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Gao L, Li Z, Xia C, Qu Y, Liu M, Yang P, Yu L, Song X. Combining manipulation of transcription factors and overexpression of the target genes to enhance lignocellulolytic enzyme production in Penicillium oxalicum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:100. [PMID: 28428823 PMCID: PMC5397729 DOI: 10.1186/s13068-017-0783-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/11/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Lignocellulolytic enzymes are the main enzymes to saccharify lignocellulose from renewable plant biomass in the bio-based economy. The production of these enzymes is transcriptionally regulated by multiple transcription factors. We previously engineered Penicillium oxalicum for improved cellulase production via manipulation of three genes in the cellulase expression regulatory network. However, the potential of combinational engineering of multiple regulators and their targets at protein abundance and activity levels has not been fully explored. RESULTS Here, we verified that a point mutation XlnRA871V in transcription factor XlnR enhanced the expression of lignocellulolytic enzymes, particularly hemicellulases, in P. oxalicum. Then, overexpression of XlnRA871V with a constitutive PDE_02864 promoter was combined with the overexpression of cellulase transcriptional activator ClrB and deletion of carbon catabolite repressor CreA. The resulted strain RE-7 showed 8.9- and 51.5-fold increased production of cellulase and xylanase relative to the starting strain M12, respectively. Further overexpression of two major cellulase genes cbh1-2 and eg1 enabled an additional 13.0% improvement of cellulase production. In addition, XlnRA871V led to decreased production of β-glucosidase and amylase, which could be attributed to the reduced transcription of corresponding enzyme-encoding genes. CONCLUSIONS The results illustrated that combinational manipulation of the involved transcription factors and their target genes was a viable strategy for efficient production of lignocellulolytic enzymes in filamentous fungi. The striking negative effect of XlnRA871V mutation on amylase production was also highlighted.
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Affiliation(s)
- Liwei Gao
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 Shandong China
| | - Zhonghai Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 Shandong China
- Department of Bioengineering, Qilu University of Technology, Jinan, 250353 Shandong China
| | - Chengqiang Xia
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 Shandong China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 Shandong China
- National Glycoengineering Research Center, Shandong University, Shan Da Nan Road 27, Jinan, Shandong 250100 China
| | - Meng Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 Shandong China
| | - Piao Yang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 Shandong China
| | - Lele Yu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 Shandong China
| | - Xin Song
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 Shandong China
- National Glycoengineering Research Center, Shandong University, Shan Da Nan Road 27, Jinan, Shandong 250100 China
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Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP. Regulators of plant biomass degradation in ascomycetous fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:152. [PMID: 28616076 PMCID: PMC5468973 DOI: 10.1186/s13068-017-0841-x] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/05/2023]
Abstract
Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Schuerg T, Prahl JP, Gabriel R, Harth S, Tachea F, Chen CS, Miller M, Masson F, He Q, Brown S, Mirshiaghi M, Liang L, Tom LM, Tanjore D, Sun N, Pray TR, Singer SW. Xylose induces cellulase production in Thermoascus aurantiacus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:271. [PMID: 29167701 PMCID: PMC5688616 DOI: 10.1186/s13068-017-0965-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/07/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Lignocellulosic biomass is an important resource for renewable production of biofuels and bioproducts. Enzymes that deconstruct this biomass are critical for the viability of biomass-based biofuel production processes. Current commercial enzyme mixtures have limited thermotolerance. Thermophilic fungi may provide enzyme mixtures with greater thermal stability leading to more robust processes. Understanding the induction of biomass-deconstructing enzymes in thermophilic fungi will provide the foundation for strategies to construct hyper-production strains. RESULTS Induction of cellulases using xylan was demonstrated during cultivation of the thermophilic fungus Thermoascus aurantiacus. Simulated fed-batch conditions with xylose induced comparable levels of cellulases. These fed-batch conditions were adapted to produce enzymes in 2 and 19 L bioreactors using xylose and xylose-rich hydrolysate from dilute acid pretreatment of corn stover. Enzymes from T. aurantiacus that were produced in the xylose-fed bioreactor demonstrated comparable performance in the saccharification of deacetylated, dilute acid-pretreated corn stover when compared to a commercial enzyme mixture at 50 °C. The T. aurantiacus enzymes retained this activity at of 60 °C while the commercial enzyme mixture was largely inactivated. CONCLUSIONS Xylose induces both cellulase and xylanase production in T. aurantiacus and was used to produce enzymes at up to the 19 L bioreactor scale. The demonstration of induction by xylose-rich hydrolysate and saccharification of deacetylated, dilute acid-pretreated corn stover suggests a scenario to couple biomass pretreatment with onsite enzyme production in a biorefinery. This work further demonstrates the potential for T. aurantiacus as a thermophilic platform for cellulase development.
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Affiliation(s)
- Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Chyi-Shin Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Matthew Miller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Fabrice Masson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Qian He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Sarah Brown
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Mona Mirshiaghi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ling Liang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Lauren M. Tom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ning Sun
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Todd R. Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
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Samal A, Craig JP, Coradetti ST, Benz JP, Eddy JA, Price ND, Glass NL. Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:225. [PMID: 28947916 PMCID: PMC5609067 DOI: 10.1186/s13068-017-0901-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/05/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plant biomass degradation by fungal-derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applications for degradation of plant cell wall polysaccharides. However, incomplete knowledge of biomolecular networks responsible for plant cell wall deconstruction impedes experimental efforts in this direction. RESULTS To expand this knowledge base, a detailed network of reactions important for deconstruction of plant cell wall polysaccharides into simple sugars was constructed for the filamentous fungus Neurospora crassa. To reconstruct this network, information was integrated from five heterogeneous data types: functional genomics, transcriptomics, proteomics, genetics, and biochemical characterizations. The combined information was encapsulated into a feature matrix and the evidence weighted to assign annotation confidence scores for each gene within the network. Comparative analyses of RNA-seq and ChIP-seq data shed light on the regulation of the plant cell wall degradation network, leading to a novel hypothesis for degradation of the hemicellulose mannan. The transcription factor CLR-2 was subsequently experimentally shown to play a key role in the mannan degradation pathway of N. crassa. CONCLUSIONS Here we built a network that serves as a scaffold for integration of diverse experimental datasets. This approach led to the elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi and a novel function for the transcription factor CLR-2. This expanding network will aid in efforts to rationally engineer industrially relevant hyper-production strains.
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Affiliation(s)
- Areejit Samal
- Institute for Systems Biology, Seattle, WA 98109 USA
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704 USA
- The Institute of Mathematical Sciences, Homi Bhabha National Institute, Chennai, 600113 India
- The Abdus Salam International Centre for Theoretical Physics, 34151 Trieste, Italy
| | - James P. Craig
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Samuel T. Coradetti
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - J. Philipp Benz
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704 USA
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - James A. Eddy
- Institute for Systems Biology, Seattle, WA 98109 USA
| | | | - N. Louise Glass
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
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Disruption of non-anchored cell wall protein NCW-1 promotes cellulase production by increasing cellobiose uptake in Neurospora crassa. Biotechnol Lett 2016; 39:545-551. [DOI: 10.1007/s10529-016-2274-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/20/2016] [Indexed: 12/16/2022]
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106
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Internalization of Heterologous Sugar Transporters by Endogenous α-Arrestins in the Yeast Saccharomyces cerevisiae. Appl Environ Microbiol 2016; 82:7074-7085. [PMID: 27694235 PMCID: PMC5118918 DOI: 10.1128/aem.02148-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/23/2016] [Indexed: 01/03/2023] Open
Abstract
When expressed in Saccharomyces cerevisiae using either of two constitutive yeast promoters (PGK1prom and CCW12prom), the transporters CDT-1 and CDT-2 from the filamentous fungus Neurospora crassa are able to catalyze, respectively, active transport and facilitated diffusion of cellobiose (and, for CDT-2, also xylan and its derivatives). In S. cerevisiae, endogenous permeases are removed from the plasma membrane by clathrin-mediated endocytosis and are marked for internalization through ubiquitinylation catalyzed by Rsp5, a HECT class ubiquitin:protein ligase (E3). Recruitment of Rsp5 to specific targets is mediated by a 14-member family of endocytic adaptor proteins, termed α-arrestins. Here we demonstrate that CDT-1 and CDT-2 are subject to α-arrestin-mediated endocytosis, that four α-arrestins (Rod1, Rog3, Aly1, and Aly2) are primarily responsible for this internalization, that the presence of the transport substrate promotes transporter endocytosis, and that, at least for CDT-2, residues located in its C-terminal cytosolic domain are necessary for its efficient endocytosis. Both α-arrestin-deficient cells expressing CDT-2 and otherwise wild-type cells expressing CDT-2 mutants unresponsive to α-arrestin-driven internalization exhibit an increased level of plasma membrane-localized transporter compared to that of wild-type cells, and they grow, utilize the transport substrate, and generate ethanol anaerobically better than control cells. IMPORTANCE Ethanolic fermentation of the breakdown products of plant biomass by budding yeast Saccharomyces cerevisiae remains an attractive biofuel source. To achieve this end, genes for heterologous sugar transporters and the requisite enzyme(s) for subsequent metabolism have been successfully expressed in this yeast. For one of the heterologous transporters examined in this study, we found that the amount of this protein residing in the plasma membrane was the rate-limiting factor for utilization of the cognate carbon source (cellobiose) and its conversion to ethanol.
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107
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Hernández‐Guzmán A, Flores‐Martínez A, Ponce‐Noyola P, Villagómez‐Castro JC. Purification and characterization of an extracellular β-glucosidase from Sporothrix schenckii. FEBS Open Bio 2016; 6:1067-1077. [PMID: 27833847 PMCID: PMC5095144 DOI: 10.1002/2211-5463.12108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/28/2016] [Accepted: 07/25/2016] [Indexed: 01/27/2023] Open
Abstract
An extracellular β-glucosidase (E.C. 3.2.1.21), induced by cellulose in the mycelial form of human pathogen fungus Sporothrix schenckii, was purified to homogeneity using hydroxyapatite (HAp) adsorption chromatography in batch and Sephacryl S200-HR size exclusion chromatography. The molecular mass of the purified enzyme was estimated to be 197 kDa by size exclusion chromatography with a subunit of 96.8 kDa determined by SDS/PAGE. The β-glucosidase exhibited optimum catalytic activity at pH 5.5/45 °C and was relatively stable for up to 24 h at 45 °C. Isoelectric focusing displayed an enzyme with a pI value of 4.0. Its activity was inhibited by Fe2+ but not by any other ions or chelating agents. Km and Vmax values of the purified enzyme were 0.012 mm and 2.56 nmol·min-1·mg-1, respectively, using 4-methylumbelliferyl β-D-glucopyranoside (4-MUG) as the substrate and 44.14 mm and 22.49 nmol·min-1·mg-1 when p-nitrophenyl β-D-glucopyranoside (p-NPG) was used. The purified β-glucosidase was active against cellobioside, laminarin, 4-MUG, and p-NPG and slightly active against 4-methylumbelliferyl β-D-cellobioside and p-nitrophenyl β-D-cellobioside but did not hydrolyze 4-methylumbelliferyl β-D-xyloside, 4-methylumbelliferyl β-D-galactopyranoside nor 4-methylumbelliferyl α-D-glucopyranoside. In addition, the enzyme showed transglycosylation activity when it was incubated along with different oligosaccharides. Whether the transglycosylation and cellulase activities function in vivo as a mechanism involved in the degradation of cellulolytic biomass in the saprophytic stage of S. schenckii remains to be determined.
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Affiliation(s)
- Alicia Hernández‐Guzmán
- Departamento de BiologíaDivisión de Ciencias Naturales y ExactasUniversidad de GuanajuatoMéxico
| | - Alberto Flores‐Martínez
- Departamento de BiologíaDivisión de Ciencias Naturales y ExactasUniversidad de GuanajuatoMéxico
| | - Patricia Ponce‐Noyola
- Departamento de BiologíaDivisión de Ciencias Naturales y ExactasUniversidad de GuanajuatoMéxico
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108
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Corrêa TLR, dos Santos LV, Pereira GAG. AA9 and AA10: from enigmatic to essential enzymes. Appl Microbiol Biotechnol 2016; 100:9-16. [PMID: 26476647 DOI: 10.1007/s00253-015-7040-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/20/2015] [Accepted: 09/24/2015] [Indexed: 12/15/2022]
Abstract
The lignocellulosic biomass, comprised mainly of cellulose, hemicellulose, and lignin, is a strong competitor for petroleum to obtain fuels and other products because of its renewable nature, low cost, and non-competitiveness with food production when obtained from agricultural waste. Due to its recalcitrance, lignocellulosic material requires an arsenal of enzymes for its deconstruction and the consequent release of fermentable sugars. In this context, enzymes currently classified as auxiliary activity 9 (AA9/formerly GH61) and 10 (AA10/formerly CBM 33) or lytic polysaccharide monooxygenases (LPMO) have emerged as cellulase boosting enzymes. AA9 and AA10 are the new paradigm for deconstruction of lignocellulosic biomass by enhancing the activity and decreasing the loading of classical enzymes to the reaction and, consequently, reducing costs of the hydrolysis step in the second-generation ethanol production chain. In view of that disclosed above, the goal of this work is to review experimental data that supports the relevance of AA9 and AA10 for the biomass deconstruction field.
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109
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Reilly MC, Magnuson JK, Baker SE. Approaches to understanding protein hypersecretion in fungi. FUNGAL BIOL REV 2016. [DOI: 10.1016/j.fbr.2016.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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110
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Brown NA, Ries LNA, Reis TF, Rajendran R, Corrêa dos Santos RA, Ramage G, Riaño-Pachón DM, Goldman GH. RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:145. [PMID: 27437031 PMCID: PMC4950808 DOI: 10.1186/s13068-016-0558-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/24/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Sugarcane is one of the world's most profitable crops. Waste steam-exploded sugarcane bagasse (SEB) is a cheap, abundant, and renewable lignocellulosic feedstock for the next-generation biofuels. In nature, fungi seldom exist as planktonic cells, similar to those found in the nutrient-rich environment created within an industrial fermenter. Instead, fungi predominantly form biofilms that allow them to thrive in hostile environments. RESULTS In turn, we adopted an RNA-sequencing approach to interrogate how the model fungus, Aspergillus nidulans, adapts to SEB, revealing the induction of carbon starvation responses and the lignocellulolytic machinery, in addition to morphological adaptations. Genetic analyses showed the importance of hydrophobins for growth on SEB. The major hydrophobin, RodA, was retained within the fungal biofilm on SEB fibres. The StuA transcription factor that regulates fungal morphology was up-regulated during growth on SEB and controlled hydrophobin gene induction. The absence of the RodA or DewC hydrophobins reduced biofilm formation. The loss of a RodA or a functional StuA reduced the retention of the hydrolytic enzymes within the vicinity of the fungus. Hence, hydrophobins promote biofilm formation on SEB, and may enhance lignocellulose utilisation via promoting a compact substrate-enzyme-fungus structure. CONCLUSION This novel study highlights the importance of hydrophobins to the formation of biofilms and the efficient deconstruction of lignocellulose.
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Affiliation(s)
- Neil Andrew Brown
- />Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Laure N. A. Ries
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila F. Reis
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Ranjith Rajendran
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, The University of Glasgow, Glasgow, UK
| | - Renato Augusto Corrêa dos Santos
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, SP CEP 13083-970 Brazil
| | - Gordon Ramage
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, The University of Glasgow, Glasgow, UK
| | - Diego Mauricio Riaño-Pachón
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, SP CEP 13083-970 Brazil
| | - Gustavo H. Goldman
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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Vu VV, Marletta MA. Starch-degrading polysaccharide monooxygenases. Cell Mol Life Sci 2016; 73:2809-19. [PMID: 27170366 PMCID: PMC11108391 DOI: 10.1007/s00018-016-2251-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 01/08/2023]
Abstract
Polysaccharide degradation by hydrolytic enzymes glycoside hydrolases (GHs) is well known. More recently, polysaccharide monooxygenases (PMOs, also known as lytic PMOs or LPMOs) were found to oxidatively degrade various polysaccharides via a copper-dependent hydroxylation. PMOs were previously thought to be either GHs or carbohydrate binding modules (CBMs), and have been re-classified in carbohydrate active enzymes (CAZY) database as auxiliary activity (AA) families. These enzymes include cellulose-active fungal PMOs (AA9, formerly GH61), chitin- and cellulose-active bacterial PMOs (AA10, formerly CBM33), and chitin-active fungal PMOs (AA11). These PMOs significantly boost the activity of GHs under industrially relevant conditions, and thus have great potential in the biomass-based biofuel industry. PMOs that act on starch are the latest PMOs discovered (AA13), which has expanded our perspectives in PMOs studies and starch degradation. Starch-active PMOs have many common structural features and biochemical properties of the PMO superfamily, yet differ from other PMO families in several important aspects. These differences likely correlate, at least in part, to the differences in primary and higher order structures of starch and cellulose, and chitin. In this review we will discuss the discovery, structural features, biochemical and biophysical properties, and possible biological functions of starch-active PMOs, as well as their potential application in the biofuel, food, and other starch-based industries. Important questions regarding various aspects of starch-active PMOs and possible economical driving force for their future studies will also be highlighted.
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Affiliation(s)
- Van V Vu
- NTT Hi-Tech Institute (NHTI), Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh City, Vietnam
| | - Michael A Marletta
- Department of Chemistry and Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720-3220, USA.
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Daly P, van Munster JM, Kokolski M, Sang F, Blythe MJ, Malla S, Velasco de Castro Oliveira J, Goldman GH, Archer DB. Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression. Fungal Genet Biol 2016; 102:4-21. [PMID: 27150814 PMCID: PMC5476202 DOI: 10.1016/j.fgb.2016.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/20/2016] [Accepted: 04/29/2016] [Indexed: 12/15/2022]
Abstract
First genome-wide transcriptional response in fungal mixed species straw cultures. In mixed cultures, rRNA abundance was used to predict RNA-seq read abundance. Subset of P. chrysogenum CAZy with mixed cultures increased abundance pattern. Lack of overall higher CAZy transcripts/activities due to inter-species antagonism. Induction of secondary metabolite producing gene clusters in mixed cultures.
Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw. Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement. This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study.
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Affiliation(s)
- Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Jolanda M van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Fei Sang
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Martin J Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Sunir Malla
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro 10000, Campinas, São Paulo 13083-100, Brazil.
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, São Paulo 14040-903, Brazil.
| | - David B Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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Kracher D, Scheiblbrandner S, Felice AKG, Breslmayr E, Preims M, Ludwicka K, Haltrich D, Eijsink VGH, Ludwig R. Extracellular electron transfer systems fuel cellulose oxidative degradation. Science 2016; 352:1098-101. [DOI: 10.1126/science.aaf3165] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/15/2016] [Indexed: 01/19/2023]
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114
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Schneider WDH, Gonçalves TA, Uchima CA, Couger MB, Prade R, Squina FM, Dillon AJP, Camassola M. Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:66. [PMID: 26989443 PMCID: PMC4794826 DOI: 10.1186/s13068-016-0476-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/02/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND The enzymatic degradation of lignocellulosic materials by fungal enzyme systems has been extensively studied due to its effectiveness in the liberation of fermentable sugars for bioethanol production. Recently, variants of the fungus Penicillium echinulatum have been described as a great producer of cellulases and considered a promising strain for the bioethanol industry. RESULTS Penicillium echinulatum, wild-type 2HH and its mutant strain S1M29, were grown on four different carbon sources: cellulose, sugar cane bagasse pretreated by steam explosion (SCB), glucose, and glycerol for 120 h. Samples collected at 24, 96, and 120 h were used for enzymatic measurement, and the 96-h one was also used for secretome analysis by 1D-PAGE LC-MS/MS. A total of 165 proteins were identified, and more than one-third of these proteins belong to CAZy families. Glycosyl hydrolases (GH) are the most abundant group, being represented in larger quantities by GH3, 5, 17, 43, and 72. Cellobiohydrolases, endoglucanases, β-glycosidases, xylanases, β-xylosidases, and mannanases were found, and in minor quantities, pectinases, ligninases, and amylases were also found. Swollenin and esterases were also identified. CONCLUSIONS Our study revealed differences in the two strains of P. echinulatum in several aspects in which the mutation improved the production of enzymes related to lignocellulosic biomass deconstruction. Considering the spectral counting analysis, the mutant strain S1M29 was more efficient in the production of enzymes involved in cellulose and hemicellulose degradation, despite having a nearly identical CAZy enzymatic repertoire. Moreover, S1M29 secretes more quantities of protein on SCB than on cellulose, relevant information when considering the production of cellulases using raw materials at low cost. Glucose, and especially glycerol, were used mainly for the production of amylases and ligninases.
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Affiliation(s)
- Willian Daniel Hahn Schneider
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
| | - Thiago Augusto Gonçalves
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
- />Department of Biochemistry, Institute of Biology, State University of Campinas (UNICAMP), Campinas, São Paulo Brazil
| | - Cristiane Akemi Uchima
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
| | - Matthew Brian Couger
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 South Innovation Way, Stillwater, OK 74078 USA
| | - Rolf Prade
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 South Innovation Way, Stillwater, OK 74078 USA
| | - Fabio Marcio Squina
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
| | - Aldo José Pinheiro Dillon
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
| | - Marli Camassola
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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Tang SL, Bubner P, Bauer S, Somerville CR. O-Glycan analysis of cellobiohydrolase I from Neurospora crassa. Glycobiology 2016; 26:670-7. [PMID: 26762173 DOI: 10.1093/glycob/cww004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/08/2016] [Indexed: 11/14/2022] Open
Abstract
We describe here the composition of the O-linked glycans on the Neurospora crassa cellobiohydrolase I (CBHI), which accounts for approximately 40% of the protein secreted by cells growing in the presence of cellulose. CBHI is O-glycosylated with six types of linear, and three types of branched, O-glycans containing approximately equal amounts of mannose and galactose. In addition to the classic fungal O-glycans with reducing end mannoses, we also identified reducing end galactoses which suggest the existence of a protein-O-galactosyltransferase in N. crassa Because of the excellent genetic resources available for N. crassa, the knowledge of the CBHI O-glycans may enable the future evaluation of the role of O-glycosylation on cellulase function and the development of directed O-glycan/cellulase engineering.
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Affiliation(s)
- Shu-Lun Tang
- Energy Biosciences Institute, University of California Berkeley, 2151 Berkeley Way MC 5230, Berkeley, CA 94720, USA
| | - Patricia Bubner
- Energy Biosciences Institute, University of California Berkeley, 2151 Berkeley Way MC 5230, Berkeley, CA 94720, USA
| | - Stefan Bauer
- Energy Biosciences Institute, University of California Berkeley, 2151 Berkeley Way MC 5230, Berkeley, CA 94720, USA
| | - Chris R Somerville
- Energy Biosciences Institute, University of California Berkeley, 2151 Berkeley Way MC 5230, Berkeley, CA 94720, USA
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117
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Zhang X, Qu Y, Qin Y. Expression and chromatin structures of cellulolytic enzyme gene regulated by heterochromatin protein 1. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:206. [PMID: 27729944 PMCID: PMC5048463 DOI: 10.1186/s13068-016-0624-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/24/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Heterochromatin protein 1 (HP1, homologue HepA in Penicillium oxalicum) binding is associated with a highly compact chromatin state accompanied by gene silencing or repression. HP1 loss leads to the derepression of gene expression. We investigated HepA roles in regulating cellulolytic enzyme gene expression, as an increasingly number of studies have suggested that cellulolytic enzyme gene expression is not only regulated by transcription factors, but is also affected by the chromatin status. RESULTS Among the genes that exhibited significant differences between the hepA deletion strain (ΔhepA) and the wild type (WT), most (95.0 %) were upregulated in ΔhepA compared with WT. The expression of the key transcription factor for cellulolytic enzyme gene (e.g., repressor CreA and activator ClrB) increased significantly. However, the deletion of hepA led to downregulation of prominent extracellular cellulolytic enzyme genes. Among the top 10 extracellular glycoside hydrolases (Amy15A, Amy13A, Cel7A/CBHI, Cel61A, Chi18A, Cel3A/BGLI, Xyn10A, Cel7B/EGI, Cel5B/EGII, and Cel6A/CBHII), in which secretion amount is from the highest to the tenth in P. oxalicum secretome, eight genes, including two amylase genes (amy15A and amy13A), all five cellulase genes (cel7A/cbh1, cel6A/cbh2, cel7B/eg1, cel5B/eg2, and cel3A/bgl1), and the cellulose-active LPMO gene (cel61A) expression were downregulated. Results of chromatin accessibility real-time PCR (CHART-PCR) showed that the chromatin of all three tested upstream regions opened specifically because of the deletion of hepA in the case of two prominent cellulase genes cel7A/cbh1 and cel7B/eg1. However, the open chromatin status did not occur along with the activation of cellulolytic enzyme gene expression. The overexpression of hepA upregulated the cellulolytic enzyme gene expression without chromatin modification. The overexpression of hepA remarkably activated the cellulolytic enzyme synthesis, not only in WT (~150 % filter paper activity (FPA) increase), but also in the industry strain RE-10 (~20-30 % FPA increase). CONCLUSIONS HepA is required for chromatin condensation of prominent cellulase genes. However, the opening of chromatin mediated by the deletion of hepA was not positively correlated with cellulolytic enzyme gene activation. HepA is actually a positive regulator for cellulolytic enzyme gene expression and could be a promising target for genetic modification to improve cellulolytic enzyme synthesis.
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Affiliation(s)
- Xiujun Zhang
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan, 250100 China
- Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, 250100 China
| | - Yinbo Qu
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan, 250100 China
| | - Yuqi Qin
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan, 250100 China
- Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, 250100 China
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118
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A novel proteomics sample preparation method for secretome analysis of Hypocrea jecorina growing on insoluble substrates. J Proteomics 2016; 131:104-112. [DOI: 10.1016/j.jprot.2015.10.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/21/2015] [Accepted: 10/12/2015] [Indexed: 11/23/2022]
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119
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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120
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A Neurospora crassa ÿ-glucosidase with potential for lignocellulose hydrolysis shows strong glucose tolerance and stimulation by glucose and xylose. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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121
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Pellegrin C, Morin E, Martin FM, Veneault-Fourrey C. Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins. Front Microbiol 2015; 6:1278. [PMID: 26635749 PMCID: PMC4649063 DOI: 10.3389/fmicb.2015.01278] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/31/2015] [Indexed: 12/20/2022] Open
Abstract
Fungi are major players in the carbon cycle in forest ecosystems due to the wide range of interactions they have with plants either through soil degradation processes by litter decayers or biotrophic interactions with pathogenic and ectomycorrhizal symbionts. Secretion of fungal proteins mediates these interactions by allowing the fungus to interact with its environment and/or host. Ectomycorrhizal (ECM) symbiosis independently appeared several times throughout evolution and involves approximately 80% of trees. Despite extensive physiological studies on ECM symbionts, little is known about the composition and specificities of their secretomes. In this study, we used a bioinformatics pipeline to predict and analyze the secretomes of 49 fungal species, including 11 ECM fungi, wood and soil decayers and pathogenic fungi to tackle the following questions: (1) Are there differences between the secretomes of saprophytic and ECM fungi? (2) Are small-secreted proteins (SSPs) more abundant in biotrophic fungi than in saprophytic fungi? and (3) Are there SSPs shared between ECM, saprotrophic and pathogenic fungi? We showed that the number of predicted secreted proteins is similar in the surveyed species, independently of their lifestyle. The secretome from ECM fungi is characterized by a restricted number of secreted CAZymes, but their repertoires of secreted proteases and lipases are similar to those of saprotrophic fungi. Focusing on SSPs, we showed that the secretome of ECM fungi is enriched in SSPs compared with other species. Most of the SSPs are coded by orphan genes with no known PFAM domain or similarities to known sequences in databases. Finally, based on the clustering analysis, we identified shared- and lifestyle-specific SSPs between saprotrophic and ECM fungi. The presence of SSPs is not limited to fungi interacting with living plants as the genome of saprotrophic fungi also code for numerous SSPs. ECM fungi shared lifestyle-specific SSPs likely involved in symbiosis that are good candidates for further functional analyses.
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Affiliation(s)
- Clement Pellegrin
- UMR 1136 Interactions Arbres/Microorganismes, Université de LorraineVandoeuvre-lès-Nancy, France
- UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Institut National de la Recherche Agronomique, INRA-NancyChampenoux, France
| | - Emmanuelle Morin
- UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Institut National de la Recherche Agronomique, INRA-NancyChampenoux, France
| | - Francis M. Martin
- UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Institut National de la Recherche Agronomique, INRA-NancyChampenoux, France
| | - Claire Veneault-Fourrey
- UMR 1136 Interactions Arbres/Microorganismes, Université de LorraineVandoeuvre-lès-Nancy, France
- UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Institut National de la Recherche Agronomique, INRA-NancyChampenoux, France
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122
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The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts. FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-015-0351-8] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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123
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Li Z, Yao G, Wu R, Gao L, Kan Q, Liu M, Yang P, Liu G, Qin Y, Song X, Zhong Y, Fang X, Qu Y. Synergistic and Dose-Controlled Regulation of Cellulase Gene Expression in Penicillium oxalicum. PLoS Genet 2015; 11:e1005509. [PMID: 26360497 PMCID: PMC4567317 DOI: 10.1371/journal.pgen.1005509] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 08/17/2015] [Indexed: 11/24/2022] Open
Abstract
Filamentous fungus Penicillium oxalicum produces diverse lignocellulolytic enzymes, which are regulated by the combinations of many transcription factors. Here, a single-gene disruptant library for 470 transcription factors was constructed and systematically screened for cellulase production. Twenty transcription factors (including ClrB, CreA, XlnR, Ace1, AmyR, and 15 unknown proteins) were identified to play putative roles in the activation or repression of cellulase synthesis. Most of these regulators have not been characterized in any fungi before. We identified the ClrB, CreA, XlnR, and AmyR transcription factors as critical dose-dependent regulators of cellulase expression, the core regulons of which were identified by analyzing several transcriptomes and/or secretomes. Synergistic and additive modes of combinatorial control of each cellulase gene by these regulatory factors were achieved, and cellulase expression was fine-tuned in a proper and controlled manner. With one of these targets, the expression of the major intracellular β-glucosidase Bgl2 was found to be dependent on ClrB. The Bgl2-deficient background resulted in a substantial gene activation by ClrB and proved to be closely correlated with the relief of repression mediated by CreA and AmyR during cellulase induction. Our results also signify that probing the synergistic and dose-controlled regulation mechanisms of cellulolytic regulators and using it for reconstruction of expression regulation network (RERN) may be a promising strategy for cellulolytic fungi to develop enzyme hyper-producers. Based on our data, ClrB was identified as focal point for the synergistic activation regulation of cellulase expression by integrating cellulolytic regulators and their target genes, which refined our understanding of transcriptional-regulatory network as a “seesaw model” in which the coordinated regulation of cellulolytic genes is established by counteracting activators and repressors. Cellulolytic fungi have evolved into sophisticated lignocellulolytic systems to adapt to their natural habitat. This trait is important for filamentous fungi, which are the main source of cellulases utilized to degrade lignocellulose to fermentable sugars. Penicillium oxalicum, which produces lignocellulolytic enzymes with more diverse components than Trichoderma reesei, has the capacity to secrete large amounts of cellulases. Meanwhile, cellulase expression is regulated by a complex network involved in many transcription factors in this organism. To better understand how cellulase genes are systematically regulated in P. oxalicum, we employed molecular genetics to uncover the cellulolytic transcription factors on a genome-wide scale. We discovered the synergistic and tunable regulation of cellulase expression by integrating cellulolytic regulators and their target genes, which refined our understanding of transcriptional-regulatory network as a “seesaw model” in which the coordinated regulation of cellulolytic genes is established by counteracting activators and repressors.
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Affiliation(s)
- Zhonghai Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Guangshan Yao
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Ruimei Wu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Liwei Gao
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Qinbiao Kan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Meng Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Piao Yang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Yuqi Qin
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong, China
| | - Xin Song
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong, China
- * E-mail:
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Blackman LM, Cullerne DP, Torreña P, Taylor J, Hardham AR. RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica. PLoS One 2015; 10:e0136899. [PMID: 26332397 PMCID: PMC4558045 DOI: 10.1371/journal.pone.0136899] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.
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Affiliation(s)
- Leila M. Blackman
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
- * E-mail:
| | - Darren P. Cullerne
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
- Agriculture Flagship, CSIRO, Canberra ACT, Australia
| | - Pernelyn Torreña
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
| | - Jen Taylor
- Agriculture Flagship, CSIRO, Canberra ACT, Australia
| | - Adrienne R. Hardham
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
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Pei X, Fan F, Lin L, Chen Y, Sun W, Zhang S, Tian C. Involvement of the adaptor protein 3 complex in lignocellulase secretion in Neurospora crassa revealed by comparative genomic screening. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:124. [PMID: 26300971 PMCID: PMC4545925 DOI: 10.1186/s13068-015-0302-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/30/2015] [Indexed: 06/02/2023]
Abstract
BACKGROUND Lignocellulase hypersecretion has been achieved in industrial fungal workhorses such as Trichoderma reesei, but the underlying mechanism associated with this process is not well understood. Although previous comparative genomic studies have revealed that the mutagenic T. reesei strain RUT-C30 harbors hundreds of mutations compared with its parental strain QM6a, how these mutations actually contribute to the hypersecretion phenotype remains to be elucidated. RESULTS In this study, we systematically screened gene knockout (KO) mutants in the cellulolytic fungus Neurospora crassa, which contains orthologs of potentially defective T. reesei RUT-C30 mutated genes. Of the 86 deletion mutants screened in N. crassa, 12 exhibited lignocellulase production more than 25% higher than in the wild-type (WT) strain and 4 showed nearly 25% lower secretion. We observed that the deletion of Ncap3m (NCU03998), which encodes the μ subunit of the adaptor protein 3 (AP-3) complex in N. crassa, led to the most significant increase in lignocellulase secretion under both Avicel and xylan culture conditions. Moreover, strains lacking the β subunit of the AP-3 complex, encoded by Ncap3b (NCU06569), had a similar phenotype to ΔNcap3m, suggesting that the AP-3 complex is involved in lignocellulase secretion in N. crassa. We also found that the transcriptional abundance of major lignocellulase genes in ΔNcap3m was maintained at a relatively higher level during the late stage of fermentation compared with the WT, which might add to the hypersecretion phenotype. Finally, we found that importation of the T. reesei ap3m ortholog Trap3m into ΔNcap3m can genetically restore secretion of lignocellulases to normal levels, which suggests that the effect of the AP-3 complex on lignocellulase secretion is conserved in cellulolytic ascomycetes. CONCLUSIONS Using the model cellulolytic fungus N. crassa, we explored potential hypersecretion-related mutations in T. reesei strain RUT-C30. Through systematic genetic screening of 86 corresponding orthologous KO mutants in N. crassa, we identified several genes, particularly those encoding the AP-3 complex that contribute to lignocellulase secretion. These findings will be useful for strain improvement in future lignocellulase and biomass-based chemical production.
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Affiliation(s)
- Xue Pei
- />College of Plant Sciences, Jilin University, Changchun, 130062 China
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Feiyu Fan
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Liangcai Lin
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yong Chen
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Shihong Zhang
- />College of Plant Sciences, Jilin University, Changchun, 130062 China
| | - Chaoguang Tian
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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126
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Li X, Chomvong K, Yu VY, Liang JM, Lin Y, Cate JHD. Cellobionic acid utilization: from Neurospora crassa to Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:120. [PMID: 26279678 PMCID: PMC4537572 DOI: 10.1186/s13068-015-0303-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/31/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Economical production of fuels and chemicals from plant biomass requires the efficient use of sugars derived from the plant cell wall. Neurospora crassa, a model lignocellulosic degrading fungus, is capable of breaking down the complex structure of the plant cell wall. In addition to cellulases and hemicellulases, N. crassa secretes lytic polysaccharide monooxygenases (LPMOs), which cleave cellulose by generating oxidized sugars-particularly aldonic acids. However, the strategies N. crassa employs to utilize these sugars are unknown. RESULTS We identified an aldonic acid utilization pathway in N. crassa, comprised of an extracellular hydrolase (NCU08755), cellobionic acid transporter (CBT-1, NCU05853) and cellobionic acid phosphorylase (CAP, NCU09425). Extracellular cellobionic acid could be imported directly by CBT-1 or cleaved to gluconic acid and glucose by a β-glucosidase (NCU08755) outside the cells. Intracellular cellobionic acid was further cleaved to glucose 1-phosphate and gluconic acid by CAP. However, it remains unclear how N. crassa utilizes extracellular gluconic acid. The aldonic acid pathway was successfully implemented in Saccharomyces cerevisiae when N. crassa gluconokinase was co-expressed, resulting in cellobionic acid consumption in both aerobic and anaerobic conditions. CONCLUSIONS We successfully identified a branched aldonic acid utilization pathway in N. crassa and transferred its essential components into S. cerevisiae, a robust industrial microorganism.
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Affiliation(s)
- Xin Li
- />Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Kulika Chomvong
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Vivian Yaci Yu
- />Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Julie M Liang
- />Department of Chemistry, University of California, Berkeley, CA USA
| | - Yuping Lin
- />Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Jamie H D Cate
- />Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
- />Department of Chemistry, University of California, Berkeley, CA USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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127
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Tan TC, Kracher D, Gandini R, Sygmund C, Kittl R, Haltrich D, Hällberg BM, Ludwig R, Divne C. Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation. Nat Commun 2015; 6:7542. [PMID: 26151670 PMCID: PMC4507011 DOI: 10.1038/ncomms8542] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/19/2015] [Indexed: 02/06/2023] Open
Abstract
A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-binding cytochrome (CYT) connected via a flexible linker to a flavin-dependent dehydrogenase (DH). Electrons are generated from cellobiose oxidation catalysed by DH and shuttled via CYT to LPMO. Here we present structural analyses that provide a comprehensive picture of CDH conformers, which govern the electron transfer between redox centres. Using structure-based site-directed mutagenesis, rapid kinetics analysis and molecular docking, we demonstrate that flavin-to-haem interdomain electron transfer (IET) is enabled by a haem propionate group and that rapid IET requires a closed CDH state in which the propionate is tightly enfolded by DH. Following haem reduction, CYT reduces LPMO to initiate oxygen activation at the copper centre and subsequent cellulose depolymerization.
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Affiliation(s)
- Tien-Chye Tan
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
| | - Daniel Kracher
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Rosaria Gandini
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
| | - Christoph Sygmund
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Roman Kittl
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - B. Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm S-17177, Sweden
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22603, Germany; and Centre for Structural Systems Biology (CSSB), DESY-Campus, Hamburg 22603, Germany
| | - Roland Ludwig
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Christina Divne
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
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128
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Montenegro-Montero A, Goity A, Larrondo LF. The bZIP Transcription Factor HAC-1 Is Involved in the Unfolded Protein Response and Is Necessary for Growth on Cellulose in Neurospora crassa. PLoS One 2015; 10:e0131415. [PMID: 26132395 PMCID: PMC4488935 DOI: 10.1371/journal.pone.0131415] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/02/2015] [Indexed: 12/15/2022] Open
Abstract
High protein secretion capacity in filamentous fungi requires an extremely efficient system for protein synthesis, folding and transport. When the folding capacity of the endoplasmic reticulum (ER) is exceeded, a pathway known as the unfolded protein response (UPR) is triggered, allowing cells to mitigate and cope with this stress. In yeast, this pathway relies on the transcription factor Hac1, which mediates the up-regulation of several genes required under these stressful conditions. In this work, we identified and characterized the ortholog of the yeast HAC1 gene in the filamentous fungus Neurospora crassa. We show that its mRNA undergoes an ER stress-dependent splicing reaction, which in N. crassa removes a 23 nt intron and leads to a change in the open reading frame. By disrupting the N. crassa hac-1 gene, we determined it to be crucial for activating UPR and for proper growth in the presence of ER stress-inducing chemical agents. Neurospora is naturally found growing on dead plant material, composed primarily by lignocellulose, and is a model organism for the study of plant cell wall deconstruction. Notably, we found that growth on cellulose, a substrate that requires secretion of numerous enzymes, imposes major demands on ER function and is dramatically impaired in the absence of hac-1, thus broadening the range of physiological functions of the UPR in filamentous fungi. Growth on hemicellulose however, another carbon source that necessitates the secretion of various enzymes for its deconstruction, is not impaired in the mutant nor is the amount of proteins secreted on this substrate, suggesting that secretion, as a whole, is unaltered in the absence of hac-1. The characterization of this signaling pathway in N. crassa will help in the study of plant cell wall deconstruction by fungi and its manipulation may result in important industrial biotechnological applications.
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Affiliation(s)
- Alejandro Montenegro-Montero
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandra Goity
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F. Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail:
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129
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Miao Y, Liu D, Li G, Li P, Xu Y, Shen Q, Zhang R. Genome-wide transcriptomic analysis of a superior biomass-degrading strain of A. fumigatus revealed active lignocellulose-degrading genes. BMC Genomics 2015; 16:459. [PMID: 26076650 PMCID: PMC4469458 DOI: 10.1186/s12864-015-1658-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/28/2015] [Indexed: 12/14/2022] Open
Abstract
Background Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability. Results The 29-million base-pair genome of Z5 was sequenced and 9540 protein-coding genes were predicted and annotated. Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases and pectinases involved in lignocellulosic biomass degradation. Transcriptional responses of A. fumigatus Z5 induced by sucrose, oat spelt xylan, Avicel PH-101 and rice straw were compared. There were 444, 1711 and 1386 significantly differently expressed genes in xylan, cellulose and rice straw, respectively, when compared to sucrose as a control condition. Conclusions Combined analysis of the genomic and transcriptomic data provides a comprehensive understanding of the responding mechanisms to the most abundant natural polysaccharides in A. fumigatus. This study provides a basis for further analysis of genes shown to be highly induced in the presence of polysaccharide substrates and also the information which could prove useful for biomass degradation and heterologous protein expression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1658-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youzhi Miao
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China.
| | - Dongyang Liu
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China.
| | - Guangqi Li
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China.
| | - Pan Li
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China.
| | - Yangchun Xu
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China.
| | - Qirong Shen
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China.
| | - Ruifu Zhang
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China. .,Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P.R. China.
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130
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Abstract
Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance-β-glucan synthesis, trehalose production, and cold-induced RNA helicases-were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter-lignin peroxidases, cellobiohydrolases, and crystalline cellulases-were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.
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Affiliation(s)
- Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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131
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Kim IJ, Nam KH, Yun EJ, Kim S, Youn HJ, Lee HJ, Choi IG, Kim KH. Optimization of synergism of a recombinant auxiliary activity 9 from Chaetomium globosum with cellulase in cellulose hydrolysis. Appl Microbiol Biotechnol 2015; 99:8537-47. [PMID: 25936375 PMCID: PMC4768223 DOI: 10.1007/s00253-015-6592-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/14/2015] [Accepted: 04/01/2015] [Indexed: 01/16/2023]
Abstract
Auxiliary activity family 9 (AA9, formerly known as glycoside hydrolase family 61 or polysaccharide monooxygenase) is a group of fungal proteins that were recently found to have a significant synergism with cellulase in cellulose hydrolysis via the oxidative cleavage of glycosidic bonds of cellulose chains. In this study, we report the active expression of a recombinant fungal AA9 from Chaetomium globosum (CgAA9) in a bacterial host, Escherichia coli, and the optimization of its synergistic activity in cellulose hydrolysis by using cellulase. The recombinant CgAA9 (0.9 mg/g cellulose) exhibited 1.7-fold synergism in the hydrolysis of Avicel when incubated with 0.9 filter paper units of Celluclast 1.5 L/g cellulose. The first study of the active expression of AA9 using a bacterial host and its synergistic optimization could be useful for the industrial application of AA9 for the saccharification of lignocellulose.
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Affiliation(s)
- In Jung Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Ki Hyun Nam
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Eun Ju Yun
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Sooah Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Hak Jin Youn
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Hee Jin Lee
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea.
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Nair RA, Geethu C, Sangwan A, Pillai PP. Sequence and Bioinformatic Analysis of Family 1 Glycoside Hydrolase (GH) 1 Gene from the Oomycete Pythium myriotylum Drechsler. Appl Biochem Biotechnol 2015; 176:772-81. [PMID: 25877398 DOI: 10.1007/s12010-015-1610-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 04/06/2015] [Indexed: 11/30/2022]
Abstract
The oomycetous phytopathogen Pythium myriotylum secretes cellulases for growth/nutrition of the necrotroph. Cellulases are multi-enzyme system classified into different glycoside hydrolase (GH) families. The present study deals with identification and characterization of GH gene sequence from P. myriotylum by a PCR strategy using consensus primers. Cloning of the full-length gene sequence using genome walker strategy resulted in identification of 1230-bp P. myriotylum GH gene sequence, designated as PmGH1. Analysis revealed that PmGH1 encodes a predicted cytoplasmic 421 amino acid protein with an apparent molecular weight of 46.77 kDa and a theoretical pI of 8.11. Tertiary structure of the deduced amino acid sequence showed typical (α/β)8 barrel folding of family 1 GHs. Sequence characterization of PmGH1 identified the conserved active site residues, viz., Glu 181 and Glu 399, that function as acid-base catalyst and catalytically active nucleophile, respectively. Binding sites for N-acetyl-D-glucosamine (NAG) were revealed in the PmGH1 3D structure with Glu181 and Glu399 positioned on either side to form a catalytic pair. Phylogenetic analysis indicated a closer affiliation of PmGH1 with sequences of GH1 family. Results presented are first attempts providing novel insights into the evolutionary and functional perspectives of the identified P. myriotylum GH.
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Affiliation(s)
- R Aswati Nair
- School of Biotechnology, National Institute of Technology Calicut (NITC), Calicut, Kerala, India,
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133
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Fan F, Ma G, Li J, Liu Q, Benz JP, Tian C, Ma Y. Genome-wide analysis of the endoplasmic reticulum stress response during lignocellulase production in Neurospora crassa. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:66. [PMID: 25883682 PMCID: PMC4399147 DOI: 10.1186/s13068-015-0248-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/27/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lignocellulolytic fungal cells suffer endoplasmic reticulum (ER) stress during lignocellulase synthesis; however, an understanding of this integrated process on a genome-wide scale remains poor. Here, we undertook a systematic investigation of this process in Neurospora crassa (N. crassa) using transcriptomic analysis coupled with genetic screens. RESULTS A set of 766 genes was identified as the ER stress response targets (ESRTs) in N. crassa under cellulose utilization conditions. Among these, the expression of 223 and 186 genes showed dependence on IRE-1 and HAC-1, respectively. A total of 527 available mutants for ESRT genes were screened, 249 of which exhibited ER stress susceptibility, including 100 genes with unknown function. Disruption of ire-1 or hac-1 in N. crassa did not affect transcriptional induction of lignocellulase genes by cellulose but severely affected secretion of the corresponding enzymes. A global investigation of transcription factors (TFs) discovered three novel regulators (RES-1, RES-2, RRG-2) involved in lignocellulase secretion. Production of lignocellulases in Δres-1 increased by more than 30% in comparison to wild type (WT), while secretion decreased by nearly 30% in strains Δres-2 and Δrrg-2. Transcriptional profiling of the three TF mutants suggests they are deeply involved in lignocellulase secretion and ER stress response. CONCLUSIONS Here, we determined the transcriptional scope of the ER stress response during lignocellulase synthesis in the model cellulolytic fungus N. crassa. Through genome-wide mutant screening and analysis, dozens of novel genes were discovered to be involved in the process. The findings of this work will be useful for strain improvement to facilitate lignocellulase and biomass-based chemical production.
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Affiliation(s)
- Feiyu Fan
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
- />University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049 China
| | - Guoli Ma
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
- />University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049 China
| | - Jingen Li
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
- />University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049 China
| | - Qian Liu
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
| | - Johan Philipp Benz
- />Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - Chaoguang Tian
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
| | - Yanhe Ma
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
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Functional Analysis of Two l-Arabinose Transporters from Filamentous Fungi Reveals Promising Characteristics for Improved Pentose Utilization in Saccharomyces cerevisiae. Appl Environ Microbiol 2015; 81:4062-70. [PMID: 25841015 DOI: 10.1128/aem.00165-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/31/2015] [Indexed: 11/20/2022] Open
Abstract
Limited uptake is one of the bottlenecks for l-arabinose fermentation from lignocellulosic hydrolysates in engineered Saccharomyces cerevisiae. This study characterized two novel l-arabinose transporters, LAT-1 from Neurospora crassa and MtLAT-1 from Myceliophthora thermophila. Although the two proteins share high identity (about 83%), they display different substrate specificities. Sugar transport assays using the S. cerevisiae strain EBY.VW4000 indicated that LAT-1 accepts a broad substrate spectrum. In contrast, MtLAT-1 appeared much more specific for l-arabinose. Determination of the kinetic properties of both transporters revealed that the Km values of LAT-1 and MtLAT-1 for l-arabinose were 58.12 ± 4.06 mM and 29.39 ± 3.60 mM, respectively, with corresponding Vmax values of 116.7 ± 3.0 mmol/h/g dry cell weight (DCW) and 10.29 ± 0.35 mmol/h/g DCW, respectively. In addition, both transporters were found to use a proton-coupled symport mechanism and showed only partial inhibition by d-glucose during l-arabinose uptake. Moreover, LAT-1 and MtLAT-1 were expressed in the S. cerevisiae strain BSW2AP containing an l-arabinose metabolic pathway. Both recombinant strains exhibited much faster l-arabinose utilization, greater biomass accumulation, and higher ethanol production than the control strain. In conclusion, because of higher maximum velocities and reduced inhibition by d-glucose, the genes for the two characterized transporters are promising targets for improved l-arabinose utilization and fermentation in S. cerevisiae.
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135
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Beeson WT, Vu VV, Span EA, Phillips CM, Marletta MA. Cellulose degradation by polysaccharide monooxygenases. Annu Rev Biochem 2015; 84:923-46. [PMID: 25784051 DOI: 10.1146/annurev-biochem-060614-034439] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polysaccharide monooxygenases (PMOs), also known as lytic PMOs (LPMOs), enhance the depolymerization of recalcitrant polysaccharides by hydrolytic enzymes and are found in the majority of cellulolytic fungi and actinomycete bacteria. For more than a decade, PMOs were incorrectly annotated as family 61 glycoside hydrolases (GH61s) or family 33 carbohydrate-binding modules (CBM33s). PMOs have an unusual surface-exposed active site with a tightly bound Cu(II) ion that catalyzes the regioselective hydroxylation of crystalline cellulose, leading to glycosidic bond cleavage. The genomes of some cellulolytic fungi contain more than 20 genes encoding cellulose-active PMOs, suggesting a diversity of biological activities. PMOs show great promise in reducing the cost of conversion of lignocellulosic biomass to fermentable sugars; however, many questions remain about their reaction mechanism and biological function. This review addresses, in depth, the structural and mechanistic aspects of oxidative depolymerization of cellulose by PMOs and considers their biological function and phylogenetic diversity.
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Affiliation(s)
- William T Beeson
- Department of Chemistry, University of California, Berkeley, California 94720
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136
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Bianco L, Perrotta G. Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis. Int J Mol Sci 2015; 16:5803-29. [PMID: 25775160 PMCID: PMC4394507 DOI: 10.3390/ijms16035803] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/17/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022] Open
Abstract
Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.
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Affiliation(s)
- Linda Bianco
- UTTRI-GENER Genetics and Genomics for Energy and Environment Laboratory-ENEA TRISAIA Research Center, 75025 Rotondella (Matera), Italy.
| | - Gaetano Perrotta
- UTTRI-GENER Genetics and Genomics for Energy and Environment Laboratory-ENEA TRISAIA Research Center, 75025 Rotondella (Matera), Italy.
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137
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Shrestha P, Ibáñez AB, Bauer S, Glassman SI, Szaro TM, Bruns TD, Taylor JW. Fungi isolated from Miscanthus and sugarcane: biomass conversion, fungal enzymes, and hydrolysis of plant cell wall polymers. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:38. [PMID: 25784958 PMCID: PMC4362644 DOI: 10.1186/s13068-015-0221-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/04/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Biofuel use is one of many means of addressing global change caused by anthropogenic release of fossil fuel carbon dioxide into Earth's atmosphere. To make a meaningful reduction in fossil fuel use, bioethanol must be produced from the entire plant rather than only its starch or sugars. Enzymes produced by fungi constitute a significant percentage of the cost of bioethanol production from non-starch (i.e., lignocellulosic) components of energy crops and agricultural residues. We, and others, have reasoned that fungi that naturally deconstruct plant walls may provide the best enzymes for bioconversion of energy crops. RESULTS Previously, we have reported on the isolation of 106 fungi from decaying leaves of Miscanthus and sugarcane (Appl Environ Microbiol 77:5490-504, 2011). Here, we thoroughly analyze 30 of these fungi including those most often found on decaying leaves and stems of these plants, as well as four fungi chosen because they are well-studied for their plant cell wall deconstructing enzymes, for wood decay, or for genetic regulation of plant cell wall deconstruction. We extend our analysis to assess not only their ability over an 8-week period to bioconvert Miscanthus cell walls but also their ability to secrete total protein, to secrete enzymes with the activities of xylanases, exocellulases, endocellulases, and beta-glucosidases, and to remove specific parts of Miscanthus cell walls, that is, glucan, xylan, arabinan, and lignin. CONCLUSION This study of fungi that bioconvert energy crops is significant because 30 fungi were studied, because the fungi were isolated from decaying energy grasses, because enzyme activity and removal of plant cell wall components were recorded in addition to biomass conversion, and because the study period was 2 months. Each of these factors make our study the most thorough to date, and we discovered fungi that are significantly superior on all counts to the most widely used, industrial bioconversion fungus, Trichoderma reesei. Many of the best fungi that we found are in taxonomic groups that have not been exploited for industrial bioconversion and the cultures are available from the Centraalbureau voor Schimmelcultures in Utrecht, Netherlands, for all to use.
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Affiliation(s)
- Prachand Shrestha
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - Ana B Ibáñez
- />Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Stefan Bauer
- />Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Sydney I Glassman
- />Department of Environmental Science Policy and Management, University of California, Berkeley, CA 94720 USA
| | - Timothy M Szaro
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - Thomas D Bruns
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - John W Taylor
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
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138
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Sancar C, Sancar G, Ha N, Cesbron F, Brunner M. Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora. BMC Biol 2015; 13:17. [PMID: 25762222 PMCID: PMC4381671 DOI: 10.1186/s12915-015-0126-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/03/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Circadian clocks control rhythmic expression of a large number of genes in coordination with the 24 hour day-night cycle. The mechanisms generating circadian rhythms, their amplitude and circadian phase are dependent on a transcriptional network of immense complexity. Moreover, the contribution of post-transcriptional mechanisms in generating rhythms in RNA abundance is not known. RESULTS Here, we analyzed the clock-controlled transcriptome of Neurospora crassa together with temporal profiles of elongating RNA polymerase II. Our data indicate that transcription contributes to the rhythmic expression of the vast majority of clock-controlled genes (ccgs) in Neurospora. The ccgs accumulate in two main clusters with peak transcription and expression levels either at dawn or dusk. Dawn-phased genes are predominantly involved in catabolic and dusk-phased genes in anabolic processes, indicating a clock-controlled temporal separation of the physiology of Neurospora. Genes whose expression is strongly dependent on the core circadian activator WCC fall mainly into the dawn-phased cluster while rhythmic genes regulated by the glucose-dependent repressor CSP1 fall predominantly into the dusk-phased cluster. Surprisingly, the number of rhythmic transcripts increases about twofold in the absence of CSP1, indicating that rhythmic expression of many genes is attenuated by the activity of CSP1. CONCLUSIONS The data indicate that the vast majority of transcript rhythms in Neurospora are generated by dawn and dusk specific transcription. Our observations suggest a substantial plasticity of the circadian transcriptome with respect to the number of rhythmic genes as well as amplitude and phase of the expression rhythms and emphasize a major role of the circadian clock in the temporal organization of metabolism and physiology.
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Affiliation(s)
- Cigdem Sancar
- Heidelberg University Biochemistry Center, Heidelberg, Germany.
| | - Gencer Sancar
- Heidelberg University Biochemistry Center, Heidelberg, Germany.
| | - Nati Ha
- Heidelberg University Biochemistry Center, Heidelberg, Germany.
| | | | - Michael Brunner
- Heidelberg University Biochemistry Center, Heidelberg, Germany. .,University of Heidelberg Biochemistry Center, Im Neuenheimer Feld 328, Heidelberg, D-69120, Germany.
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139
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O'Neill EC, Field RA. Enzymatic synthesis using glycoside phosphorylases. Carbohydr Res 2015; 403:23-37. [PMID: 25060838 PMCID: PMC4336185 DOI: 10.1016/j.carres.2014.06.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 05/29/2014] [Accepted: 06/09/2014] [Indexed: 01/10/2023]
Abstract
Carbohydrate phosphorylases are readily accessible but under-explored catalysts for glycoside synthesis. Their use of accessible and relatively stable sugar phosphates as donor substrates underlies their potential. A wide range of these enzymes has been reported of late, displaying a range of preferences for sugar donors, acceptors and glycosidic linkages. This has allowed this class of enzymes to be used in the synthesis of diverse carbohydrate structures, including at the industrial scale. As more phosphorylase enzymes are discovered, access to further difficult to synthesise glycosides will be enabled. Herein we review reported phosphorylase enzymes and the glycoside products that they have been used to synthesise.
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Affiliation(s)
- Ellis C O'Neill
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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140
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Li X, Yu VY, Lin Y, Chomvong K, Estrela R, Park A, Liang JM, Znameroski EA, Feehan J, Kim SR, Jin YS, Glass NL, Cate JHD. Expanding xylose metabolism in yeast for plant cell wall conversion to biofuels. eLife 2015; 4. [PMID: 25647728 PMCID: PMC4338637 DOI: 10.7554/elife.05896] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/02/2015] [Indexed: 12/18/2022] Open
Abstract
Sustainable biofuel production from renewable biomass will require the efficient and complete use of all abundant sugars in the plant cell wall. Using the cellulolytic fungus Neurospora crassa as a model, we identified a xylodextrin transport and consumption pathway required for its growth on hemicellulose. Reconstitution of this xylodextrin utilization pathway in Saccharomyces cerevisiae revealed that fungal xylose reductases act as xylodextrin reductases, producing xylosyl-xylitol oligomers as metabolic intermediates. These xylosyl-xylitol intermediates are generated by diverse fungi and bacteria, indicating that xylodextrin reduction is widespread in nature. Xylodextrins and xylosyl-xylitol oligomers are then hydrolyzed by two hydrolases to generate intracellular xylose and xylitol. Xylodextrin consumption using a xylodextrin transporter, xylodextrin reductases and tandem intracellular hydrolases in cofermentations with sucrose and glucose greatly expands the capacity of yeast to use plant cell wall-derived sugars and has the potential to increase the efficiency of both first-generation and next-generation biofuel production. DOI:http://dx.doi.org/10.7554/eLife.05896.001 Plants can be used to make ‘biofuels’, which are more sustainable alternatives to traditional fuels made from petroleum. Unfortunately, most biofuels are currently made from simple sugars or starch extracted from parts of plants that we also use for food, such as the grains of cereal crops. Making biofuels from the parts of the plant that are not used for food—for example, the stems or leaves—would enable us to avoid a trade-off between food and fuel production. However, most of the sugars in these parts of the plant are locked away in the form of large, complex carbohydrates called cellulose and hemicellulose, which form the rigid cell wall surrounding each plant cell. Currently, the industrial processes that can be used to make biofuels from plant cell walls are expensive and use a lot of energy. They involve heating or chemically treating the plant material to release the cellulose and hemicellulose. Then, large quantities of enzymes are added to break these carbohydrates down into simple sugars that can then be converted into alcohol (a biofuel) by yeast. Fungi may be able to provide us with a better solution. Many species are able to grow on plants because they can break down cellulose and hemicellulose into simple sugars they can use for energy. If the genes involved in this process could be identified and inserted into yeast it may provide a new, cheaper method to make biofuels from plant cell walls. To address this challenge, Li et al. studied how the fungus Neurospora crassa breaks down hemicellulose. This study identified a protein that can transport molecules of xylodextrin—which is found in hemicellulose—into the cells of the fungus, and two enzymes that break down the xylodextrin to make simple sugars, using a previously unknown chemical intermediate. When Li et al. inserted the genes that make the transport protein and the enzymes into yeast, the yeast were able to use plant cell wall material to make simple sugars and convert these to alcohol. The yeast used more of the xylodextrin when they were grown with an additional source of energy, such as the sugars glucose or sucrose. Li et al.'s findings suggest that giving yeast the ability to break down hemicellulose has the potential to improve the efficiency of biofuel production. The next challenge will be to improve the process so that the yeast can convert the xylodextrin and simple sugars more rapidly. DOI:http://dx.doi.org/10.7554/eLife.05896.002
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Affiliation(s)
- Xin Li
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Vivian Yaci Yu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Yuping Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Kulika Chomvong
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Raíssa Estrela
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Annsea Park
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Julie M Liang
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Elizabeth A Znameroski
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Joanna Feehan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Soo Rin Kim
- Institute for Genomic Biology, University of Illinois, Urbana, United States
| | - Yong-Su Jin
- Institute for Genomic Biology, University of Illinois, Urbana, United States
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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Wang B, Cai P, Sun W, Li J, Tian C, Ma Y. A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:21. [PMID: 25691917 PMCID: PMC4330645 DOI: 10.1186/s13068-015-0208-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/20/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND Crop residue is an abundant, low-cost plant biomass material available worldwide for use in the microbial production of enzymes, biofuels, and valuable chemicals. However, the diverse chemical composition and complex structure of crop residues are more challenging for efficient degradation by microbes than are homogeneous polysaccharides. In this study, the transcriptional responses of Neurospora crassa to various plant straws were analyzed using RNA-Seq, and novel beneficial factors for biomass-induced enzyme production were evaluated. RESULTS Comparative transcriptional profiling of N. crassa grown on five major crop straws of China (barley, corn, rice, soybean, and wheat straws) revealed a highly overlapping group of 430 genes, the biomass commonly induced core set (BICS). A large proportion of induced carbohydrate-active enzyme (CAZy) genes (82 out of 113) were also conserved across the five plant straws. Excluding 178 genes within the BICS that were also upregulated under no-carbon conditions, the remaining 252 genes were defined as the biomass regulon (BR). Interestingly, 88 genes were only induced by plant biomass and not by three individual polysaccharides (Avicel, xylan, and pectin); these were denoted as the biomass unique set (BUS). Deletion of one BUS gene, the transcriptional regulator rca-1, significantly improved lignocellulase production using plant biomass as the sole carbon source, possibly functioning via de-repression of the regulator clr-2. Thus, this result suggests that rca-1 is a potential engineering target for biorefineries, especially for plant biomass direct microbial conversion processes. CONCLUSIONS Transcriptional profiling revealed a large core response to different sources of plant biomass in N. crassa. The sporulation regulator rca-1 was identified as beneficial for biomass-based enzyme production.
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Affiliation(s)
- Bang Wang
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Pengli Cai
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenliang Sun
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chaoguang Tian
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yanhe Ma
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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142
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Reilly MC, Qin L, Craig JP, Starr TL, Glass NL. Deletion of homologs of the SREBP pathway results in hyper-production of cellulases in Neurospora crassa and Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:121. [PMID: 26288653 PMCID: PMC4539670 DOI: 10.1186/s13068-015-0297-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/24/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND The filamentous fungus Neurospora crassa efficiently utilizes plant biomass and is a model organism for genetic, molecular and cellular biology studies. Here, a set of 567 single-gene deletion strains was assessed for cellulolytic activity as compared to the wild-type parental strain. Mutant strains included were those carrying a deletion in: (1) genes encoding proteins homologous to those implicated in the Saccharomyces cerevisiae secretion apparatus; (2) genes that are homologous to those known to differ between the Trichoderma reesei hyper-secreting strain RUT-C30 and its ancestral wild-type strain; (3) genes encoding proteins identified in the secretome of N. crassa when cultured on plant biomass and (4) genes encoding proteins predicted to traverse the secretory pathway. RESULTS The 567 single-gene deletion collection was cultured on crystalline cellulose and a comparison of levels of secreted protein and cellulase activity relative to the wild-type strain resulted in the identification of seven hyper-production and 18 hypo-production strains. Some of these deleted genes encoded proteins that are likely to act in transcription, protein synthesis and intracellular trafficking, but many encoded fungal-specific proteins of undetermined function. Characterization of several mutants peripherally linked to protein processing or secretion showed that the hyper- or hypo-production phenotypes were primarily a response to cellulose. The altered secretome of these strains was not limited to the production of cellulolytic enzymes, yet was part of the cellulosic response driven by the cellulase transcription factor CLR-2. Mutants implicated the loss of the SREBP pathway, which has been found to regulate ergosterol biosynthesis genes in response to hypoxic conditions, resulted in a hyper-production phenotype. Deletion of two SREBP pathway components in T. reesei also conferred a hyper-production phenotype under cellulolytic conditions. CONCLUSIONS These studies demonstrate the utility of screening the publicly available N. crassa single-gene deletion strain collection for a particular phenotype. Mutants in a predicted E3 ligase and its target SREBP transcription factor played an unanticipated role in protein production under cellulolytic conditions. Furthermore, phenotypes similar to those observed in N. crassa were seen following the targeted deletion of orthologous SREBP pathway loci in T. reesei, a fungal species commonly used in industrial enzyme production.
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Affiliation(s)
- Morgann C Reilly
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Lina Qin
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - James P Craig
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Trevor L Starr
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - N Louise Glass
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
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143
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Liaud N, Giniés C, Navarro D, Fabre N, Crapart S, Gimbert IH, Levasseur A, Raouche S, Sigoillot JC. RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger. Fungal Biol Biotechnol 2014; 1:1-14. [PMID: 26457194 PMCID: PMC4599204 DOI: 10.1186/s40694-014-0003-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/23/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers. RESULTS In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study. CONCLUSIONS By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production.
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Affiliation(s)
- Nadège Liaud
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Christian Giniés
- INRA, UMR 1260, « Nutrition, Obésité et Risque Thrombotique », Marseille, F-13385 France
- INSERM, UMR 1062, « Nutrition, Obésité et Risque Thrombotique », Marseille, F-13385 France
- Université d’Aix-Marseille, UMR 1260, « Nutrition, Obésité et Risque Thrombotique », Faculté de Médecine, Marseille, F-13385 France
| | - David Navarro
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- INRA, International Center for Microbial Resources collection-Filamentous fungi CIRM-CF, Marseille, F-13288 France
| | - Nicolas Fabre
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Sylvaine Crapart
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Isabelle Herpoël- Gimbert
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
| | - Anthony Levasseur
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
| | - Sana Raouche
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Polytech’ Marseille (ex ESIL), UMR 1163 BCF - INRA / AMU, 163 Avenue de Luminy CP 925, Marseille, F-13288 France
| | - Jean-Claude Sigoillot
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
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144
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Cai P, Wang B, Ji J, Jiang Y, Wan L, Tian C, Ma Y. The putative cellodextrin transporter-like protein CLP1 is involved in cellulase induction in Neurospora crassa. J Biol Chem 2014; 290:788-96. [PMID: 25398875 DOI: 10.1074/jbc.m114.609875] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Neurospora crassa recently has become a novel system to investigate cellulase induction. Here, we discovered a novel membrane protein, cellodextrin transporter-like protein 1 (CLP1; NCU05853), a putative cellodextrin transporter-like protein that is a critical component of the cellulase induction pathway in N. crassa. Although CLP1 protein cannot transport cellodextrin, the suppression of cellulase induction by this protein was discovered on both cellobiose and Avicel. The co-disruption of the cellodextrin transporters cdt2 and clp1 in strain Δ3βG formed strain CPL7. With induction by cellobiose, cellulase production was enhanced 6.9-fold in CPL7 compared with Δ3βG. We also showed that the suppression of cellulase expression by CLP1 occurred by repressing the expression of cellodextrin transporters, particularly cdt1 expression. Transcriptome analysis of the hypercellulase-producing strain CPL7 showed that the cellulase expression machinery was dramatically stimulated, as were the cellulase enzyme genes including the inducer transporters and the major transcriptional regulators.
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Affiliation(s)
- Pengli Cai
- From the Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bang Wang
- From the Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jingxiao Ji
- From the Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yongsheng Jiang
- From the Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Li Wan
- From the Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chaoguang Tian
- From the Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- From the Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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145
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Molecular profiling of the Phytophthora plurivora secretome: a step towards understanding the cross-talk between plant pathogenic oomycetes and their hosts. PLoS One 2014; 9:e112317. [PMID: 25372870 PMCID: PMC4221288 DOI: 10.1371/journal.pone.0112317] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/05/2014] [Indexed: 02/06/2023] Open
Abstract
The understanding of molecular mechanisms underlying host–pathogen interactions in plant diseases is of crucial importance to gain insights on different virulence strategies of pathogens and unravel their role in plant immunity. Among plant pathogens, Phytophthora species are eliciting a growing interest for their considerable economical and environmental impact. Plant infection by Phytophthora phytopathogens is a complex process coordinated by a plethora of extracellular signals secreted by both host plants and pathogens. The characterization of the repertoire of effectors secreted by oomycetes has become an active area of research for deciphering molecular mechanisms responsible for host plants colonization and infection. Putative secreted proteins by Phytophthora species have been catalogued by applying high-throughput genome-based strategies and bioinformatic approaches. However, a comprehensive analysis of the effective secretome profile of Phytophthora is still lacking. Here, we report the first large-scale profiling of P. plurivora secretome using a shotgun LC-MS/MS strategy. To gain insight on the molecular signals underlying the cross-talk between plant pathogenic oomycetes and their host plants, we also investigate the quantitative changes of secreted protein following interaction of P. plurivora with the root exudate of Fagus sylvatica which is highly susceptible to the root pathogen. We show that besides known effectors, the expression and/or secretion levels of cell-wall-degrading enzymes were altered following the interaction with the host plant root exudate. In addition, a characterization of the F. sylvatica root exudate was performed by NMR and amino acid analysis, allowing the identification of the main released low-molecular weight components, including organic acids and free amino acids. This study provides important insights for deciphering the extracellular network involved in the highly susceptible P. plurivora-F. sylvatica interaction.
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146
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Brown NA, Dos Reis TF, Goinski AB, Savoldi M, Menino J, Almeida MT, Rodrigues F, Goldman GH. The Aspergillus nidulans signalling mucin MsbA regulates starvation responses, adhesion and affects cellulase secretion in response to environmental cues. Mol Microbiol 2014; 94:1103-1120. [PMID: 25294314 DOI: 10.1111/mmi.12820] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2014] [Indexed: 01/27/2023]
Abstract
In the heterogeneous semi-solid environment naturally occupied by lignocellulolytic fungi the majority of nutrients are locked away as insoluble plant biomass. Hence, lignocellulolytic fungi must actively search for, and attach to, a desirable source of nutrients. During growth on lignocellulose a period of carbon deprivation provokes carbon catabolite derepression and scavenging hydrolase secretion. Subsequently, starvation and/or contact sensing was hypothesized to play a role in lignocellulose attachment and degradation. In Aspergillus nidulans the extracellular signalling mucin, MsbA, influences growth under nutrient-poor conditions including lignocellulose. Cellulase secretion and activity was affected by MsbA via a mechanism that was independent of cellulase transcription. MsbA modulated both the cell wall integrity and filamentous growth MAPK pathways influencing adhesion, biofilm formation and secretion. The constitutive activation of MsbA subsequently enhanced cellulase activity by increasing the secretion of the cellobiohydrolase, CbhA, while improved substrate attachment and may contribute to an enhanced starvation response. Starvation and/or contact sensing therefore represents a new dimension to the already multifaceted regulation of cellulase activity.
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Affiliation(s)
- Neil Andrew Brown
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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147
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Abstract
The recently discovered fungal and bacterial polysaccharide monooxygenases (PMOs) are capable of oxidatively cleaving chitin, cellulose, and hemicelluloses that contain β(1→4) linkages between glucose or substituted glucose units. They are also known collectively as lytic PMOs, or LPMOs, and individually as AA9 (formerly GH61), AA10 (formerly CBM33), and AA11 enzymes. PMOs share several conserved features, including a monocopper center coordinated by a bidentate N-terminal histidine residue and another histidine ligand. A bioinformatic analysis using these conserved features suggested several potential new PMO families in the fungus Neurospora crassa that are likely to be active on novel substrates. Herein, we report on NCU08746 that contains a C-terminal starch-binding domain and an N-terminal domain of previously unknown function. Biochemical studies showed that NCU08746 requires copper, oxygen, and a source of electrons to oxidize the C1 position of glycosidic bonds in starch substrates, but not in cellulose or chitin. Starch contains α(1→4) and α(1→6) linkages and exhibits higher order structures compared with chitin and cellulose. Cellobiose dehydrogenase, the biological redox partner of cellulose-active PMOs, can serve as the electron donor for NCU08746. NCU08746 contains one copper atom per protein molecule, which is likely coordinated by two histidine ligands as shown by X-ray absorption spectroscopy and sequence analysis. Results indicate that NCU08746 and homologs are starch-active PMOs, supporting the existence of a PMO superfamily with a much broader range of substrates. Starch-active PMOs provide an expanded perspective on studies of starch metabolism and may have potential in the food and starch-based biofuel industries.
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148
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Kim IJ, Lee HJ, Choi IG, Kim KH. Synergistic proteins for the enhanced enzymatic hydrolysis of cellulose by cellulase. Appl Microbiol Biotechnol 2014; 98:8469-80. [PMID: 25129610 DOI: 10.1007/s00253-014-6001-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 01/09/2023]
Abstract
Reducing the enzyme loadings for enzymatic saccharification of lignocellulose is required for economically feasible production of biofuels and biochemicals. One strategy is addition of small amounts of synergistic proteins to cellulase mixtures. Synergistic proteins increase the activity of cellulase without causing significant hydrolysis of cellulose. Synergistic proteins exert their activity by inducing structural modifications in cellulose. Recently, synergistic proteins from various biological sources, including bacteria, fungi, and plants, were identified based on genomic data, and their synergistic activities were investigated. Currently, an up-to-date overview of several aspects of synergistic proteins, such as their functions, action mechanisms and synergistic activity, are important for future industrial application. In this review, we summarize the current state of research on four synergistic proteins: carbohydrate-binding modules, plant expansins, expansin-like proteins, and Auxiliary Activity family 9 (formerly GH61) proteins. This review provides critical information to aid in promoting research on the development of efficient and industrially feasible synergistic proteins.
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Affiliation(s)
- In Jung Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
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149
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Xiong Y, Sun J, Glass NL. VIB1, a link between glucose signaling and carbon catabolite repression, is essential for plant cell wall degradation by Neurospora crassa. PLoS Genet 2014; 10:e1004500. [PMID: 25144221 PMCID: PMC4140635 DOI: 10.1371/journal.pgen.1004500] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/27/2014] [Indexed: 11/18/2022] Open
Abstract
Filamentous fungi that thrive on plant biomass are the major producers of hydrolytic enzymes used to decompose lignocellulose for biofuel production. Although induction of cellulases is regulated at the transcriptional level, how filamentous fungi sense and signal carbon-limited conditions to coordinate cell metabolism and regulate cellulolytic enzyme production is not well characterized. By screening a transcription factor deletion set in the filamentous fungus Neurospora crassa for mutants unable to grow on cellulosic materials, we identified a role for the transcription factor, VIB1, as essential for cellulose utilization. VIB1 does not directly regulate hydrolytic enzyme gene expression or function in cellulosic inducer signaling/processing, but affects the expression level of an essential regulator of hydrolytic enzyme genes, CLR2. Transcriptional profiling of a Δvib-1 mutant suggests that it has an improper expression of genes functioning in metabolism and energy and a deregulation of carbon catabolite repression (CCR). By characterizing new genes, we demonstrate that the transcription factor, COL26, is critical for intracellular glucose sensing/metabolism and plays a role in CCR by negatively regulating cre-1 expression. Deletion of the major player in CCR, cre-1, or a deletion of col-26, did not rescue the growth of Δvib-1 on cellulose. However, the synergistic effect of the Δcre-1; Δcol-26 mutations circumvented the requirement of VIB1 for cellulase gene expression, enzyme secretion and cellulose deconstruction. Our findings support a function of VIB1 in repressing both glucose signaling and CCR under carbon-limited conditions, thus enabling a proper cellular response for plant biomass deconstruction and utilization.
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Affiliation(s)
- Yi Xiong
- Plant and Microbial Biology Department and The Energy Biosciences Institute, The University of California, Berkeley, Berkeley, California, United States of America
| | - Jianping Sun
- Plant and Microbial Biology Department and The Energy Biosciences Institute, The University of California, Berkeley, Berkeley, California, United States of America
| | - N. Louise Glass
- Plant and Microbial Biology Department and The Energy Biosciences Institute, The University of California, Berkeley, Berkeley, California, United States of America
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150
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Balestrini R, Bonfante P. Cell wall remodeling in mycorrhizal symbiosis: a way towards biotrophism. FRONTIERS IN PLANT SCIENCE 2014; 5:237. [PMID: 24926297 PMCID: PMC4044974 DOI: 10.3389/fpls.2014.00237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/12/2014] [Indexed: 05/05/2023]
Abstract
Cell walls are deeply involved in the molecular talk between partners during plant and microbe interactions, and their role in mycorrhizae, i.e., the widespread symbiotic associations established between plant roots and soil fungi, has been investigated extensively. All mycorrhizal interactions achieve full symbiotic functionality through the development of an extensive contact surface between the plant and fungal cells, where signals and nutrients are exchanged. The exchange of molecules between the fungal and the plant cytoplasm takes place both through their plasma membranes and their cell walls; a functional compartment, known as the symbiotic interface, is thus defined. Among all the symbiotic interfaces, the complex intracellular interface of arbuscular mycorrhizal (AM) symbiosis has received a great deal of attention since its first description. Here, in fact, the host plasma membrane invaginates and proliferates around all the developing intracellular fungal structures, and cell wall material is laid down between this membrane and the fungal cell surface. By contrast, in ectomycorrhizae (ECM), where the fungus grows outside and between the root cells, plant and fungal cell walls are always in direct contact and form the interface between the two partners. The organization and composition of cell walls within the interface compartment is a topic that has attracted widespread attention, both in ecto- and endomycorrhizae. The aim of this review is to provide a general overview of the current knowledge on this topic by integrating morphological observations, which have illustrated cell wall features during mycorrhizal interactions, with the current data produced by genomic and transcriptomic approaches.
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Affiliation(s)
- Raffaella Balestrini
- Institute for Sustainable Plant Protection, National Research CouncilTorino, Italy
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of TorinoTorino, Italy
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