in a similar level of expression to that observed upon inoculation with the wild-type strain. Response to pathogen infection was also enhanced in the plants inoculated with the Taswo1 overexpressing strains, and surprisingly, an intermediate level of protection was achieved with the mutant strains. Tolerance to abiotic stresses was also higher in plants inoculated with the Taswo1 overexpressing strains but was similar in plants inoculated with the wild-type or the mutant strains. Compatible osmolyte production in drought conditions was studied. This study may contribute to improving Trichoderma biocontrol and biofertilization abilities.
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Hamann PRV, de M B Silva L, Gomes TC, Noronha EF. Assembling mini-xylanosomes with Clostridium thermocellum XynA, and their properties in lignocellulose deconstruction. Enzyme Microb Technol 2021; 150:109887. [PMID: 34489040 DOI: 10.1016/j.enzmictec.2021.109887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 12/01/2022]
Abstract
Lignocellulose is a prominent source of carbohydrates to be used in biorefineries. One of the main challenges associated with its use is the low yields obtained during enzymatic hydrolysis, as well as the high cost associate with enzyme acquisition. Despite the great attention in using the fraction composed by hexoses, nowadays, there is a growing interest in enzymatic blends to deconstruct the pentose-rich fraction. Among the organisms studied as a source of enzymes to lignocellulose deconstruction, the anaerobic bacterium Clostridium thermocellum stands out. Most of the remarkable performance of C. thermocellum in degrading cellulose is related to its capacity to assemble enzymes into well-organized enzymatic complexes, cellulosomes. A mini-version of a cellulosome was designed in the present study, using the xylanase XynA and the N-terminus portion of scaffolding protein, mCipA, harboring one CBM3 and two cohesin I domains. The formed mini-xylanosome displayed maximum activity between 60 and 70 °C in a pH range from 6 to 8. Although biochemical properties of complexed/non-complexed enzymes were similar, the formed xylanosome displayed higher hydrolysis at 60 and 70 °C for alkali-treated sugarcane bagasse. Lignocellulose deconstruction using fungal secretome and the mini-xylanosome resulted in higher d-glucose yield, and the addition of the mCipA scaffolding protein enhanced cellulose deconstruction when coupled with fungal enzymes. Results obtained in this study demonstrated that the assembling of xylanases into mini-xylanosomes could improve sugarcane deconstruction, and the mCipA protein can work as a cellulose degradation enhancer.
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Affiliation(s)
- Pedro R V Hamann
- University of Brasilia, Cell Biology Department, Enzymology Laboratory, Brazil.
| | - Luísa de M B Silva
- University of Brasilia, Cell Biology Department, Enzymology Laboratory, Brazil
| | - Tainah C Gomes
- University of Brasilia, Cell Biology Department, Enzymology Laboratory, Brazil
| | - Eliane F Noronha
- University of Brasilia, Cell Biology Department, Enzymology Laboratory, Brazil.
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Pimentel PSSR, de Oliveira JB, Astolfi-Filho S, Pereira N. Enzymatic Hydrolysis of Lignocellulosic Biomass Using an Optimized Enzymatic Cocktail Prepared from Secretomes of Filamentous Fungi Isolated from Amazonian Biodiversity. Appl Biochem Biotechnol 2021; 193:3915-3935. [PMID: 34410613 DOI: 10.1007/s12010-021-03642-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022]
Abstract
The use of lignocellulosic biomass (LCB) has emerged as one of the main strategies for generating renewable biofuels. For the efficient use of such feedstock, pre-treatments are essential. The hydrolysis of cellulose - major component of LCB - demands enzymatic cocktails with improved efficiency to generate fermentable sugars. In this scenario, lignocellulolytic fungi have enormous potential for the development of efficient enzyme platforms. In this study, two enzymatic cocktails were developed for hydrolysis of two lignocellulosic biomasses: industrial cellulose pulp and cassava peel. The solid biomass ratio in relation to the protein content of the enzyme cocktail was performed by experimental design. The optimized cocktail for the hydrolysis of cellulose pulp (AMZ 1) was composed, in protein base, by 43% of Aspergillus sp. LMI03 enzyme extract and 57% of T. reesei QM9414, while the optimal enzyme cocktail for cassava peel hydrolysis (AMZ 2) was composed by 50% of Aspergillus sp. LMI03 enzyme extract, 25% of the extract of P. citrinum LMI01 and 25% of T. reesei. The ratio between solids and protein loading for AMZ 1 cocktail performance was 52 g/L solids and 30 mg protein/g solids, resulting in a hydrolytic efficiency of 93%. For the AMZ 2 cocktail, the hydrolytic efficiency was 78% for an optimized ratio of 78 g/L solids and 19 mg protein/g solids. These results indicate that cocktails formulated with enzymatic extracts of P. citrinum LMI01, Aspergillus sp. LMI03, and T. reesei QM9414 are excellent alternatives for efficient hydrolysis of plant biomass and for other processes that depend on biocatalysis.
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Affiliation(s)
| | - Jessica Batista de Oliveira
- Multi Institutional Biotechnology Graduate Program, Federal University of Amazonas, Manaus, 69067-005, Brazil
| | - Spartaco Astolfi-Filho
- Centro de Apoio Multidisciplinar (CAM), Federal University of Amazonas, Manaus, 69067-005, Brazil
| | - Nei Pereira
- Laboratory of Bioprocess Development, Center of Biofuels, Oil and Derivatives, School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-594, Brazil
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Abstract
Brown rot fungi release massive amounts of carbon from forest deadwood, particularly at high latitudes. These fungi degrade wood by generating small reactive oxygen species (ROS) to loosen lignocellulose, to then selectively remove carbohydrates. The ROS mechanism has long been considered the key adaptation defining brown rot wood decomposition, but recently, we found preliminary evidence that fungal glycoside hydrolases (GHs) implicated in early cell wall loosening might have been adapted to tolerate ROS stress and to synergize with ROS to loosen woody lignocellulose. In the current study, we found more specifically that side chain hemicellulases that help in the early deconstruction of the lignocellulosic complex are significantly more tolerant of ROS in the brown rot fungus Rhodonia placenta than in a white rot fungus (Trametes versicolor) and a soft rot fungus (Trichoderma reesei). Using proteomics to understand the extent of tolerance, we found that significant oxidation of secreted R. placenta proteins exposed to ROS was less than half of the oxidation observed for T. versicolor or T. reesei. The principal oxidative modifications observed in all cases were monooxidation and dioxidation/trioxidation (mainly in methionine and tryptophan residues), some of which were critical for enzyme activity. At the peptide level, we found that GHs in R. placenta were the least ROS affected among our tested fungi. These results confirm and describe underlying mechanisms of tolerance in early-secreted brown rot fungal hemicellulases. These enzymatic adaptations may have been as important as nonenzymatic ROS pathway adaptations in brown rot fungal evolution.
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Zhang P, Cui M, Huang R, Qi W, Thielemans W, He Z, Su R. Enhanced enzymatic hydrolysis of cellulose by endoglucanase via expansin pretreatment and the addition of zinc ions. BIORESOURCE TECHNOLOGY 2021; 333:125139. [PMID: 33882384 DOI: 10.1016/j.biortech.2021.125139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
One of the major limitations of lignocellulose conversion is the relatively low efficiency of cellulases. Expansins can act as an accessory protein to loosen the rigid cellulose structure and promote cellulose hydrolysis. However, the synergistic action of expansin is not well understood. In this study, we employed quartz crystal microbalance with dissipation to real-time monitor the adsorption of Bacillus subtilis expansin (BsEXLX1) and endoglucanase I (Cel7B) and the hydrolysis of cellulose. The effects of pH, temperature, and zinc ions on the initial adsorption rate and adsorption capacity of BsEXLX1 were examined. When 36.5 mM of zinc ions was added, the irreversible adsorption ratio of BsEXLX1 further increased to 4.63 times the value in the absence of zinc ions, whereas the initial adsorption rate and the hydrolysis rate constants of Cel7B could reach 2.16 times and 2.05 times the values in the absence of zinc ions, respectively.
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Affiliation(s)
- Peiqian Zhang
- State Key Laboratory of Chemical Engineering, Tianjin Key Laboratory of Membrane Science and Desalination Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Sustainable Materials Lab, Department of Chemical Engineering, KU Leuven, campus Kulak Kortrijk, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
| | - Mei Cui
- State Key Laboratory of Chemical Engineering, Tianjin Key Laboratory of Membrane Science and Desalination Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Renliang Huang
- School of Marine Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, Tianjin Key Laboratory of Membrane Science and Desalination Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Wim Thielemans
- Sustainable Materials Lab, Department of Chemical Engineering, KU Leuven, campus Kulak Kortrijk, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
| | - Zhimin He
- State Key Laboratory of Chemical Engineering, Tianjin Key Laboratory of Membrane Science and Desalination Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, Tianjin Key Laboratory of Membrane Science and Desalination Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; School of Marine Science and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China.
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35
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Ali A, Ellinger B, Brandt SC, Betzel C, Rühl M, Wrenger C, Schlüter H, Schäfer W, Brognaro H, Gand M. Genome and Secretome Analysis of Staphylotrichum longicolleum DSM105789 Cultured on Agro-Residual and Chitinous Biomass. Microorganisms 2021; 9:1581. [PMID: 34442660 PMCID: PMC8398502 DOI: 10.3390/microorganisms9081581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
Staphylotrichum longicolleum FW57 (DSM105789) is a prolific chitinolytic fungus isolated from wood, with a chitinase activity of 0.11 ± 0.01 U/mg. We selected this strain for genome sequencing and annotation, and compiled its growth characteristics on four different chitinous substrates as well as two agro-industrial waste products. We found that the enzymatic mixture secreted by FW57 was not only able to digest pre-treated sugarcane bagasse, but also untreated sugarcane bagasse and maize leaves. The efficiency was comparable to a commercial enzymatic cocktail, highlighting the potential of the S. longicolleum enzyme mixture as an alternative pretreatment method. To further characterize the enzymes, which efficiently digested polymers such as cellulose, hemicellulose, pectin, starch, and lignin, we performed in-depth mass spectrometry-based secretome analysis using tryptic peptides from in-gel and in-solution digestions. Depending on the growth conditions, we were able to detect from 442 to 1092 proteins, which were annotated to identify from 134 to 224 putative carbohydrate-active enzymes (CAZymes) in five different families: glycoside hydrolases, auxiliary activities, carbohydrate esterases, polysaccharide lyases, glycosyl transferases, and proteins containing a carbohydrate-binding module, as well as combinations thereof. The FW57 enzyme mixture could be used to replace commercial enzyme cocktails for the digestion of agro-residual substrates.
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Affiliation(s)
- Arslan Ali
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi 75270, Pakistan
- Institute of Clinical Chemistry and Laboratory Medicine, Diagnostic Center, Section Mass Spectrometry & Proteomics, Campus Research, Martinistr. 2, N27, Medical Center Hamburg-Eppendorf, Universität Hamburg, 20246 Hamburg, Germany
| | - Bernhard Ellinger
- Department ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany;
| | - Sophie C. Brandt
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Department Biology and Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Gießen, Germany;
| | - Carsten Wrenger
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Biomedical Science Institute, University of São Paulo, Av. Lineu Prestes, 2415, São Paulo CEP 05508-900, Brazil
| | - Hartmut Schlüter
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Institute of Clinical Chemistry and Laboratory Medicine, Diagnostic Center, Section Mass Spectrometry & Proteomics, Campus Research, Martinistr. 2, N27, Medical Center Hamburg-Eppendorf, Universität Hamburg, 20246 Hamburg, Germany
| | - Wilhelm Schäfer
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Biomedical Science Institute, University of São Paulo, Av. Lineu Prestes, 2415, São Paulo CEP 05508-900, Brazil
| | - Martin Gand
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
- Institute of Food Chemistry and Food Biotechnology, Department Biology and Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Gießen, Germany;
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Sukumaran RK, Christopher M, Kooloth-Valappil P, Sreeja-Raju A, Mathew RM, Sankar M, Puthiyamadam A, Adarsh VP, Aswathi A, Rebinro V, Abraham A, Pandey A. Addressing challenges in production of cellulases for biomass hydrolysis: Targeted interventions into the genetics of cellulase producing fungi. BIORESOURCE TECHNOLOGY 2021; 329:124746. [PMID: 33610429 DOI: 10.1016/j.biortech.2021.124746] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Lignocellulosic materials are the favoured feedstock for biorefineries due to their abundant availability and non-completion with food. Biobased technologies for refining these materials are limited mainly by the cost of biomass hydrolyzing enzymes, typically sourced from filamentous fungi. Therefore, considerable efforts have been directed at improving the quantity and quality of secreted lignocellulose degrading enzymes from fungi in order to attain overall economic viability. Process improvements and media engineering probably have reached their thresholds and further production enhancements require modifying the fungal metabolism to improve production and secretion of these enzymes. This review focusses on the types and mechanisms of action of known fungal biomass degrading enzymes, our current understanding of the genetic control exerted on their expression, and possible routes for intervention, especially on modulating catabolite repression, transcriptional regulators, signal transduction, secretion pathways etc., in order to improve enzyme productivity, activity and stability.
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Affiliation(s)
- Rajeev K Sukumaran
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Meera Christopher
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Prajeesh Kooloth-Valappil
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - AthiraRaj Sreeja-Raju
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Reshma M Mathew
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Meena Sankar
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Anoop Puthiyamadam
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Velayudhanpillai-Prasannakumari Adarsh
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Aswathi Aswathi
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Valan Rebinro
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Amith Abraham
- Department of Chemical Engineering, Hanyang University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
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Zhang H, Wang Y, Brunecky R, Yao B, Xie X, Zheng F, Luo H. A Swollenin From Talaromyces leycettanus JCM12802 Enhances Cellulase Hydrolysis Toward Various Substrates. Front Microbiol 2021; 12:658096. [PMID: 33854492 PMCID: PMC8039133 DOI: 10.3389/fmicb.2021.658096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/10/2021] [Indexed: 12/02/2022] Open
Abstract
Swollenins exist within some fungal species and are candidate accessory proteins for the biodegradation of cellulosic substrates. Here, we describe the identification of a swollenin gene, Tlswo, in Talaromyces leycettanus JCM12802. Tlswo was successfully expressed in both Trichoderma reesei and Pichia pastoris. Assay results indicate that TlSWO is capable of releasing reducing sugars from lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin. The specific activity of TlSWO toward lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin is 9.0 ± 0.100, 8.9 ± 0.100, 2.3 ± 0.002 and 0.79 ± 0.002 U/mg, respectively. Additionally, TlSWO had disruptive activity on Avicel and a synergistic effect with cellobiohydrolases, increasing the activity on pretreated corn stover by up to 72.2%. The functional diversity of TlSWO broadens its applicability in experimental settings, and indicating that it may be a promising candidate for future industrial applications.
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Affiliation(s)
- Honghai Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangming Xie
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Fei Zheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Huiying Luo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Pang AP, Wang H, Zhang F, Hu X, Wu FG, Zhou Z, Wang W, Lu Z, Lin F. High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:77. [PMID: 33771193 PMCID: PMC8004424 DOI: 10.1186/s13068-021-01926-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/11/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Knowledge with respect to regulatory systems for cellulase production is prerequisite for exploitation of such regulatory networks to increase cellulase production, improve fermentation efficiency and reduce the relevant production cost. The target of rapamycin (TOR) signaling pathway is considered as a central signaling hub coordinating eukaryotic cell growth and metabolism with environmental inputs. However, how and to what extent the TOR signaling pathway and rapamycin are involved in cellulase production remain elusive. RESULT At the early fermentation stage, high-dose rapamycin (100 μM) caused a temporary inhibition effect on cellulase production, cell growth and sporulation of Trichoderma reesei RUT-C30 independently of the carbon sources, and specifically caused a tentative morphology defect in RUT-C30 grown on cellulose. On the contrary, the lipid content of T. reesei RUT-C30 was not affected by rapamycin. Accordingly, the transcriptional levels of genes involved in the cellulase production were downregulated notably with the addition of rapamycin. Although the mRNA levels of the putative rapamycin receptor trFKBP12 was upregulated significantly by rapamycin, gene trTOR (the downstream effector of the rapamycin-FKBP12 complex) and genes associated with the TOR signaling pathways were not changed markedly. With the deletion of gene trFKBP12, there is no impact of rapamycin on cellulase production, indicating that trFKBP12 mediates the observed temporary inhibition effect of rapamycin. CONCLUSION Our study shows for the first time that only high-concentration rapamycin induced a transient impact on T. reesei RUT-C30 at its early cultivation stage, demonstrating T. reesei RUT-C30 is highly resistant to rapamycin, probably due to that trTOR and its related signaling pathways were not that sensitive to rapamycin. This temporary influence of rapamycin was facilitated by gene trFKBP12. These findings add to our knowledge on the roles of rapamycin and the TOR signaling pathways play in T. reesei.
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Affiliation(s)
- Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhihua Zhou
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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39
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Liu C, Bi J, Kang L, Zhou J, Liu X, Liu Z, Yuan S. The molecular mechanism of stipe cell wall extension for mushroom stipe elongation growth. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2020.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Impact of NaOH Concentration on Deweaving of Cotton Fabric in Aqueous Solutions. SUSTAINABILITY 2021. [DOI: 10.3390/su13042015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In the past decade, there has been increasing attention paid to the recycling of cotton fabric waste. In the present study, different concentrations of sodium hydroxide (NaOH) ranging from 1 M to 4 M were used to thermomechanically deweave cotton fabric. The fabrics treated with 1 M NaOH and 2 M NaOH were partially deweaved, whereas those treated with 3 M NaOH and 4 M NaOH were completely deweaved. Fourier-transform infrared (FTIR) spectroscopy was applied to analyze the chemistry and structure of the cotton fabric. The FTIR spectra indicated that the structure of cotton fabrics treated with 1–2 M NaOH were similar to that of pristine fabric, while the presence of NaOH was observed. In the case of samples treated with 3–4 M NaOH, both the peak positions and the band intensities were changed, in addition to the formation of cellulose II. FTIR spectra for the recycled NaOH-treated cotton fabrics were compared, and no major structural changes were identified. A post-treatment with deionized (DI) water removed excess Na+ ions, with the sample showing a similar molecular structure to that of the pristine material. These results suggest the feasibility of recycling aqueous NaOH for post-washing treatment as a new method for recycling cellulosic fabric waste.
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Tsumura R, Sawada K, Kunitake E, Sumitani JI, Kawaguchi T, Tani S. A component of the septation initiation network complex, AaSepM, is involved in multiple cellulose-responsive signaling pathways in Aspergillus aculeatus. Appl Microbiol Biotechnol 2021; 105:1535-1546. [PMID: 33481069 DOI: 10.1007/s00253-021-11110-7] [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] [Received: 09/08/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
Various carbohydrate-active enzymes in Aspergillus are produced in response to physiological inducers, which is regulated at the transcriptional level. To elucidate the induction mechanisms in Aspergillus, we screened for new regulators involved in cellulose-responsive induction from approximately 10,000 Aspergillus aculeatus T-DNA-inserted mutants. We constructed the T-DNA-inserted mutant library using the host strain harboring the orotidine 5'-monophosphate decarboxylase gene (pyrG) under the control of the FIII-avicelase gene (cbhI) promoter. Thus, candidate mutants deficient in cellulose-responsive induction were positively screened via counter selection against 5-fluoroorotic acid (5-FOA). Among less than two hundred 5-FOA-resistant mutants, one mutant that the T-DNA inserted into the AasepM locus reduced the cbhI expression in response to cellulose. Since AaSepM is similar to Schizosaccharomyces pombe Cdc14p (E-value, 2e-20; identities, 33%), which is a component of the septation initiation network (SIN)-complex, we constructed an AasepM deletion mutant (ΔAasepM). We analyzed the expression of cellulase and xylanase genes in response to cellulose, septation, and conidiation in ΔAasepM. The AasepM deletion leads to delayed septation and decreased formation of the conidium chain in A. aculeatus but does not affect hyphal growth on minimal media. We also confirmed AaSepM's involvement in multiple cellulose-responsive signaling pathways of cellulase and xylanase genes under the control of the ManR-dependent, XlnR-dependent, and ManR- and XlnR-independent signaling pathways. KEY POINTS : • A new regulator for cellulolytic gene expression has been identified. • AaSepM is involved in septation and conidiation in A. aculeatus. • AasepM is involved in multiple cellulose-responsive signaling pathways.
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Affiliation(s)
- Ryosuke Tsumura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan
| | - Kazumi Sawada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan
| | - Emi Kunitake
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan.,Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, 514-8507, Japan
| | - Jun-Ichi Sumitani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan
| | - Takashi Kawaguchi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan
| | - Shuji Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan.
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42
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Wu H, Nakazawa T, Xu H, Yang R, Bao D, Kawauchi M, Sakamoto M, Honda Y. Comparative transcriptional analyses of Pleurotus ostreatus mutants on beech wood and rice straw shed light on substrate-biased gene regulation. Appl Microbiol Biotechnol 2021; 105:1175-1190. [PMID: 33415371 DOI: 10.1007/s00253-020-11087-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/15/2020] [Accepted: 12/28/2020] [Indexed: 11/25/2022]
Abstract
Distinct wood degraders occupying their preferred habitats have biased enzyme repertoires that are well fitted to their colonized substrates. Pleurotus ostreatus, commonly found on wood, has evolved its own enzyme-producing traits. In our previous study, transcriptional shifts in several P. ostreatus delignification-defective mutants, including Δhir1 and Δgat1 strains, were analyzed, which revealed the downregulation of ligninolytic genes and the upregulation of cellulolytic and xylanolytic genes when compared to their parental strain 20b on beech wood sawdust medium (BWS). In this study, rice straw (RS) was used as an alternative substrate to examine the transcriptional responses of P. ostreatus to distinct substrates. The vp1 gene and a cupredoxin-encoding gene were significantly upregulated in the 20b strain on RS compared with that on BWS, reflecting their distinct regulation patterns. The overall expression level of genes encoding glucuronidases was also higher on RS than on BWS, showing a good correlation with the substrate composition. Transcriptional alterations in the mutants (Δhir1 or Δgat1 versus 20b strain) on RS were similar to those on BWS, and the extracellular lignocellulose-degrading enzyme activities and lignin-degrading ability of the mutants on RS were consistent with the transcriptional alterations of the corresponding enzyme-encoding genes. However, transcripts of specific genes encoding enzymes belonging to the same CAZyme family exhibited distinct alteration patterns in the mutant strains grown on RS compared to those grown on BWS. These findings provide new insights into the molecular mechanisms underlying the transcriptional regulation of lignocellulolytic genes in P. ostreatus.Key Points• P. ostreatus expressed variable enzymatic repertoire-related genes in response to distinct substrates.• A demand to upregulate the cellulolytic genes seems to be present in ligninolysis-deficient mutants.• The regulation of some specific genes probably driven by the demand is dependent on the substrate.
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Affiliation(s)
- Hongli Wu
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Haibo Xu
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ruiheng Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Dapeng Bao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
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Rocha J, Shapiro LR, Kolter R. A horizontally acquired expansin gene increases virulence of the emerging plant pathogen Erwinia tracheiphila. Sci Rep 2020; 10:21743. [PMID: 33303810 PMCID: PMC7729394 DOI: 10.1038/s41598-020-78157-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
Erwinia tracheiphila is a bacterial plant pathogen that causes a fatal wilt infection in some cucurbit crop plants. Wilt symptoms are thought to be caused by systemic bacterial colonization through xylem that impedes sap flow. However, the genetic determinants of within-plant movement are unknown for this pathogen species. Here, we find that E. tracheiphila has horizontally acquired an operon with a microbial expansin (exlx) gene adjacent to a glycoside hydrolase family 5 (gh5) gene. Plant inoculation experiments with deletion mutants in the individual genes (Δexlx and Δgh5) and the full operon (Δexlx-gh5) resulted in decreased severity of wilt symptoms, decreased mortality rate, and impaired systemic colonization compared to the Wt strain. Co-inoculation experiments with Wt and Δexlx-gh5 rescued the movement defect of the mutant strain, suggesting that expansin and GH5 function extracellularly. Together, these results show that expansin-GH5 contributes to systemic movement through xylem, leading to rapid wilt symptom development and higher rates of plant death. The presence of expansin genes in diverse species of bacterial and fungal wilt-inducing pathogens suggests that microbial expansin proteins may be an under-appreciated virulence factor for many pathogen species.
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Affiliation(s)
- Jorge Rocha
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Conacyt-Centro de Investigación y Desarrollo en Agrobiotecnología Alimentaria, San Agustin Tlaxiaca, 42163, Hidalgo, Mexico.
| | - Lori R Shapiro
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
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Narváez-Barragán DA, Tovar-Herrera OE, Segovia L, Serrano M, Martinez-Anaya C. Expansin-related proteins: biology, microbe-plant interactions and associated plant-defense responses. MICROBIOLOGY-SGM 2020; 166:1007-1018. [PMID: 33141007 DOI: 10.1099/mic.0.000984] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Expansins, cerato-platanins and swollenins (which we will henceforth refer to as expansin-related proteins) are a group of microbial proteins involved in microbe-plant interactions. Although they share very low sequence similarity, some of their composing domains are near-identical at the structural level. Expansin-related proteins have their target in the plant cell wall, in which they act through a non-enzymatic, but still uncharacterized, mechanism. In most cases, mutagenesis of expansin-related genes affects plant colonization or plant pathogenesis of different bacterial and fungal species, and thus, in many cases they are considered virulence factors. Additionally, plant treatment with expansin-related proteins activate several plant defenses resulting in the priming and protection towards subsequent pathogen encounters. Plant-defence responses induced by these proteins are reminiscent of pattern-triggered immunity or hypersensitive response in some cases. Plant immunity to expansin-related proteins could be caused by the following: (i) protein detection by specific host-cell receptors, (ii) alterations to the cell-wall-barrier properties sensed by the host, (iii) displacement of cell-wall polysaccharides detected by the host. Expansin-related proteins may also target polysaccharides on the wall of the microbes that produced them under certain physiological instances. Here, we review biochemical, evolutionary and biological aspects of these relatively understudied proteins and different immune responses they induce in plant hosts.
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Affiliation(s)
- Delia A Narváez-Barragán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62110 Cuernavaca Morelos, Mexico
| | - Omar E Tovar-Herrera
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, BeerSheva, Israel
| | - Lorenzo Segovia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62110 Cuernavaca Morelos, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62110 Cuernavaca Morelos, Mexico
| | - Claudia Martinez-Anaya
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62110 Cuernavaca Morelos, Mexico
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Delabona PDS, Codima CA, Ramoni J, Zubieta MP, de Araújo BM, Farinas CS, Pradella JGDC, Seiboth B. The impact of putative methyltransferase overexpression on the Trichoderma harzianum cellulolytic system for biomass conversion. BIORESOURCE TECHNOLOGY 2020; 313:123616. [PMID: 32563792 DOI: 10.1016/j.biortech.2020.123616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
Trichoderma harzianum has attracting attention for its potential alternative use in biofuel production, due to a recognized competence for high diversity glycoside hydrolases (GH) enzyme complex, including higher β-glucosidases and auxiliary proteins, using low-cost carbon sources. This strain constitutively overexpressed the global regulator putative methyltransferase - LAE1, in order to improve the GHs production. The recombinant strain achieved 79-fold increase in lae1 expression and high GHs productivity. The evaluation of the LAE1 impact to induce the GHs used soluble and lignocellulose inexpensive carbon sources in a stirred-tank bioreactor. Using sugarcane bagasse with sucrose, the overexpression of lae1 resulted in significantly increment of gh61b (31x), cel7a (25x), bgl1(20x) and xyn3 (20x) genes expression. Reducing sugar released from pretreated sugarcane bagasse, which hydrolyzed by recombinant crude enzyme cocktail, achieved 41% improvement. Therefore, lae1 overexpression effectively is a promising improving GHs target for biomass degradation by T. harzianum.
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Affiliation(s)
- Priscila da Silva Delabona
- National Centre of Research in Energy and Materials, High-tech Pole II, 10000 Giuseppe Maximo Scolfaro St, P.O Box 6192, Campinas, SP, Brazil; Synthetic Biology and Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1a, A-1060 Vienna, Austria; Federal University of Goiás (UFG), Samambaia Campus, Goiânia, GO, Brazil.
| | - Carla Aloia Codima
- National Centre of Research in Energy and Materials, High-tech Pole II, 10000 Giuseppe Maximo Scolfaro St, P.O Box 6192, Campinas, SP, Brazil
| | - Jonas Ramoni
- Synthetic Biology and Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1a, A-1060 Vienna, Austria
| | - Mariane Paludetti Zubieta
- National Centre of Research in Energy and Materials, High-tech Pole II, 10000 Giuseppe Maximo Scolfaro St, P.O Box 6192, Campinas, SP, Brazil
| | | | | | - José Geraldo da Cruz Pradella
- National Centre of Research in Energy and Materials, High-tech Pole II, 10000 Giuseppe Maximo Scolfaro St, P.O Box 6192, Campinas, SP, Brazil
| | - Bernhard Seiboth
- Synthetic Biology and Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1a, A-1060 Vienna, Austria
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46
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Lohoff C, Buchholz PCF, Le Roes-Hill M, Pleiss J. Expansin Engineering Database: A navigation and classification tool for expansins and homologues. Proteins 2020; 89:149-162. [PMID: 32862462 DOI: 10.1002/prot.26001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/16/2020] [Accepted: 08/25/2020] [Indexed: 11/07/2022]
Abstract
Expansins have the remarkable ability to loosen plant cell walls and cellulose material without showing catalytic activity and therefore have potential applications in biomass degradation. To support the study of sequence-structure-function relationships and the search for novel expansins, the Expansin Engineering Database (ExED, https://exed.biocatnet.de) collected sequence and structure data on expansins from Bacteria, Fungi, and Viridiplantae, and expansin-like homologues such as carbohydrate binding modules, glycoside hydrolases, loosenins, swollenins, cerato-platanins, and EXPNs. Based on global sequence alignment and protein sequence network analysis, the sequences are highly diverse. However, many similarities were found between the expansin domains. Newly created profile hidden Markov models of the two expansin domains enable standard numbering schemes, comprehensive conservation analyses, and genome annotation. Conserved key amino acids in the expansin domains were identified, a refined classification of expansins and carbohydrate binding modules was proposed, and new sequence motifs facilitate the search of novel candidate genes and the engineering of expansins.
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Affiliation(s)
- Caroline Lohoff
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Marilize Le Roes-Hill
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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47
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Valenzuela-Riffo F, Parra-Palma C, Ramos P, Morales-Quintana L. Molecular and structural insights into FaEXPA5, an alpha-expansin protein related with cell wall disassembly during ripening of strawberry fruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:581-589. [PMID: 32711363 DOI: 10.1016/j.plaphy.2020.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Cell wall modification is one of the main factors that produce the tissue softening during ripening of many fruit including strawberry (Fragaria x ananassa). Expansins have been studied for over 20 years as a class of the important cell growth regulators, and in the last years these have been related with the fruit softening. In strawberry, five partial sequences of the expansins genes were described in the past, this analysis showed that FaEXP5 partial gene was present throughout fruit development, but was more strongly expressed during ripening. Now, we reported the full length of this α-expansin (FaEXPA5), whose had been related with fruit softening, and the protein structural was described by homology model. Their transcript accumulation during softening was confirmed by qRT-PCR, displaying a high accumulation rate during fruit ripening. In silico analysis of promoter sequence showed four ABA and two auxin cis-regulatory elements, potentially responsible for the expression patterns observed in response to the hormone treatments. Additionally, 3D protein model displayed two domains and one open groove characteristic of expansin structures. The protein-ligand interactions were evaluated by molecular dynamic (MD) simulation using three different long structure ligands (a cellulose fiber, a xyloglucan fiber (XXXG type), and a pectin fiber as control). Favorable interactions were observed with xyloglucan and cellulose, being cellulose the best ligand with lower RMSD value. Additionally, MD simulations showed that FaEXPA5 can interact with the ligands through residues present in the open groove along the two domains.
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Affiliation(s)
- Felipe Valenzuela-Riffo
- Programa de Doctorado en Ciencias Mención Ingeniería Genética, Instituto de Ciencias Biológicas, Universidad de Talca, Chile
| | - Carolina Parra-Palma
- Programa de Doctorado en Ciencias Mención Ingeniería Genética, Instituto de Ciencias Biológicas, Universidad de Talca, Chile
| | - Patricio Ramos
- Instituto de Ciencias Biológicas, Universidad de Talca, Chile; Núcleo Científico Multidisciplinario-DI, Universidad de Talca, Chile.
| | - Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédica, Facultad Ciencias de La Salud, Universidad Autónoma de Chile, Talca, Chile.
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Østby H, Hansen LD, Horn SJ, Eijsink VGH, Várnai A. Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives. J Ind Microbiol Biotechnol 2020; 47:623-657. [PMID: 32840713 PMCID: PMC7658087 DOI: 10.1007/s10295-020-02301-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Efficient saccharification of lignocellulosic biomass requires concerted development of a pretreatment method, an enzyme cocktail and an enzymatic process, all of which are adapted to the feedstock. Recent years have shown great progress in most aspects of the overall process. In particular, increased insights into the contributions of a wide variety of cellulolytic and hemicellulolytic enzymes have improved the enzymatic processing step and brought down costs. Here, we review major pretreatment technologies and different enzyme process setups and present an in-depth discussion of the various enzyme types that are currently in use. We pay ample attention to the role of the recently discovered lytic polysaccharide monooxygenases (LPMOs), which have led to renewed interest in the role of redox enzyme systems in lignocellulose processing. Better understanding of the interplay between the various enzyme types, as they may occur in a commercial enzyme cocktail, is likely key to further process improvements.
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Affiliation(s)
- Heidi Østby
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Line Degn Hansen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway.
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Zhang W, Liu C, Qu M, Pan K, OuYang K, Song X, Zhao X. Construction and characterization of a chimeric enzyme of swollenin and xylanase to improve soybean straw hydrolysis. Int J Biol Macromol 2020; 156:558-564. [PMID: 32311404 DOI: 10.1016/j.ijbiomac.2020.04.101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/18/2020] [Accepted: 04/14/2020] [Indexed: 12/27/2022]
Abstract
A study was carried out to produce a fusion protein (Swo-Xyn) using the Trichoderma reesei swollenin and Lentinula edodes xylanase and to investigate its characteristics and application in degrading soybean straw. In parallel, L. edodes xylanase (Xyn) alone was used as a control protein in application tests. The Swo-Xyn was recombined, expressed and produced by Pichia pastoris and had the maximum activity at 40 °C and pH 3.0 using xylan as substrate. The Swo-Xyn exhibited preferential hydrolysis of Xylan. The Swo-Xyn had slight low Km value (23.90 vs. 25.36 mg/ml) but significantly low Vmax value (162.4 vs. 227.2 μmol/mg·min) and specific activity (18.82 vs. 38.97 U/mg) relative to the Xyn. The Swo-Xyn activity was enhanced by Zn2+ in dose dependent manners with the peak activity at 30 mM of Zn2+. The Swo-Xyn could tolerate 15% of methanol, ethanol, aceton, and DMSO with >60% residual activity. The Swo-Xyn had the greater tolerance to SDS, EDTA, 2-ME than the Xyn and could be activated by DTT, Triton X-100, and Tween 20. Compared with the Xyn, the hydrolysis and sequent cellulose enzymolysis of soybean straw could be better improved by the Swo-Xyn. The Swo-Xyn should be more useful for improving the utilization of soybean straw.
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Affiliation(s)
- Wenjing Zhang
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Chanjuan Liu
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Mingren Qu
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Ke Pan
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Kehui OuYang
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xiaozhen Song
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xianghui Zhao
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
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50
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Chase WR, Zhaxybayeva O, Rocha J, Cosgrove DJ, Shapiro LR. Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution. THE NEW PHYTOLOGIST 2020; 226:921-938. [PMID: 31930503 DOI: 10.1111/nph.16428] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/19/2019] [Indexed: 05/23/2023]
Abstract
Plants must rearrange the network of complex carbohydrates in their cell walls during normal growth and development. To accomplish this, all plants depend on proteins called expansins that nonenzymatically loosen noncovalent bonding between cellulose microfibrils. Surprisingly, expansin genes have more recently been found in some bacteria and microbial eukaryotes, where their biological functions are largely unknown. Here, we reconstruct a comprehensive phylogeny of microbial expansin genes. We find these genes in all eukaryotic microorganisms that have structural cell wall cellulose, suggesting expansins evolved in ancient marine microorganisms long before the evolution of land plants. We also find expansins in an unexpectedly high diversity of bacteria and fungi that do not have cellulosic cell walls. These bacteria and fungi inhabit varied ecological contexts, mirroring the diversity of terrestrial and aquatic niches where plant and/or algal cellulosic cell walls are present. The microbial expansin phylogeny shows evidence of multiple horizontal gene transfer events within and between bacterial and eukaryotic microbial lineages, which may in part underlie their unusually broad phylogenetic distribution. Overall, expansins are unexpectedly widespread in bacteria and eukaryotes, and the contribution of these genes to microbial ecological interactions with plants and algae has probbaly been underappreciated.
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Affiliation(s)
- William R Chase
- Department of Biology, Pennsylvania State University, University Park, PA, 16801, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA
| | - Jorge Rocha
- Department of Microbiology and Immunology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Daniel J Cosgrove
- Department of Biology, Pennsylvania State University, University Park, PA, 16801, USA
| | - Lori R Shapiro
- Department of Microbiology and Immunology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
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