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Ning YN, Tian D, Zhao S, Feng JX. Regulation of genes encoding polysaccharide-degrading enzymes in Penicillium. Appl Microbiol Biotechnol 2024; 108:16. [PMID: 38170318 DOI: 10.1007/s00253-023-12892-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 01/05/2024]
Abstract
Penicillium fungi, including Penicillium oxalicum, can secrete a range of efficient plant-polysaccharide-degrading enzymes (PPDEs) that is very useful for sustainable bioproduction, using renewable plant biomass as feedstock. However, the low efficiency and high cost of PPDE production seriously hamper the industrialization of processes based on PPDEs. In Penicillium, the expression of PPDE genes is strictly regulated by a complex regulatory system and molecular breeding to modify this system is a promising way to improve fungal PPDE yields. In this mini-review, we present an update on recent research progress concerning PPDE distribution and function, the regulatory mechanism of PPDE biosynthesis, and molecular breeding to produce PPDE-hyperproducing Penicillium strains. This review will facilitate future development of fungal PPDE production through metabolic engineering and synthetic biology, thereby promoting PPDE industrial biorefinery applications. KEY POINTS: • This mini review summarizes PPDE distribution and function in Penicillium. • It updates progress on the regulatory mechanism of PPDE biosynthesis in Penicillium. • It updates progress on breeding of PPDE-hyperproducing Penicillium strains.
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Affiliation(s)
- Yuan-Ni Ning
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Di Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China.
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China.
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2
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Randhawa A, A Ogunyewo O, Jawed K, Yazdani SS. Calcium signaling positively regulates cellulase translation and secretion in a Clr-2-overexpressing, catabolically derepressed strain of Penicillium funiculosum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:21. [PMID: 38336687 PMCID: PMC10858516 DOI: 10.1186/s13068-023-02448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/13/2023] [Indexed: 02/12/2024]
Abstract
BACKGROUND Low-cost cellulase production is vital to sustainable second-generation biorefineries. The catabolically derepressed strain of Penicillium funiculosum NCIM1228 (PfMig188 or ∆Mig1) secretes a superior set of cellulolytic enzymes, that are most suitable for 2G biorefineries. At a 3% (w/w) load, the ∆Mig1 secretome can release > 80% of fermentable sugars from lignocellulose at a 15% (w/v) biomass load, irrespective of the type of biomass and pretreatment. The robustness of the secretome can be further increased by improving the cellulase production capacity of the fungal strain. RESULTS We began by identifying the transcription factor responsible for cellulase production in NCIM1228. An advanced RNA-seq screen identified three genes, clr-2, ctf1a and ctf1b; the genes were cloned under their native promoters and transformed into NCIM1228. Of the three, clr-2 overexpression led to twofold higher cellulase production than the parent strain and was thus identified as the transcriptional activator of cellulase in NCIM1228. Next, we overexpressed clr-2 in ∆Mig1 and expected an exponential increase in cellulolytic attributes accredited to the reinforced activation mechanisms, conjoint with diminished negative regulation. Although clr-2 overexpression increased the transcript levels of cellulase genes in ∆Mig1, there was no increase in cellulase yield. Even a further increase in the transcript levels of clr-2 via a stronger promoter was ineffective. However, when the CaCO3 concentration was increased to 5 g/l in the growth medium, we achieved a 1.5-fold higher activity of 6.4 FPU/ml in the ∆Mig1 strain with clr-2 overexpression. Enthused by the calcium effect, a transcriptomic screen for genes encoding Ca2+-activated kinase identified ssp1, whose overexpression could further increase cellulase yield to ~ 7.5 FPU/ml. Investigation of the mechanism revealed that calcium signaling exclusively enhances the translation and secretion of cellulase in Penicillium funiculosum. CONCLUSIONS Our study identifies for the first time that cellulose activates two discrete signaling events to govern cellulase transcription and posttranscriptional processes (translation, processing and secretion) in P. funiculosum NCIM1228. Whereas Clr-2, the transcriptional activator of cellulase, governs transcription, calcium signaling specifically activates cellulase translation and secretion.
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Affiliation(s)
- Anmoldeep Randhawa
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
- AMITY University, Mohali, Punjab, 140306, India.
| | - Olusola A Ogunyewo
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Kamran Jawed
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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Xia C, Qi X, Song X. Cumulative expression of heterologous XlnR regulatory modules and AraR A731V in Penicillium oxalicum enhances saccharification efficiency of corn stover and corn fiber. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:18. [PMID: 38303075 PMCID: PMC10835966 DOI: 10.1186/s13068-024-02464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/03/2024]
Abstract
Penicillium oxalicum engineered strain DB2 and its mutant strains with multiple regulatory modules were constructed. Mutant strain RE-4-2 with two regulatory modules showed a significant increase in the reducing sugar released from corn stover and corn fiber as well as in the conversion of cellulose than DB2. RE-5-2 with three regulatory modules showed a further increase in reducing sugar released from corn stover and the conversion of cellulose on the basis of RE-4-2. RE-4-2-AraRA731V constructed by overexpressing AraRA731V in RE-4-2 showed an increase of 7.2 times and 1.2 times in arabinofuranosidase and xylosidase activities, respectively. Reducing sugar yield and cellulose conversion of corn stover and corn fiber by RE-4-2-AraRA731V were further increased.
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Affiliation(s)
- Chengqiang Xia
- College of Animal Science, Shanxi Agriculture University, Minxiannan Road 1, Jinzhong, 030801, Shanxi, China
| | - Xiaoyu Qi
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250100, Shandong, China
| | - Xin Song
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China.
- National Glycoengineering Research Center, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China.
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4
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Zhao Q, Yang Z, Xiao Z, Zhang Z, Xing J, Liang H, Gao L, Zhao J, Qu Y, Liu G. Structure-guided engineering of transcriptional activator XYR1 for inducer-free production of lignocellulolytic enzymes in Trichoderma reesei. Synth Syst Biotechnol 2023; 8:732-740. [PMID: 38187093 PMCID: PMC10770280 DOI: 10.1016/j.synbio.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/29/2023] [Accepted: 11/15/2023] [Indexed: 01/09/2024] Open
Abstract
The filamentous fungus Trichoderma reesei is widely used for the production of lignocellulolytic enzymes in industry. XYR1 is the major transcriptional activator of cellulases and hemicellulases in T. reesei. However, rational engineering of XYR1 for improved lignocellulolytic enzymes production has been limited by the lack of structure information. Here, alanine 873 was identified as a new potential target for the engineering of XYR1 based on its structure predicted by AlphaFold2. The mutation of this residue to tyrosine enabled significantly enhanced production of xylanolytic enzymes in the medium with cellulose as the carbon source. Moreover, xylanase and cellulase production increased by 56.7- and 3.3-fold, respectively, when glucose was used as the sole carbon source. Under both conditions, the improvements of lignocellulolytic enzyme production were higher than those in the previously reported V821F mutant. With the enriched hemicellulases and cellulases, the crude enzymes secreted by the A873Y mutant strain produced 51 % more glucose and 52 % more xylose from pretreated corn stover than those of the parent strain. The results provide a novel strategy for engineering the lignocellulolytic enzyme-producing capacity of T. reesei, and would be helpful for understanding the molecular mechanisms of XYR1 regulation.
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Affiliation(s)
- Qinqin Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zezheng Yang
- Taishan College, Shandong University, Qingdao, 266237, China
| | - Ziyang Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jing Xing
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Huiqi Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Liwei Gao
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Taishan College, Shandong University, Qingdao, 266237, China
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5
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Zhao S, Zhang T, Hasunuma T, Kondo A, Zhao XQ, Feng JX. Every road leads to Rome: diverse biosynthetic regulation of plant cell wall-degrading enzymes in filamentous fungi Penicillium oxalicum and Trichoderma reesei. Crit Rev Biotechnol 2023:1-21. [PMID: 38035670 DOI: 10.1080/07388551.2023.2280810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/16/2023] [Indexed: 12/02/2023]
Abstract
Cellulases and xylanases are plant cell wall-degrading enzymes (CWDEs) that are critical to sustainable bioproduction based on renewable lignocellulosic biomass to reduce carbon dioxide emission. Currently, these enzymes are mainly produced from filamentous fungi, especially Trichoderma reesei and Penicillium oxalicum. However, an in-depth comparison of these two producers has not been performed. Although both P. oxalicum and T. reesei harbor CWDE systems, they exhibit distinct features regulating the production of these enzymes, mainly through different transcriptional regulatory networks. This review presents the strikingly different modes of genome-wide regulation of cellulase and xylanase biosynthesis in P. oxalicum and T. reesei, including sugar transporters, signal transduction cascades, transcription factors, chromatin remodeling, and three-dimensional organization of chromosomes. In addition, different molecular breeding approaches employed, based on the understanding of the regulatory networks, are summarized. This review highlights the existence of very different regulatory modes leading to the efficient regulation of CWDE production in filamentous fungi, akin to the adage that "every road leads to Rome." An understanding of this divergence may help further improvements in fungal enzyme production through the metabolic engineering and synthetic biology of certain fungal species.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
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Kerkaert JD, Huberman LB. Regulation of nutrient utilization in filamentous fungi. Appl Microbiol Biotechnol 2023; 107:5873-5898. [PMID: 37540250 PMCID: PMC10983054 DOI: 10.1007/s00253-023-12680-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
Organisms must accurately sense and respond to nutrients to survive. In filamentous fungi, accurate nutrient sensing is important in the establishment of fungal colonies and in continued, rapid growth for the exploitation of environmental resources. To ensure efficient nutrient utilization, fungi have evolved a combination of activating and repressing genetic networks to tightly regulate metabolic pathways and distinguish between preferred nutrients, which require minimal energy and resources to utilize, and nonpreferred nutrients, which have more energy-intensive catabolic requirements. Genes necessary for the utilization of nonpreferred carbon sources are activated by transcription factors that respond to the presence of the specific nutrient and repressed by transcription factors that respond to the presence of preferred carbohydrates. Utilization of nonpreferred nitrogen sources generally requires two transcription factors. Pathway-specific transcription factors respond to the presence of a specific nonpreferred nitrogen source, while another transcription factor activates genes in the absence of preferred nitrogen sources. In this review, we discuss the roles of transcription factors and upstream regulatory genes that respond to preferred and nonpreferred carbon and nitrogen sources and their roles in regulating carbon and nitrogen catabolism. KEY POINTS: • Interplay of activating and repressing transcriptional networks regulates catabolism. • Nutrient-specific activating transcriptional pathways provide metabolic specificity. • Repressing regulatory systems differentiate nutrients in mixed nutrient environments.
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Affiliation(s)
- Joshua D Kerkaert
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Lori B Huberman
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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7
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Zhao S, Mo LX, Li WT, Jiang LL, Meng YY, Ou JF, Liao LS, Yan YS, Luo XM, Feng JX. Arginine methyltransferases PRMT2 and PRMT3 are essential for biosynthesis of plant-polysaccharide-degrading enzymes in Penicillium oxalicum. PLoS Genet 2023; 19:e1010867. [PMID: 37523410 PMCID: PMC10414604 DOI: 10.1371/journal.pgen.1010867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/10/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Many filamentous fungi produce plant-polysaccharide-degrading enzymes (PPDE); however, the regulatory mechanism of this process is poorly understood. A Gal4-like transcription factor, CxrA, is essential for mycelial growth and PPDE production in Penicillium oxalicum. Its N-terminal region, CxrAΔ207-733 is required for the regulatory functions of whole CxrA, and contains a DNA-binding domain (CxrAΔ1-16&Δ59-733) and a methylated arginine (R) 94. Methylation of R94 is mediated by an arginine N-methyltransferase, PRMT2 and appears to induce dimerization of CxrAΔ1-60. Overexpression of prmt2 in P. oxalicum increases PPDE production by 41.4-95.1% during growth on Avicel, compared with the background strain Δku70;hphR+. Another arginine N-methyltransferase, PRMT3, appears to assist entry of CxrA into the nucleus, and interacts with CxrAΔ1-60 in vitro under Avicel induction. Deletion of prmt3 resulted in 67.0-149.7% enhanced PPDE production by P. oxalicum. These findings provide novel insights into the regulatory mechanism of fungal PPDE production.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Li-Xiang Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Wen-Tong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Lian-Li Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Yi-Yuan Meng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Jian-Feng Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Yu-Si Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People’s Republic of China
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8
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Dong CD, Patel AK, Madhavan A, Chen CW, Singhania RR. Significance of glycans in cellulolytic enzymes for lignocellulosic biorefinery - A review. BIORESOURCE TECHNOLOGY 2023; 379:128992. [PMID: 37011847 DOI: 10.1016/j.biortech.2023.128992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
Lignocellulosic (LC) biomass is the most abundant renewable resource for mankind gravitating society towards sustainable solution for energy that can reduce the carbon footprint. The economic feasibility of 'biomass biorefinery' depends upon the efficiency cellulolytic enzymes which is the main crux. Its high production cost and low efficiencies are the major limitations, that need to be resolved. As the complexity of the genome increases, so does the complexity of the proteome, further facilitated by protein post-translational modifications (PTMs). Glycosylation is regarded the major PTMs and hardly any recent work is focused on importance of glycosylation in cellulase. By modifying protein side chains and glycans, superior cellulases with improved stability and efficiency can be obtained. Functional proteomics relies heavily on PTMs because they regulate activity, localization, and interactions with protein, lipid, nucleic acid, and cofactor molecules. O- and N- glycosylation in cellulases influences its characteristics adding positive attributes to the enzymes.
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Affiliation(s)
- Cheng-Di Dong
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Anil Kumar Patel
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, India
| | - Aravind Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam, Kerala 690 525, India
| | - Chiu-Wen Chen
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Reeta Rani Singhania
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, India.
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Zhao S, Wang JX, Hou R, Ning YN, Chen ZX, Liu Q, Luo XM, Feng JX. Novel Transcription Factor CXRD Regulates Cellulase and Xylanase Biosynthesis in Penicillium oxalicum under Solid-State Fermentation. Appl Environ Microbiol 2023; 89:e0036023. [PMID: 37191516 PMCID: PMC10305053 DOI: 10.1128/aem.00360-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
Penicillium oxalicum produces an integrated, extracellular cellulase and xylanase system, strictly regulated by several transcription factors. However, the understanding of the regulatory mechanism of cellulase and xylanase biosynthesis in P. oxalicum is limited, particularly under solid-state fermentation (SSF) conditions. In our study, deletion of a novel gene, cxrD (cellulolytic and xylanolytic regulator D), resulted in 49.3 to 2,230% enhanced production of cellulase and xylanase, except for 75.0% less xylanase at 2 days, compared with the P. oxalicum parental strain, when cultured on solid medium containing wheat bran plus rice straw for 2 to 4 days after transfer from glucose. In addition, the deletion of cxrD delayed conidiospore formation, leading to 45.1 to 81.8% reduced asexual spore production and altered mycelial accumulation to various extents. Comparative transcriptomics and real-time quantitative reverse transcription-PCR found that CXRD dynamically regulated the expression of major cellulase and xylanase genes and conidiation-regulatory gene brlA under SSF. In vitro electrophoretic mobility shift assays demonstrated that CXRD bound to the promoter regions of these genes. The core DNA sequence 5'-CYGTSW-3' was identified to be specifically bound by CXRD. These findings will contribute to understanding the molecular mechanism of negative regulation of fungal cellulase and xylanase biosynthesis under SSF. IMPORTANCE Application of plant cell wall-degrading enzymes (CWDEs) as catalysts in biorefining of lignocellulosic biomass into bioproducts and biofuels reduces both chemical waste production and carbon footprint. The filamentous fungus Penicillium oxalicum can secrete integrated CWDEs, with potential for industrial application. Solid-state fermentation (SSF), simulating the natural habitat of soil fungi, such as P. oxalicum, is used for CWDE production, but a limited understanding of CWDE biosynthesis hampers the improvement of CWDE yields through synthetic biology. Here, we identified a novel transcription factor CXRD, which negatively regulates the biosynthesis of cellulase and xylanase in P. oxalicum under SSF, providing a potential target for genetic engineering to improve CWDE production.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People’s Republic of China
| | - Jiu-Xiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People’s Republic of China
| | - Run Hou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People’s Republic of China
| | - Yuan-Ni Ning
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People’s Republic of China
| | - Zhao-Xing Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People’s Republic of China
| | - Qi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People’s Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People’s Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People’s Republic of China
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Li J, Chen Y, Gao A, Wei L, Wei D, Wang W. Simultaneous Production of Cellulase and β-Carotene in the Filamentous Fungus Trichoderma reesei. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6358-6365. [PMID: 37042195 DOI: 10.1021/acs.jafc.3c00690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
β-Carotene is an indispensable additive in beverage, cosmetic, feed, and pharmaceutical production. The fermentation industry annually generates abundant waste mycelia from Trichoderma reesei (T. reesei), a pivotal industrial strain for cellulase and heterologous protein production. In this study, we constructed a T. reesei cell factory for β-carotene production for the first time. Four key enzymes, CarRP, CarB, GGS1/CrtE, and HMG1, were overexpressed in T. reesei. The concentrations of medium components, including tryptone and glucose, were optimized. The modified strain accumulated β-carotene at a titer of 218.8 mg/L in flask culture. We achieved cellulase production (FPase, 22.33 IU/mL) with the concomitant production of β-carotene (286.63 mg/L) from T. reesei in a jar. Overall, this study offers a novel and unique approach to address the costly waste mycelium management process using T. reesei industrial strains that simultaneously produce proteins and carotenoids.
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Affiliation(s)
- Jing Li
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yumeng Chen
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ao Gao
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Liujing Wei
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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11
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Kun RS, Garrigues S, Peng M, Keymanesh K, Lipzen A, Ng V, Tejomurthula S, Grigoriev IV, de Vries RP. The transcriptional activator ClrB is crucial for the degradation of soybean hulls and guar gum in Aspergillus niger. Fungal Genet Biol 2023; 165:103781. [PMID: 36801368 DOI: 10.1016/j.fgb.2023.103781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
Low-cost plant substrates, such as soybean hulls, are used for various industrial applications. Filamentous fungi are important producers of Carbohydrate Active enZymes (CAZymes) required for the degradation of these plant biomass substrates. CAZyme production is tightly regulated by several transcriptional activators and repressors. One such transcriptional activator is CLR-2/ClrB/ManR, which has been identified as a regulator of cellulase and mannanase production in several fungi. However, the regulatory network governing the expression of cellulase and mannanase encoding genes has been reported to differ between fungal species. Previous studies showed that Aspergillus niger ClrB is involved in the regulation of (hemi-)cellulose degradation, although its regulon has not yet been identified. To reveal its regulon, we cultivated an A. niger ΔclrB mutant and control strain on guar gum (a galactomannan-rich substrate) and soybean hulls (containing galactomannan, xylan, xyloglucan, pectin and cellulose) to identify the genes that are regulated by ClrB. Gene expression data and growth profiling showed that ClrB is indispensable for growth on cellulose and galactomannan and highly contributes to growth on xyloglucan in this fungus. Therefore, we show that A. niger ClrB is crucial for the utilization of guar gum and the agricultural substrate, soybean hulls. Moreover, we show that mannobiose is most likely the physiological inducer of ClrB in A. niger and not cellobiose, which is considered to be the inducer of N. crassa CLR-2 and A. nidulans ClrB.
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Affiliation(s)
- Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Keykhosrow Keymanesh
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Sravanthi Tejomurthula
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Igor V Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - 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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12
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Hu Y, Liu Z, Xu S, Zhao Q, Liu G, Song X, Qu Y, Qin Y. The interaction between the histone acetyltransferase complex Hat1-Hat2 and transcription factor AmyR provides a molecular brake to regulate amylase gene expression. Mol Microbiol 2023; 119:471-491. [PMID: 36760021 DOI: 10.1111/mmi.15036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/15/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
The chromatin structure is generally regulated by chromatin remodelers and histone modifiers, which affect DNA replication, repair, and levels of transcription. The first identified histone acetyltransferase was Hat1/KAT1, which belongs to lysine (K) acetyltransferases. The catalytic subunit Hat1 and the regulatory subunit Hat2 make up the core HAT1 complex. In this study, the results of tandem affinity purification and mass spectrometry and bimolecular fluorescence complementation proved that the Penicillium oxalicum PoHat1-Hat2 is the transcriptional cofactor of the sequence-specific transcription factor PoAmyR, a transcription activator essential for the transcription of amylase gene. ChIP-qPCR results demonstrated that the complex PoHat1-Hat2 is recruited by PoAmyR to the promoters of prominent amylase genes Poamy13A and Poamy15A and performs histone H4 lysine12 acetylation. The result of the yeast two-hybrid test indicated that PoHat2 is the subunit that directly interacts with PoAmyR. PoHat1-Hat2 acts as the molecular brake of the PoAmyR-regulating transcription of amylase genes. A putative model for amylase gene regulation by PoAmyR-Hat2-Hat1 was constructed. Our paper is the first report that the Hat1-Hat2 complex acts as a cofactor for sequence-specific TF to regulate gene expression and explains the mechanism of TF AmyR regulating amylase genes expression.
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Affiliation(s)
- Yueyan Hu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China.,Shandong Lishan Biotechnology Co., Ltd, Jinan, China
| | - Zhongjiao Liu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shaohua Xu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qinqin Zhao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guodong Liu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Xin Song
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Yinbo Qu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Yuqi Qin
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China.,NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-based Medicine, Shandong University, Qingdao, China
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13
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Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
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14
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Chatterjee S, Venkata Mohan S. Fungal biorefinery for sustainable resource recovery from waste. BIORESOURCE TECHNOLOGY 2022; 345:126443. [PMID: 34852279 DOI: 10.1016/j.biortech.2021.126443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Depletion of natural resources and negative impact of fossil fuels on environment are becoming a global concern. The concept of biorefinery is one of the alternative platforms for the production of biofuels and chemicals. Valorisation of biological resources through complete utilization of waste, reusing secondary products and generating energy to power the process are the key principles of biorefinery. Agricultural residues and biogenic municipal solid wastes are getting importance as a potential feedstock for the generation of bioproducts. This communication reviews and highlights the scope of yeast and fungi as a potent candidate for the synthesis of gamut of bioproducts in an integrated approach addressing sustainability and circular bioeconomy. It also provides a close view on importance of microbes in biorefinery, feedstock pretreatment strategies for renewable sugar production, cultivation systems and yeast and fungi based products. Integrated closed loop approach towards multiple product generation with zero waste discharge is also discussed.
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Affiliation(s)
- Sulogna Chatterjee
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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15
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Xu G, Guo H, Yan M, Jia Z, Li Z, Chen M, Bao X. An actin‐like protein
Po
ARP9
involves in the regulation of development and cellulase and amylase expression in
Penicillium oxalicum. J Appl Microbiol 2022; 132:2894-2905. [DOI: 10.1111/jam.15466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/28/2021] [Accepted: 01/23/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Gen Xu
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Hao Guo
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Mengdi Yan
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Zhilei Jia
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Zhonghai Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Mei Chen
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
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16
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Zhang X, Hu Y, Liu G, Liu M, Li Z, Zhao J, Song X, Zhong Y, Qu Y, Wang L, Qin Y. The complex Tup1-Cyc8 bridges transcription factor ClrB and putative histone methyltransferase LaeA to activate the expression of cellulolytic genes. Mol Microbiol 2022; 117:1002-1022. [PMID: 35072962 DOI: 10.1111/mmi.14885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
The degradation of lignocellulosic biomass by cellulolytic enzymes is involved in the global carbon cycle. The hydrolysis of lignocellulosic biomass into fermentable sugars is potential as excellent industrial resource to produce a variety of chemical products. The production of cellulolytic enzymes is regulated mainly at the transcriptional level in filamentous fungi. Transcription factor ClrB and the putative histone methyltransferase LaeA, are both necessary for the expression of cellulolytic genes. However, the mechanism by which transcription factors and methyltransferase coordinately regulate cellulolytic genes is still unknown. Here, we reveal a transcriptional regulatory mechanism involving Penicillium oxalicum transcription factor ClrB (PoClrB), complex Tup1-Cyc8, and putative histone methyltransferase LaeA (PoLaeA). As the transcription factor, PoClrB binds the targeted promoters of cellulolytic genes, recruits PoTup1-Cyc8 complex via direct interaction with PoTup1. PoTup1 interacts with PoCyc8 to form the coactivator complex PoTup1-Cyc8. Then, PoTup1 recruits putative histone methyltransferase PoLaeA to modify the chromatin structure of the upstream region of cellulolytic genes, thereby facilitating the binding of transcription machinery to activating the corresponding cellulolytic gene expression. Our results contribute to a better understanding of complex transcriptional regulation mechanisms of cellulolytic genes and will be valuable for lignocellulosic biorefining.
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Affiliation(s)
- Xiujun Zhang
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.,School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yueyan Hu
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Guodong Liu
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Meng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Zhonghai Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.,State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xin Song
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yinbo Qu
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, Qingdao, China.,State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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17
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Xia C, Gao L, Li Z, Liu G, Song X. Functional analysis of the transcriptional activator XlnR of Penicillium oxalicum. J Appl Microbiol 2021; 132:1112-1120. [PMID: 34467597 DOI: 10.1111/jam.15276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/31/2021] [Accepted: 08/23/2021] [Indexed: 12/01/2022]
Abstract
AIMS The aim of this article is to study the functional features of Penicillium oxalicum transcriptional activator XlnR. METHODS AND RESULTS The yeast reporter system was used to identify transcriptional activation domain of XlnR in P. oxalicum. The expression cassette was introduced into the xlnR locus of P. oxalicum by homologous recombination. In this study, several putative structural domains in P. oxalicum XlnR were predicted by bioinformatics analysis, and the transcriptional activation domain (351-694 region) was identified in XlnR relying on reporter gene system in yeast. In addition, the amino acid at XlnR 871 site (alanine) located in the regulatory region could influence the regulatory activity of XlnR directly. When the alanine at XlnR 871 site was replaced by stronger hydrophobic amino acid (e.g. valine or isoleucine), the regulatory activity will be greatly improved, especially for the regulation of hemicellulase genes expression. When alanine at XlnR 871 site was mutated to a hydrophilic amino acid (e.g. aspartic acid or arginine), the regulatory activity of XlnR will be reduced. CONCLUSIONS The 351-694 region of P. oxalicum XlnR was identified as transcriptional activation domain, and the regulatory activity of XlnR was greatly influenced by hydrophobicity of amino acid at 871 site of XlnR in P. oxalicum. SIGNIFICANCE AND IMPACT OF THE STUDY The results will provide an effective target site to regulate the activity of XlnR and improve cellulase production of P. oxalicum.
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Affiliation(s)
- Chengqiang Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong Province, China.,College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi Province, China
| | - Liwei Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong Province, China
| | - Zhonghai Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong Province, China.,National Glycoengineering Research Center, Shandong University, Qingdao, Shandong Province, China
| | - Xin Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong Province, China.,National Glycoengineering Research Center, Shandong University, Qingdao, Shandong Province, China
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18
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Gao L, He X, Guo Y, Wu Z, Zhao J, Liu G, Qu Y. Combinatorial Engineering of Transcriptional Activators in Penicillium oxalicum for Improved Production of Corn-Fiber-Degrading Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2539-2548. [PMID: 33619954 DOI: 10.1021/acs.jafc.0c07659] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Enzymatic conversion of corn fiber to fermentable sugars is beneficial to improving the economic efficiency of corn processing. In this work, the filamentous fungus Penicillium oxalicum was found to secrete enzymes for efficient saccharification of un-pretreated corn fiber. Separate engineering of transcriptional activators ClrB, XlnR, and AraR led to enhanced production of different sets of lignocellulolytic enzymes. Particularly, the enzymes produced by XlnR- and AraR-engineered strains showed a synergistic effect in corn fiber saccharification. Combinatorial engineering of all three activators generated a strain MCAX with 3.1- to 51.0-fold increases in lignocellulolytic enzyme production compared with the parent strain. In addition, the enzymes of strain MCAX released significantly more fermentable sugars from corn fiber than those of the parent strain at the same protein dosage. The results suggest that this strain has potential for on-site production of enzymes for corn fiber saccharification.
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Affiliation(s)
- Liwei Gao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 11 Keyuanjingsi Road, 266101 Qingdao, China
| | - Xin He
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Yingjie Guo
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Zehua Wu
- Research and Development Department, Shandong Shouguang Juneng Golden Corn Co., Ltd., Anshun Street, Shouguang, 262700 Weifang, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
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19
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Carbon Catabolite Repression Governs Diverse Physiological Processes and Development in Aspergillus nidulans. mBio 2021; 13:e0373421. [PMID: 35164551 PMCID: PMC8844935 DOI: 10.1128/mbio.03734-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Carbon catabolite repression (CCR) is a common phenomenon of microorganisms that enable efficient utilization of carbon nutrients, critical for the fitness of microorganisms in the wild and for pathogenic species to cause infection. In most filamentous fungal species, the conserved transcription factor CreA/Cre1 mediates CCR. Previous studies demonstrated a primary function for CreA/Cre1 in carbon metabolism; however, the phenotype of creA/cre1 mutants indicated broader roles. The global function and regulatory mechanism of this wide-domain transcription factor has remained elusive. Here, we applied two powerful genomics methods (transcriptome sequencing and chromatin immunoprecipitation sequencing) to delineate the direct and indirect roles of Aspergillus nidulans CreA across diverse physiological processes, including secondary metabolism, iron homeostasis, oxidative stress response, development, N-glycan biosynthesis, unfolded protein response, and nutrient and ion transport. The results indicate intricate connections between the regulation of carbon metabolism and diverse cellular functions. Moreover, our work also provides key mechanistic insights into CreA regulation and identifies CreA as a master regulator controlling many transcription factors of different regulatory networks. The discoveries for this highly conserved transcriptional regulator in a model fungus have important implications for CCR in related pathogenic and industrial species. IMPORTANCE The ability to scavenge and use a wide range of nutrients for growth is crucial for microorganisms' survival in the wild. Carbon catabolite repression (CCR) is a transcriptional regulatory phenomenon of both bacteria and fungi to coordinate the expression of genes required for preferential utilization of carbon sources. Since carbon metabolism is essential for growth, CCR is central to the fitness of microorganisms. In filamentous fungi, CCR is mediated by the conserved transcription factor CreA/Cre1, whose function in carbon metabolism has been well established. However, the global roles and regulatory mechanism of CreA/Cre1 are poorly defined. This study uncovers the direct and indirect functions of CreA in the model organism Aspergillus nidulans over diverse physiological processes and development and provides mechanistic insights into how CreA controls different regulatory networks. The work also reveals an interesting functional divergence between filamentous fungal and yeast CreA/Cre1 orthologues.
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20
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Okal EJ, Aslam MM, Karanja JK, Nyimbo WJ. Mini review: Advances in understanding regulation of cellulase enzyme in white-rot basidiomycetes. Microb Pathog 2020; 147:104410. [PMID: 32707312 DOI: 10.1016/j.micpath.2020.104410] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 12/17/2022]
Abstract
White-rot basidiomycetic fungi have gained a lot of scientific attention in recent years owing to their ability to produce cellulase enzymes that are of great importance in numerous industrial applications. This has seen a rise in number of studies seeking to comprehend both physical and molecular mechanisms that regulate the production of cellulase enzymes in these fungi. Cellulase has several applications in production of food and beverages, biofuel, biological detergents, pharmaceuticals, and deinking in paper and pulp industry. Enhanced understanding of genetic mechanisms that regulate cellulase production would have utility for optimal cellulase production in white-rot basidiomycetes using biotechnology approaches. Carbon catabolite repression and various transcriptional factors such as XlnR, Cre, Clr, Ace, and gna1 control expression of genes encoding cellobiohydrolase (CBH), endoglucanase (EGL) and β-glucosidase (BGL). In this review, we have consolidated and summarised some of recent findings on genetic regulation of cellulase with an aim of highlighting the general regulatory mechanisms that underlie cellulase expressions in white-rot fungi. This review further outlines some of important transcription factors that regulate cellulase genes, and key research gaps that may need to be addressed by future research.
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Affiliation(s)
- Eyalira J Okal
- Juncao Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Mehtab Muhammad Aslam
- Center for Plant Water-Use and Nutrition Regulation, College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Cops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Joseph K Karanja
- Center for Plant Water-Use and Nutrition Regulation, College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Cops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Witness J Nyimbo
- Juncao Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
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Han L, Liu K, Ma W, Jiang Y, Hou S, Tan Y, Yuan Q, Niu K, Fang X. Redesigning transcription factor Cre1 for alleviating carbon catabolite repression in Trichoderma reesei. Synth Syst Biotechnol 2020; 5:230-235. [PMID: 32695894 PMCID: PMC7365963 DOI: 10.1016/j.synbio.2020.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/17/2020] [Accepted: 07/04/2020] [Indexed: 12/14/2022] Open
Abstract
Carbon catabolite repression (CCR), which is mainly mediated by Cre1 and triggered by glucose, leads to a decrease in cellulase production in Trichoderma reesei. Many studies have focused on modifying Cre1 for alleviating CCR. Based on the homologous alignment of CreA from wild-type Penicillium oxalicum 114–2 (Po-0) and cellulase hyperproducer JUA10-1(Po-1), we constructed a C-terminus substitution strain—Po-2—with decreased transcriptional levels of cellulase and enhanced CCR. Results revealed that the C-terminal domain of CreAPo−1 plays an important role in alleviating CCR. Furthermore, we replaced the C-terminus of Cre1 with that of CreAPo−1 in T. reesei (Tr-0) and generated Tr-1. As a control, the C-terminus of Cre1 was truncated and Tr-2 was generated. The transcriptional profiles of these transformants revealed that the C-terminal chimera greatly improves cellulase transcription in the presence of glucose and thus upregulates cellulase in the presence of glucose and weakens CCR, consistent with truncating the C-terminus of Cre1 in Tr-0. Therefore, we propose constructing a C-terminal chimera as a new strategy to improve cellulase production and alleviate CCR in the presence of glucose.
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Affiliation(s)
- Lijuan Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Kuimei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.,Rongcheng Campus, Harbin University of Science and Technology, Weihai, 264300, China
| | - Wei Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Shaoli Hou
- Shandong Henglu Biological Technology Co., Ltd, Jinan, 250000, China
| | - Yinshuang Tan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Quanquan Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.,Shandong Henglu Biological Technology Co., Ltd, Jinan, 250000, China
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Zhang T, Liu H, Lv B, Li C. Regulating Strategies for Producing Carbohydrate Active Enzymes by Filamentous Fungal Cell Factories. Front Bioeng Biotechnol 2020; 8:691. [PMID: 32733865 PMCID: PMC7360787 DOI: 10.3389/fbioe.2020.00691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022] Open
Abstract
Filamentous fungi are important eukaryotic organisms crucial in substrate degradation and carbon cycle on the earth and have been harnessed as cell factories for the production of proteins and other high value-added products in recent decades. As cell factories, filamentous fungi play a crucial role in industrial protein production as both native hosts and heterologous hosts. In this review, the regulation strategies of carbohydrate active enzyme expression at both transcription level and protein level are introduced, and the transcription regulations are highlighted with induction mechanism, signaling pathway, and promoter and transcription factor regulation. Afterward, the regulation strategies in protein level including suitable posttranslational modification, protein secretion enhancement, and protease reduction are also presented. Finally, the challenges and perspectives in this field are discussed. In this way, a comprehensive knowledge regarding carbohydrate active enzyme production regulation at both transcriptional and protein levels is provided with the particular goal of aiding in the practical application of filamentous fungi for industrial protein production.
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Affiliation(s)
- Teng Zhang
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Hu Liu
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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