1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Liu D, Garrigues S, Culleton H, McKie VA, de Vries RP. Analysis of the molecular basis for the non-amylolytic and non-proteolytic nature of Aspergillus vadensis CBS 113365. N Biotechnol 2024; 82:25-32. [PMID: 38697469 DOI: 10.1016/j.nbt.2024.04.003] [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: 12/13/2023] [Revised: 04/01/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Aspergillus vadensis CBS 113365, a close relative of A. niger, has been suggested as a more favourable alternative for recombinant protein production as it does not acidify the culture medium and produces very low levels of extracellular proteases. The aim of this study was to investigate the underlying cause of the non-amylolytic and non-proteolytic phenotype of A. vadensis CBS 113365. Our results demonstrate that the non-functionality of the amylolytic transcription factor AmyR in A. vadensis CBS 113365 is primarily attributed to the lack of functionality of its gene's promoter sequence. In contrast, a different mechanism is likely causing the lack of PrtT activity, which is the main transcriptional regulator of protease production. The findings presented here not only expand our understanding of the genetic basis behind the distinct characteristics of A. vadensis CBS 113365, but also underscore its potential as a favourable alternative for recombinant protein production.
Collapse
Affiliation(s)
- Dujuan Liu
- 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; Departament of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Helena Culleton
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Megazyme International Ireland, Bray, Co. Wicklow, Ireland
| | | | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| |
Collapse
|
3
|
Shangguan J, Qiao J, Liu H, Zhu L, Han X, Shi L, Zhu J, Liu R, Ren A, Zhao M. The CBS/H 2S signalling pathway regulated by the carbon repressor CreA promotes cellulose utilization in Ganoderma lucidum. Commun Biol 2024; 7:466. [PMID: 38632386 PMCID: PMC11024145 DOI: 10.1038/s42003-024-06180-y] [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: 10/17/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
Cellulose is an important abundant renewable resource on Earth, and the microbial cellulose utilization mechanism has attracted extensive attention. Recently, some signalling molecules have been found to regulate cellulose utilization and the discovery of underlying signals has recently attracted extensive attention. In this paper, we found that the hydrogen sulfide (H2S) concentration under cellulose culture condition increased to approximately 2.3-fold compared with that under glucose culture condition in Ganoderma lucidum. Further evidence shown that cellulase activities of G. lucidum were improved by 18.2-27.6% through increasing H2S concentration. Then, we observed that the carbon repressor CreA inhibited H2S biosynthesis in G. lucidum by binding to the promoter of cbs, a key gene for H2S biosynthesis, at "CTGGGG". In our study, we reported for the first time that H2S increased the cellulose utilization in G. lucidum, and analyzed the mechanism of H2S biosynthesis induced by cellulose. This study not only enriches the understanding of the microbial cellulose utilization mechanism but also provides a reference for the analysis of the physiological function of H2S signals.
Collapse
Affiliation(s)
- Jiaolei Shangguan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Jinjin Qiao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - He Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Lei Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xiaofei Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Jing Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Rui Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Ang Ren
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Mingwen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| |
Collapse
|
4
|
Zhu Z, Zou G, Chai S, Xiao M, Wang Y, Wang P, Zhou Z. The protein methyltransferase TrSAM inhibits cellulase gene expression by interacting with the negative regulator ACE1 in Trichoderma reesei. Commun Biol 2024; 7:375. [PMID: 38548869 PMCID: PMC10978942 DOI: 10.1038/s42003-024-06072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Protein methylation is a commonly posttranslational modification of transcriptional regulators to fine-tune protein function, however, whether this regulation strategy participates in the regulation of lignocellulase synthesis and secretion in Trichoderma reesei remains unexplored. Here, a putative protein methyltransferase (TrSAM) is screened from a T. reesei mutant with the ability to express heterologous β-glucosidase efficiently even under glucose repression. The deletion of its encoding gene trsam causes a significant increase of cellulase activities in all tested T. reesei strains, including transformants of expressing heterologous genes using cbh1 promotor. Further investigation confirms that TrSAM interacts with the cellulase negative regulator ACE1 via its amino acid residue Arg383, which causes a decrease in the ACE1-DNA binding affinity. The enzyme activity of a T. reesei strain harboring ACE1R383Q increases by 85.8%, whereas that of the strains with trsam or ace1 deletion increases by more than 100%. By contrast, the strain with ACE1R383K shows no difference to the parent strain. Taken together, our results demonstrate that TrSAM plays an important role in regulating the expression of cellulase and heterologous proteins initiated by cbh1 promotor through interacting with ACE1R383. Elimination and mutation of TrSAM and its downstream ACE1 alleviate the carbon catabolite repression (CCR) in expressing cellulase and heterologous protein in varying degrees. This provides a new solution for the exquisite modification of T. reesei chassis.
Collapse
Affiliation(s)
- Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Science, 1000 Jinqi Rd, Shanghai, 201403, China
| | - Shunxing Chai
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinmei Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China.
| |
Collapse
|
5
|
Wang B, van der Kloet F, Kes MBMJ, Luirink J, Hamoen LW. Improving gene set enrichment analysis (GSEA) by using regulation directionality. Microbiol Spectr 2024; 12:e0345623. [PMID: 38294221 PMCID: PMC10913524 DOI: 10.1128/spectrum.03456-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
To infer the biological meaning from transcriptome data, it is useful to focus on genes that are regulated by the same regulator, i.e., regulons. Unfortunately, current gene set enrichment analysis (GSEA) tools do not consider whether a gene is activated or repressed by a regulator. This distinction is crucial when analyzing regulons since a regulator can work as an activator of certain genes and as a repressor of other genes, yet both sets of genes belong to the same regulon. Therefore, simply averaging expression differences of the genes of such a regulon will not properly reflect the activity of the regulator. What makes it more complicated is the fact that many genes are regulated by different transcription factors, and current transcriptome analysis tools are unable to indicate which regulator is most likely responsible for the observed expression difference of a gene. To address these challenges, we developed the gene set enrichment analysis program GINtool. Additional features of GINtool are novel graphical representations to facilitate the visualization of gene set analyses of transcriptome data, the possibility to include functional categories as gene sets for analysis, and the option to analyze expression differences within operons, which is useful when analyzing prokaryotic transcriptome and also proteome data.IMPORTANCEMeasuring the activity of all genes in cells is a common way to elucidate the function and regulation of genes. These transcriptome analyses produce large amounts of data since genomes contain thousands of genes. The analysis of these large data sets is challenging. Therefore, we developed a new software tool called GINtool that can facilitate the analysis of transcriptome data by using prior knowledge of gene sets controlled by the same regulator, the so-called regulons. An important novelty of GINtool is that it can take into account the directionality of gene regulation in these analyses, i.e., whether a gene is activated or repressed, which is crucial to assess whether a regulon or functional category is affected. GINtool also includes new graphical methods to facilitate the visual inspection of regulation events in transcriptome data sets. These and additional analysis methods included in GINtool make it a powerful software tool to analyze transcriptome data.
Collapse
Affiliation(s)
- Biwen Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Frans van der Kloet
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Mariah B. M. J. Kes
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Joen Luirink
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Leendert W. Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Kunitake E, Kawaguchi T, Tani S. Independent, cooperative regulation of cellulolytic genes by paralogous transcription factors ClbR and ClbR2 in Aspergillus aculeatus. Biosci Biotechnol Biochem 2024; 88:212-219. [PMID: 37947258 DOI: 10.1093/bbb/zbad156] [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: 09/25/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
The cellobiose-responsive regulator ClbR, a Zn(II)2Cys6 binuclear-cluster transcription factor, is a positive regulator of carbohydrate-active enzyme (CAZyme) genes responsive to cellulose in Aspergillus aculeatus. Because Zn(II)2Cys6 transcription factors tend to dimerize with proteins of the same family, we searched for a counterpart of ClbR and identified ClbR2, which is 42% identical to ClbR, as an interacting partner of ClbR by yeast two-hybrid screening. Genetic analyses suggested that ClbR and ClbR2 cooperatively regulate the expression of CAZyme genes in response to cellulose and 1,4-β-mannobiose in A. aculeatus. CAZyme genes under the control of the transcription factor ManR were regulated by ClbR and ClbR2, whereas those controlled by the transcription factor XlnR were regulated by ClbR, but not ClbR2. These findings suggest that ClbR participates in multiple regulatory pathways in A. aculeatus by altering an interacting factor.
Collapse
Affiliation(s)
- Emi Kunitake
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Sakai, Japan
- Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Takashi Kawaguchi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Sakai, Japan
- Graduate School of Agriculture, Osaka Metropolitan University , Sakai, Japan
| | - Shuji Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Sakai, Japan
- Graduate School of Agriculture, Osaka Metropolitan University , Sakai, Japan
| |
Collapse
|
8
|
Zhang Y, Gao H, Zhao D, Chen X, Zhu F, Li Y, Xue S. Microbially-driven alkaline regulation: Organic acid secretion behavior of Penicillium oxalicum and charge neutralization in bauxite residue. ENVIRONMENTAL RESEARCH 2024; 240:117489. [PMID: 37890830 DOI: 10.1016/j.envres.2023.117489] [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: 08/27/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Microbially-driven alkaline neutralization in bauxite residue by functional microorganisms is a promising approach for the ecological rehabilitation on alkaline disposal areas. However, the alkali resistance and acid secretion mechanism of functional microorganisms are still unknown, which limits their application. Here, saline-alkaline resistance, acid production performance, and differentially expressed genes of Penicillium oxalicum (P. oxalicum, a functional fungus screened from a typical disposal area) were investigated and its bio-neutralization efficiency was evaluated. This fungus exhibited high tolerance to alkalinity (pH 12), and salinity (NaCl 2.0 M), and produced a large amount of oxalic acid to reduce the medium pH to 2.0. Transcriptome showed that alkali stress induced the overexpression of genes related to antioxidant and stress-resistant enzymes (GST, KatE) and glycolytic pathway rate-limiting enzymes (HK). The rate of glycolysis and other organic acid metabolism processes was increased with higher stress resistance of P. oxalicum. The integrated application of P. oxalicum and maize straw accelerated the dissolved organic carbon content and stabilized the leachate pH of bauxite residue at about 7.4. 3DEEM and BIOSEM analysis indicated that P. oxalicum maintained high activity in the residue leachate and continuously decomposed the maize straw for their metabolism. P. oxalicum showed strong alkaline resistance, biomass degradation capacity, and alkaline regulation potential, which should be beneficial for microbial-driven alkaline regulation in bauxite residue.
Collapse
Affiliation(s)
- Yifan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Hui Gao
- China Aluminum Mining Limited Company, Zhengzhou City, Henan Province 450041, China.
| | - Dongliang Zhao
- China Aluminum Mining Limited Company, Zhengzhou City, Henan Province 450041, China.
| | - Xueming Chen
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350108, China.
| | - Feng Zhu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Yinsheng Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Shengguo Xue
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| |
Collapse
|
9
|
Sun Q, Xu G, Li X, Li S, Jia Z, Yan M, Chen W, Shi Z, Li Z, Chen M. Functional Study of cAMP-Dependent Protein Kinase A in Penicillium oxalicum. J Fungi (Basel) 2023; 9:1203. [PMID: 38132803 PMCID: PMC10745023 DOI: 10.3390/jof9121203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Signaling pathways play a crucial role in regulating cellulase production. The pathway mediated by signaling proteins plays a crucial role in understanding how cellulase expression is regulated. In this study, using affinity purification of ClrB, we have identified sixteen proteins that potentially interact with ClrB. One of the proteins, the catalytic subunit of cAMP-dependent protein kinase A (PoPKA-C), is an important component of the cAMP/PKA signaling pathway. Knocking out PoPKA-C resulted in significant decreases in the growth, glucose utilization, and cellulose hydrolysis ability of the mutant strain. Furthermore, the cellulase activity and gene transcription levels were significantly reduced in the ΔPoPKA-C mutant, while the expression activity of CreA, a transcriptional regulator of carbon metabolism repression, was notably increased. Additionally, deletion of PoPKA-C also led to earlier timing of conidia production. The expression levels of key transcription factor genes stuA and brlA, which are involved in the production of the conidia, showed significant enhancement in the ΔPoPKA-C mutant. These findings highlight the involvement of PoPKA-C in mycelial development, conidiation, and the regulation of cellulase expression. The functional analysis of PoPKA-C provides insights into the mechanism of the cAMP/PKA signaling pathway in cellulase expression in filamentous fungi and has significant implications for the development of high-yielding cellulase strains.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - 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 250353, China; (Q.S.); (G.X.); (X.L.); (S.L.); (Z.J.); (M.Y.); (W.C.); (Z.S.)
| | - 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 250353, China; (Q.S.); (G.X.); (X.L.); (S.L.); (Z.J.); (M.Y.); (W.C.); (Z.S.)
| |
Collapse
|
10
|
Maués DB, Maraschin JC, Duarte DÂ, Antoniêto ACC, Silva RN. Overexpression of the Transcription Factor Azf1 Reveals Novel Regulatory Functions and Impacts β-Glucosidase Production in Trichoderma reesei. J Fungi (Basel) 2023; 9:1173. [PMID: 38132774 PMCID: PMC10744372 DOI: 10.3390/jof9121173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The fungus Trichoderma reesei is an essential producer of enzymes that degrade lignocellulosic biomass to produce value-added bioproducts. The cellulolytic system of T. reesei is controlled by several transcription factors (TFs) that efficiently regulate the production of these enzymes. Recently, a new TF named Azf1 was identified as a positive regulator of cellulase expression. Here, we investigated novel regulatory functions of Azf1 by its overexpression. In the mutant strain OEazf1, overexpression of azf1 was achieved under both repression and induction conditions. Although azf1 was more abundant in transcript and protein, overexpression of this TF did not activate transcription of the cellulase gene in the presence of the repressor glucose, suggesting that Azf1 may be subject to posttranslational regulation. In cellulose, the expression of swo, encoding the accessory protein swollenin, and the β-glucosidases cel1a, cel1b, cel3b, and cel3g increases in the early stages of cultivation. The increased production of these β-glucosidases increases the hydrolysis rate of cellobiose and sophorose, which activates carbon catabolite repression (CCR) and causes repression of cellulase genes and the regulator Xyr1 in the later stages of cultivation. Moreover, overexpression of azf1 led to increased cellulase activity in T. reesei during long-term cultivation in cellulose and sugarcane bagasse. Our results provide new insights into the mechanisms regulating Azf1 and novel genes that are important targets of this TF. This work contributes to a better understanding of the complex mechanisms regulating cellulase expression in T. reesei. It will contribute to the development of strains with higher production of these essential enzymes.
Collapse
Affiliation(s)
| | | | | | | | - Roberto N. Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (D.B.M.); (J.C.M.); (D.Â.D.); (A.C.C.A.)
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Alharake J, Bidard F, Aouam T, Sénamaud-Beaufort C, Margeot A, Heiss-Blanquet S. Effect of the res2 transcription factor gene deletion on protein secretion and stress response in the hyperproducer strain Trichoderma reesei Rut-C30. BMC Microbiol 2023; 23:374. [PMID: 38036984 PMCID: PMC10687790 DOI: 10.1186/s12866-023-03125-z] [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: 06/06/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND The fungus Trichoderma reesei is one of the most used industrial cellulase producers due to its high capacity of protein secretion. Strains of T. reesei with enhanced protein secretion capacity, such as Rut-C30, have been obtained after several rounds of random mutagenesis. The strain was shown to possess an expanded endoplasmic reticulum, but the genetic factors responsible for this phenotype remain still unidentified. Recently, three new transcription factors were described in Neurospora crassa which were demonstrated to be involved in protein secretion. One of them, RES2, was involved in upregulation of secretion-related genes. The aim of our present study was therefore to analyze the role of RES2, on protein secretion in the T. reesei Rut-C30 strain. RESULT Deletion of the res2 gene in Rut-C30 resulted in slightly slower growth on all substrates tested, and lower germination rate as well as lower protein secretion compared to the parental strain Rut-C30. Transcriptomic analysis of the Rut-C30 and the Δres2 mutant strain in secretion stress conditions showed remarkably few differences : 971 genes were differentially expressed (DE) in both strains while 192 genes out of 1163 (~ 16.5%) were DE in Rut-C30 only and 693 out of 1664 genes (~ 41.6%) displayed differential expression solely in Δres2. Notably, induction of protein secretion by cultivating on lactose and addition of secretion stress inducer DTT induced many genes of the secretion pathway similarly in both strains. Among the differentially expressed genes, those coding for amino acid biosynthesis genes, transporters and genes involved in lipid metabolism were found to be enriched specifically in the Δres2 strain upon exposure to lactose or DTT. Besides, redox homeostasis and DNA repair genes were specifically upregulated in the Δres2 strain, indicating an altered stress response. CONCLUSION These results indicate that in the T. reesei Rut-C30 strain, RES2 does not act as a master regulator of the secretion pathway, but it contributes to a higher protein secretion by adjusting the expression of genes involved in different steps of protein synthesis and the secretion pathway.
Collapse
Affiliation(s)
- Jawad Alharake
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France
| | - Thiziri Aouam
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France
| | - Catherine Sénamaud-Beaufort
- Département de biologie, GenomiqueENS, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, École normale supérieure, Paris, 75005, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France.
| |
Collapse
|
13
|
Xue F, Zhao Z, Gu S, Chen M, Xu J, Luo X, Li J, Tian C. The transcriptional factor Clr-5 is involved in cellulose degradation through regulation of amino acid metabolism in Neurospora crassa. BMC Biotechnol 2023; 23:50. [PMID: 38031036 PMCID: PMC10687990 DOI: 10.1186/s12896-023-00823-4] [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: 05/11/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Filamentous fungi are efficient degraders of plant biomass and the primary producers of commercial cellulolytic enzymes. While the transcriptional regulation mechanisms of cellulases have been continuously explored in lignocellulolytic fungi, the induction of cellulase production remains a complex multifactorial system, with several aspects still largely elusive. RESULTS In this study, we identified a Zn2Cys6 transcription factor, designated as Clr-5, which regulates the expression of cellulase genes by influencing amino acid metabolism in Neurospora crassa during growth on cellulose. The deletion of clr-5 caused a significant decrease in secreted protein and cellulolytic enzyme activity of N. crassa, which was partially alleviated by supplementing with yeast extract. Transcriptomic profiling revealed downregulation of not only the genes encoding main cellulases but also those related to nitrogen metabolism after disruption of Clr-5 under Avicel condition. Clr-5 played a crucial role in the utilization of multiple amino acids, especially leucine and histidine. When using leucine or histidine as the sole nitrogen source, the Δclr-5 mutant showed significant growth defects on both glucose and Avicel media. Comparative transcriptomic analysis revealed that the transcript levels of most genes encoding carbohydrate-active enzymes and those involved in the catabolism and uptake of histidine, branched-chain amino acids, and aromatic amino acids, were remarkably reduced in strain Δclr-5, compared with the wild-type N. crassa when grown in Avicel medium with leucine or histidine as the sole nitrogen source. These findings underscore the important role of amino acid metabolism in the regulation of cellulase production in N. crassa. Furthermore, the function of Clr-5 in regulating cellulose degradation is conserved among ascomycete fungi. CONCLUSIONS These findings regarding the novel transcription factor Clr-5 enhance our comprehension of the regulatory connections between amino acid metabolism and cellulase production, offering fresh prospects for the development of fungal cell factories dedicated to cellulolytic enzyme production in bio-refineries.
Collapse
Affiliation(s)
- Fanglei Xue
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhen Zhao
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Shuying Gu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Meixin Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jing Xu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Xuegang Luo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jingen Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| |
Collapse
|
14
|
Liu Z, Ma K, Zhang X, Song X, Qin Y. Different Putative Methyltransferases Have Different Effects on the Expression Patterns of Cellulolytic Genes. J Fungi (Basel) 2023; 9:1118. [PMID: 37998923 PMCID: PMC10671955 DOI: 10.3390/jof9111118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/07/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
Putative methyltranferase LaeA and LaeA-like proteins, conserved in many filamentous fungi, regulate fungal growth, development, virulence, the biosynthesis of secondary metabolites, and the production of cellulolytic enzymes. Penicillium oxaliucm is a typical fungus that produces cellulolytic enzymes. In this study, we reported the biological function of eight putative methyltransferases (PoMtr23C/D/E/F/G/H and PoMtr25A/B) containing a methyltransf_23 or methyltransf_25 domain, with a focus on their roles in the production of cellulolytic enzymes. In P. oxalicum, various methyltransferase genes displayed different transcriptional levels. The genes Pomtr23C and Pomtr25A exhibited high transcriptional levels, while Pomtr23D/E/F/G/H and Pomtr25B were transcribed constantly at low levels. The gene deletion mutants (Δmtr23C/D/E/F/G/H and Δmtr25A/B) were constructed. Various mutants have different patterns in cellulolytic enzyme production. Compared to the WT, the largest increase in filter paper activity (FPA, indicating total cellulase activity) was observed in the Δmtr23G mutant, the only mutant with a cellulolytic halo surrounding the colony. Three mutants (Δmtr23C/D and Δmtr25A) also showed increased cellulolytic enzyme production. The Δmtr23E and Δmtr25B mutants displayed decreased FPA activity, while the Δmtr23F and Δmtr23H mutants displayed similar patterns of cellulolytic enzyme production compared with the WT. The assay of transcriptional levels of cellobiohydrolase gene Pocbh1 and β-1,4-endoglucanase Poeg1 supported that higher cellulolytic gene transcription resulted in higher production of cellulolytic enzymes, and vice versa. The transcriptional levels of two transcription factors, activator XlnR and repressor CreA, were measured. The high transcription level of the PoxlnR gene in the Δmtr23D mutant should be one reason for the increased transcription of its cellulolytic enzyme gene. Both XlnR and CreA transcriptional levels increased in the Δmtr23G mutant, but the former showed a more significant increase than the latter, indicating that the activation effect predominated. The PoMtr25A is localized in the nucleus. The catalytic subunit SNF2 of the SWI/SNF chromatin-remodeling complex was found as one of the interacting proteins of PoMtr25A via tandem affinity purification coupled with mass spectrometry. PoMtr25A may affect not only the transcription of repressor CreA but also by recruiting SWI/SNF complexes that affect chromatin structure, thereby regulating the transcription of target genes.
Collapse
Affiliation(s)
- Zhongjiao Liu
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
| | - Kexuan Ma
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiujun Zhang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Xin Song
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| |
Collapse
|
15
|
Hu X, Qian Y, Gao Z, Li G, Fu F, Guo J, Shan Y. Safety evaluation and whole genome sequencing for revealing the ability of Penicillium oxalicum WX-209 to safely and effectively degrade citrus segments. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Yang T, Li X, Xu N, Guo Y, Liu G, Zhao J. Preparation of cellulose nanocrystals from commercial dissolving pulp using an engineered cellulase system. BIORESOUR BIOPROCESS 2023; 10:42. [PMID: 38647579 PMCID: PMC10992297 DOI: 10.1186/s40643-023-00658-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/21/2023] [Indexed: 04/25/2024] Open
Abstract
There is increasing attention to the production of cellulose nanocrystals (CNCs) from lignocellulosic biomass by enzymatic hydrolysis with cellulase. In this study, the feasibility of the application of a cellulase system from engineered strain Penicillium oxalicum cEES in the production of CNCs was assessed. Using commercial eucalyptus dissolving pulp (EDP) as substrate, the CNCs were successfully obtained by enzymatic hydrolysis with the cellulase cEES, and the total yields of CNCs reached 15.7% through three-step enzymatic hydrolysis of total 72 h (24 h for each step). The prepared CNCs were characterized and found that their crystallinity and thermal stability were higher than that of EDP. In the later stage of enzymatic hydrolysis, the process efficiency of enzymatic preparation of CNCs greatly decreased because of the high crystallinity of cellulosic substrate, and a simple homogenization treatment can promote the enzymatic hydrolysis, as well as produce fusiform CNCs with more uniform size and more fermentable sugar that could be further converted into fuels and bulk chemicals through fermentation. This study provides a feasible enzymatic preparation process for CNCs with engineered cellulase and commercial cellulosic materials.
Collapse
Affiliation(s)
- Tiantian Yang
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China.
| | - Nuo Xu
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China
| | - Yingjie Guo
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao, 266237, Shandong, China.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Jia Z, Yan M, Li X, Sun Q, Xu G, Li S, Chen W, Shi Z, Li Z, Chen M, Bao X. Phosducin-like protein PoPlp1 impacts cellulase and amylase expression and development in Penicillium oxalicum via the G protein-cAMP signaling pathway. Front Microbiol 2023; 14:1165701. [PMID: 37362916 PMCID: PMC10289023 DOI: 10.3389/fmicb.2023.1165701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
In this study, a phosducin-like protein, PoPlp1, was identified and functionally studied in the cellulase-producing strain Penicillium oxalicum 114-2. PoPlp1 was proven to participate in several biological processes, including mycelium development, conidiation, and expression of cellulases and amylases. With deletion of Poplp1, morphology and development varied significantly in ΔPoplp1. Colony growth, glucose utilization, and the hydrolysis capability of starch and cellulose were limited, whereas conidiation was enhanced. Based on detection of the levels of expression of transcription factors involved in asexual development, we conjectured that PoPlp1 is involved in conidiation via the major factor BrlA. We explored the effect of PoPlp1 on cellulase and amylase expression and observed that cellulase and amylase activity and major gene transcription levels were all dramatically reduced in ΔPoplp1. Deletion of PoPlp1 caused a decrease in intracellular cAMP levels, and the cellulase gene expression level of ΔPoplp1 was restored to a certain extent through external addition of cAMP. These findings demonstrate that PoPlp1 may affect cellulase and amylase expression by regulating cAMP concentration. To comprehensively explore the mechanism of PoPlp1 in regulating multiple biological processes, we performed a comparative transcriptomic analysis between strains P. oxalicum 114-2 and ΔPoplp1. The major cellulase and amylase genes were all downregulated, congrent with the results of real-time quantitative polymerase chain reaction analysis. The genes involved in the G protein-cAMP signaling pathway, including several G-protein-coupled receptors, one regulator of G protein signaling, and two cAMP phosphodiesterases, were disrupted by deletion of PoPlp1. These results confirm the positive function of PoPlp1 in the G protein-cAMP signaling pathway. This functional analysis of PoPlp1 will be very beneficial for further study of the regulatory mechanisms of cellulase expression and other biological processes in P. oxalicum 114-2 via the G protein-cAMP signaling pathway.
Collapse
|
20
|
Zhang T, Li HZ, Li WT, Tian D, Ning YN, Liang X, Tan J, Zhao YH, Luo XM, Feng JX, Zhao S. Kinase POGSK-3β modulates fungal plant polysaccharide-degrading enzyme production and development. Appl Microbiol Biotechnol 2023; 107:3605-3620. [PMID: 37119203 DOI: 10.1007/s00253-023-12548-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
The filamentous fungus Penicillium oxalicum secretes integrative plant polysaccharide-degrading enzymes (PPDEs) applicable to biotechnology. Glycogen synthase kinase-3β (GSK-3β) mediates various cellular processes in eukaryotic cells, but the regulatory mechanisms of PPDE biosynthesis in filamentous fungi remain poorly understood. In this study, POGSK-3β (POX_c04478), a homolog of GSK-3β in P. oxalicum, was characterised using biochemical, microbiological and omics approaches. Knockdown of POGSK-3β in P. oxalicum using a copper-responsive promoter replacement system led to 53.5 - 63.6%, 79.0 - 92.8% and 76.8 - 94.7% decreases in the production of filter paper cellulase, soluble starch-degrading enzyme and raw starch-degrading enzyme, respectively, compared with the parental strain ΔKu70. POGSK-3β promoted mycelial growth and conidiation. Transcriptomic profiling and real-time quantitative reverse transcription PCR analyses revealed that POGSK-3β dynamically regulated the expression of genes encoding major PPDEs, as well as fungal development-associated genes. The results broadened our understanding of the regulatory functions of GKS-3β and provided a promising target for genetic engineering to improve PPDE production in filamentous fungi. KEY POINTS: • The roles of glycogen synthase kinase-3β were investigated in P. oxalicum. • POGSK-3β regulated PPDE production, mycelial growth and conidiation. • POGSK-3β controlled the expression of major PPDE genes and regulatory genes.
Collapse
Affiliation(s)
- 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, 530004, Guangxi, China
- College of Food and Quality Engineering, Nanning University, Nanning, 530200, Guangxi, China
| | - Han-Zhi 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, 530004, Guangxi, 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, 530004, Guangxi, 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, Nanning, 530004, Guangxi, 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, 530004, Guangxi, China
| | - Xue Liang
- 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, 530004, Guangxi, China
| | - Jing Tan
- 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, 530004, Guangxi, China
| | - Yan-Hao 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, 530004, Guangxi, 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, 530004, Guangxi, 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, 530004, Guangxi, 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, Nanning, 530004, Guangxi, China.
| |
Collapse
|
21
|
Zhao Z, Gu S, Liu D, Liu D, Chen B, Li J, Tian C. The putative methyltransferase LaeA regulates mycelium growth and cellulase production in Myceliophthora thermophila. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:58. [PMID: 37013645 PMCID: PMC10071736 DOI: 10.1186/s13068-023-02313-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND Filamentous fungi with the ability to use complex carbon sources has been developed as platforms for biochemicals production. Myceliophthora thermophila has been developed as the cell factory to produce lignocellulolytic enzymes and plant biomass-based biofuels and biochemicals in biorefinery. However, low fungal growth rate and cellulose utilization efficiency are significant barriers to the satisfactory yield and productivity of target products, which needs our further exploration and improvement. RESULTS In this study, we comprehensively explored the roles of the putative methyltransferase LaeA in regulating mycelium growth, sugar consumption, and cellulases expression. Deletion of laeA in thermophile fungus Myceliophthora thermophila enhanced mycelium growth and glucose consumption significantly. Further exploration of LaeA regulatory network indicated that multiple growth regulatory factors (GRF) Cre-1, Grf-1, Grf-2, and Grf-3, which act as negative repressors of carbon metabolism, were regulated by LaeA in this fungus. We also determined that phosphoenolpyruvate carboxykinase (PCK) is the core node of the metabolic network related to fungal vegetative growth, of which enhancement partially contributed to the elevated sugar consumption and fungal growth of mutant ΔlaeA. Noteworthily, LaeA participated in regulating the expression of cellulase genes and their transcription regulator. ΔlaeA exhibited 30.6% and 5.5% increases in the peak values of extracellular protein and endo-glucanase activity, respectively, as compared to the WT strain. Furthermore, the global histone methylation assays indicated that LaeA is associated with modulating H3K9 methylation levels. The normal function of LaeA on regulating fungal physiology is dependent on methyltransferase activity. CONCLUSIONS The research presented in this study clarified the function and elucidated the regulatory network of LaeA in the regulation of fungal growth and cellulase production, which will significantly deepen our understanding about the regulation mechanism of LaeA in filamentous fungi and provides the new strategy for improvement the fermentation properties of industrial fungal strain by metabolic engineering.
Collapse
Affiliation(s)
- Zhen Zhao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuying Gu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Defei Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Dandan Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Bingchen Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jingen Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| |
Collapse
|
22
|
Ma B, Luo XM, Zhao S, Feng JX. Protein Kinase PoxMKK1 Regulates Plant-Polysaccharide-Degrading Enzyme Biosynthesis, Mycelial Growth and Conidiation in Penicillium oxalicum. J Fungi (Basel) 2023; 9:jof9040397. [PMID: 37108852 PMCID: PMC10143691 DOI: 10.3390/jof9040397] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
The ability to adapt to changing environmental conditions is crucial for living organisms, as it enables them to successfully compete in natural niches, a process which generally depends upon protein phosphorylation-mediated signaling transduction. In the present study, protein kinase PoxMKK1, an ortholog of mitogen-activated protein kinase kinase Ste7 in Saccharomyces cerevisiae, was identified and characterized in the filamentous fungus Penicillium oxalicum. Deletion of PoxMKK1 in P. oxalicum ΔPoxKu70 led the fungus to lose 64.4-88.6% and 38.0-86.1% of its plant-polysaccharide-degrading enzyme (PPDE) production on day 4 after a shift under submerged- and solid-state fermentation, respectively, compared with the control strain ΔPoxKu70. In addition, PoxMKK1 affected hypha growth and sporulation, though this was dependent on culture formats and carbon sources. Comparative transcriptomics and real-time quantitative reverse transcription PCR assay revealed that PoxMKK1 activated the expression of genes encoding major PPDEs, known regulatory genes (i.e., PoxClrB and PoxCxrB) and cellodextrin transporter genes (i.e., PoxCdtD and PoxCdtC), while it inhibited the essential conidiation-regulating genes, including PoxBrlA, PoxAbaA and PoxFlbD. Notably, regulons modulated by PoxMKK1 and its downstream mitogen-activated protein kinase PoxMK1 co-shared 611 differential expression genes, including 29 PPDE genes, 23 regulatory genes, and 16 sugar-transporter genes. Collectively, these data broaden our insights into the diverse functions of Ste7-like protein kinase, especially regulation of PPDE biosynthesis, in filamentous fungi.
Collapse
Affiliation(s)
- Bo Ma
- 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 530004, 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 530004, 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, Nanning 530004, 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 530004, China
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
A new function of a putative UDP-glucose 4-epimerase on the expression of glycoside hydrolase genes in Aspergillus aculeatus. Appl Microbiol Biotechnol 2023; 107:785-795. [PMID: 36625911 DOI: 10.1007/s00253-022-12337-8] [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: 10/15/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023]
Abstract
In order to figure out the induction mechanisms of glycoside hydrolase genes in Aspergillus aculeatus, we screened approximately 9,000 transfer DNA (T-DNA)-inserted mutants for positive regulators involved in the induction. Since the mutants possess the orotidine 5'-monophosphate decarboxylase gene as a reporter gene to monitor the cellulose-responsive expression of the cellobiohydrolase I gene (cbhI), candidate strains were isolated by counterselection against 5-fluoroorotic acid (5-FOA). One 5-FOA-resistant mutant harboring the T-DNA at the uge5 locus showed reduced cellulose utilization and cbhI expression. A. aculeatus Uge5 is homologous to Aspergillus fumigatus uge5 (Afu5g10780; E-value, 0.0; identities, 93%), which catalyzes the conversion of uridine diphosphate (UDP)-glucose to UDP-galactopyranose. The uge5 deletion mutant in A. aculeatus (Δuge5) showed reduced conidium formation on minimal media supplemented with galactose, locust bean gum (LBG), and guar gum as a carbon source. β-1,4-Endoglucanase and β-1,4-mannanase production in submerged culture containing LBG was reduced to 10% and 6% of the control strain at day 5, respectively, but no difference was observed in cultures containing wheat bran. The expression of major cellulolytic and mannolytic genes in the presence of mannobiose in Δuge5 was reduced to less than 15% of the control strain, while cellobiose-responsive expression was only modestly reduced at early inducing time points. Since all test genes were controlled by a transcription factor ManR, these data demonstrate that Uge5 is involved in inducer-dependent selective expression of genes controlled via ManR. KEY POINTS: • UDP-glucose 4-epimerase (Uge5) regulates expression of glycosyl hydrolase genes. • ManR regulates both cellobiose- and mannobiose-responsive expression. • Uge5 plays a key role in mannobiose-responsive expression.
Collapse
|
26
|
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.
Collapse
|
27
|
Xiang B, Zhao S, Chen J, Chen Y, Zhu C, Hu S, Hu Y. Engineering the filamentous fungus Penicillium oxalicum for rapid, low-background and efficient protein expression. Enzyme Microb Technol 2023; 162:110150. [DOI: 10.1016/j.enzmictec.2022.110150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/09/2022] [Accepted: 10/23/2022] [Indexed: 11/24/2022]
|
28
|
Zhao S, Xiang B, Yang L, Chen J, Zhu C, Chen Y, Cui J, Hu S, Hu Y. Genetic modifications of critical regulators provide new insights into regulation modes of raw-starch-digesting enzyme expression in Penicillium. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:62. [PMID: 35641999 PMCID: PMC9158223 DOI: 10.1186/s13068-022-02162-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022]
Abstract
Background Starch is a very abundant and renewable carbohydrate and an important feedstock for industrial applications. However, most starch-based products are not cost-efficient due to the high energy input needed in traditional enzymatic starch conversion processes. Raw-starch-digesting enzymes (RSDEs) from filamentous fungi have great commercial value in starch processing. However, the regulatory mechanisms associated with their production in filamentous fungi remain unknown. Results In this study, we reported the novel finding that cellulolytic fungus Penicillium oxalicum 114-2 has broad RSDE activity. Four regulators, including the amylase transcription activator AmyR, the catabolite repression repressor CreA, the group III G protein α subunit PGA3, and the nonhistone chromosomal protein HepA, have been found to play a crucial regulatory role in RSDE expression. Enzymatic assays revealed that RSDE production significantly increased after the overexpression of AmyR and HepA, the deletion of CreA and the dominant activation of PGA3. RT-qPCR analysis demonstrated that there is a mutual regulation mode between the four regulators, and then formed a cascade regulation mechanism that is involved in RSDE expression. Comparative transcriptomic analysis between the wild-type strain and genetically engineered strains revealed differentially expressed genes that may mediate the RSDE expression. Conclusions The four different types of regulators were systematically investigated and found to form a regulatory network controlling RSDE gene expression. Our results provide a new insight into the regulatory mechanism of fungal amylolytic enzyme expression and offer a theoretical basis to rationally improve the RSDE yield in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02162-6.
Collapse
|
29
|
Yang T, Li X, Guo Y, Zhao J, Qu Y. Preparation of nanocellulose crystal from bleached pulp with an engineering cellulase and co-production of ethanol. Carbohydr Polym 2022; 301:120291. [DOI: 10.1016/j.carbpol.2022.120291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
|
30
|
Li CX, Liu L, Zhang T, Luo XM, Feng JX, Zhao S. Three-Dimensional Genome Map of the Filamentous Fungus Penicillium oxalicum. Microbiol Spectr 2022; 10:e0212121. [PMID: 35499317 PMCID: PMC9241887 DOI: 10.1128/spectrum.02121-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 01/14/2023] Open
Abstract
Higher-order spatial organization of the chromatin in the nucleus plays crucial roles in the maintenance of cell functions and the regulation of gene expression. Three-dimensional (3D) genome sequencing has been used to great effect in mammal and plants, but the availability of 3D genomes of filamentous fungi is severely limited. Here, we performed a chromosome-level genome assembly of Penicillium oxalicum through single-molecule real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C), with a scaffold N50 of 4.07 Mb and a contig N50 of 3.81 Mb, and further elucidated the 3D genome architecture of P. oxalicum. High-frequency interchromosomal contacts occurred within the centromeres and telomeres, as well as within individual chromosomes. There were 12,203 cis-interactions and 7,884 trans-interactions detected at a resolution of 1 kb. Moreover, a total of 1,099 topologically associated domains (or globules) were found, ranging in size from 2.0 to 76.0 kb. Interestingly, transcription factor-bound motifs were enriched in the globule boundaries. All the cellulase and xylanase genes were discretely distributed in the 3D model of the P. oxalicum genome as a result of few cis- and trans-interactions. Our results from this study provide a global view of chromatin interactions in the P. oxalicum genome and will act as a resource for studying spatial regulation of gene expression in filamentous fungi. IMPORTANCE The spatial structure of chromatin plays important roles in normal cell functions and the regulation of gene expression. The three-dimensional (3D) architectures of the genomes of many mammals and plants have been elucidated, but corresponding studies on filamentous fungi, which play vital roles as decomposers of organic matter in the soil, are very limited. Penicillium oxalicum is one of the predominant cellulolytic aerobic fungi in subtropical and tropical forest soils and can secrete integrative cellulase and xylanase under integrated regulatory control, degrading plant biomass highly efficiently. In the present study, we employed Hi-C technology to construct the 3D genome model of P. oxalicum strain HP7-1 and to further investigate cellulase and xylanase as well as transcription factor genes in 3D genome. These results provide a resource to achieve a deeper understanding of cell function and the regulation of gene expression in filamentous fungi.
Collapse
Affiliation(s)
- Cheng-Xi 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, Guangxi, China
- Anhui Key Laboratory of Infection and Immunity, Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, 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, Guangxi, 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, 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, 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, Nanning, Guangxi, China
| |
Collapse
|
31
|
Lenz AR, Balbinot E, de Abreu FP, de Oliveira NS, Fontana RC, de Avila E Silva S, Park MS, Lim YW, Houbraken J, Camassola M, Dillon AJP. Taxonomy, comparative genomics and evolutionary insights of Penicillium ucsense: a novel species in series Oxalica. Antonie Van Leeuwenhoek 2022; 115:1009-1029. [PMID: 35678932 DOI: 10.1007/s10482-022-01746-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/03/2022] [Indexed: 10/18/2022]
Abstract
The genomes of two Penicillium strains were sequenced and studied in this study: strain 2HH was isolated from the digestive tract of Anobium punctatum beetle larva in 1979 and the cellulase hypersecretory strain S1M29, derived from strain 2HH by a long-term mutagenesis process. With these data, the strains were reclassified and insight is obtained on molecular features related to cellulase hyperproduction and the albino phenotype of the mutant. Both strains were previously identified as Penicillium echinulatum and this investigation indicated that these should be reclassified. Phylogenetic and phenotype data showed that these strains represent a new Penicillium species in series Oxalica, for which the name Penicillium ucsense is proposed here. Six additional strains (SFC101850, SFCP10873, SFCP10886, SFCP10931, SFCP10932 and SFCP10933) collected from the marine environment in the Republic of Korea were also classified as this species, indicating a worldwide distribution of this new taxon. Compared to the closely related strain Penicillium oxalicum 114-2, the composition of cell wall-associated proteins of P. ucsense 2HH shows five fewer chitinases, considerable differences in the number of proteins related to β-D-glucan metabolism. The genomic comparison of 2HH and S1M29 highlighted single amino-acid substitutions in two major proteins (BGL2 and FlbA) that can be associated with the hyperproduction of cellulases. The study of melanin pathways shows that the S1M29 albino phenotype resulted from a single amino-acid substitution in the enzyme ALB1, a precursor of the 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis. Our study provides important knowledge towards understanding species distribution, molecular mechanisms, melanin production and cell wall biosynthesis of this new Penicillium species.
Collapse
Affiliation(s)
- Alexandre Rafael Lenz
- Bioinformatics and Computational Biology Laboratory, Institute of Biotechnology, University of Caxias Do Sul, Francisco Getúlio Vargas Street 1130, Caxias do Sul, RS, 95070-560, Brazil. .,Bahia State University, Silveira Martins Street 2555, Salvador, BA, 41150-000, Brazil.
| | - Eduardo Balbinot
- Bioinformatics and Computational Biology Laboratory, Institute of Biotechnology, University of Caxias Do Sul, Francisco Getúlio Vargas Street 1130, Caxias do Sul, RS, 95070-560, Brazil
| | - Fernanda Pessi de Abreu
- Bioinformatics and Computational Biology Laboratory, Institute of Biotechnology, University of Caxias Do Sul, Francisco Getúlio Vargas Street 1130, Caxias do Sul, RS, 95070-560, Brazil
| | - Nikael Souza de Oliveira
- Bioinformatics and Computational Biology Laboratory, Institute of Biotechnology, University of Caxias Do Sul, Francisco Getúlio Vargas Street 1130, Caxias do Sul, RS, 95070-560, Brazil
| | - Roselei Claudete Fontana
- Laboratory of Enzymes and Biomass, Institute of Biotechnology, University of Caxias Do Sul, Francisco Getúlio Vargas Street 1130, Caxias do Sul, RS, 95070-560, Brazil
| | - Scheila de Avila E Silva
- Bioinformatics and Computational Biology Laboratory, Institute of Biotechnology, University of Caxias Do Sul, Francisco Getúlio Vargas Street 1130, Caxias do Sul, RS, 95070-560, Brazil
| | - Myung Soo Park
- School of Biological Sciences and Institution of Microbiology, Seoul National University, Seoul, 08826, South Korea
| | - Young Woon Lim
- School of Biological Sciences and Institution of Microbiology, Seoul National University, Seoul, 08826, South Korea
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Marli Camassola
- Laboratory of Enzymes and Biomass, Institute of Biotechnology, University of Caxias Do Sul, Francisco Getúlio Vargas Street 1130, Caxias do Sul, RS, 95070-560, Brazil
| | - Aldo José Pinheiro Dillon
- Laboratory of Enzymes and Biomass, Institute of Biotechnology, University of Caxias Do Sul, Francisco Getúlio Vargas Street 1130, Caxias do Sul, RS, 95070-560, Brazil
| |
Collapse
|
32
|
Analysis of carbohydrate-active enzymes and sugar transporters in Penicillium echinulatum: A genome-wide comparative study of the fungal lignocellulolytic system. Gene 2022; 822:146345. [PMID: 35189252 DOI: 10.1016/j.gene.2022.146345] [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: 09/22/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 02/06/2023]
Abstract
Penicillium echinulatum 2HH is an ascomycete well known for its production of cellulolytic enzymes. Understanding lignocellulolytic and sugar uptake systems is essential to obtain efficient fungi strains for the production of bioethanol. In this study we performed a genome-wide functional annotation of carbohydrate-active enzymes and sugar transporters involved in the lignocellulolytic system of P. echinulatum 2HH and S1M29 strains (wildtype and mutant, respectively) and eleven related fungi. Additionally, signal peptide and orthology prediction were carried out. We encountered a diverse assortment of cellulolytic enzymes in P. echinulatum, especially in terms of β-glucosidases and endoglucanases. Other enzymes required for the breakdown of cellulosic biomass were also found, including cellobiohydrolases, lytic cellulose monooxygenases and cellobiose dehydrogenases. The S1M29 mutant, which is known to produce an increased cellulase activity, and the 2HH wild type strain of P. echinulatum did not show significant differences between their enzymatic repertoire. Nevertheless, we unveiled an amino acid substitution for a predicted intracellular β-glucosidase of the mutant, which might contribute to hyperexpression of cellulases through a cellodextrin induction pathway. Most of the P. echinulatum enzymes presented orthologs in P. oxalicum 114-2, supporting the presence of highly similar cellulolytic mechanisms and a close phylogenetic relationship between these fungi. A phylogenetic analysis of intracellular β-glucosidases and sugar transporters allowed us to identify several proteins potentially involved in the accumulation of intracellular cellodextrins. These may prove valuable targets in the genetic engineering of P. echinulatum focused on industrial cellulases production. Our study marks an important step in characterizing and understanding the molecular mechanisms employed by P. echinulatum in the enzymatic hydrolysis of lignocellulosic biomass.
Collapse
|
33
|
Raheja Y, Singh V, Kaur B, Basotra N, Di Falco M, Tsang A, Singh Chadha B. Combination of system biology and classical approaches for developing biorefinery relevant lignocellulolytic Rasamsonia emersonii strain. BIORESOURCE TECHNOLOGY 2022; 351:127039. [PMID: 35318142 DOI: 10.1016/j.biortech.2022.127039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The objective of this study was to develop thermophilic fungus Rasamsonia emersonii using integrated system biology tools (genomics, proteomics and transcriptional analysis) in combination with classical strain breeding approaches. Developed hyper cellulolytic mutant strain M36 showed endoglucanase (476.35 U/ml), β-glucosidase (70.54 U/ml), cellobiohydrolase (15.17 U/ml), FPase (4.89 U/ml) and xylanase (485.21 U/ml) on cellulose/gram flour based production medium. Comparison of the expression profile at proteome and transcriptional level of the developed strain and wild type parent gave detailed insight into the up-regulation of different CAZymes including glycosyl hydrolases (GH5, GH6, GH7, GH3, GH10) and auxiliary enzymes (lytic polysaccharide monooxygenase, swollenin) at system level. Furthermore, the potential of lignocellulolytic enzyme produced by the developed strain and custom designed cocktail spiked with heterologously expressed lytic polysaccharide monooxygenase from Mycothermus thermophiloides were analyzed for the hydrolysis of biorefinery relevant unwashed pretreated rice straw slurry (PRAJ and IOCL) @17% substrate loading rate.
Collapse
Affiliation(s)
- Yashika Raheja
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Varinder Singh
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Baljit Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Neha Basotra
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Marcos Di Falco
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Adrian Tsang
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | | |
Collapse
|
34
|
Application of recyclable CRISPR/Cas9 tools for targeted genome editing in the postharvest pathogenic fungi Penicillium digitatum and Penicillium expansum. Curr Genet 2022; 68:515-529. [PMID: 35298666 DOI: 10.1007/s00294-022-01236-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 01/14/2023]
Abstract
Penicillium digitatum and Penicillium expansum are plant pathogenic fungi that cause the green and blue mold diseases, respectively, leading to serious postharvest economic losses worldwide. Moreover, P. expansum can produce mycotoxins, which are hazardous compounds to human and animal health. The development of tools that allow multiple and precise genetic manipulation of these species is crucial for the functional characterization of their genes. In this sense, CRISPR/Cas9 represents an excellent opportunity for genome editing due to its efficiency, accuracy and versatility. In this study, we developed protoplast generation and transformation protocols and applied them to implement the CRISPR/Cas9 technology in both species for the first time. For this, we used a self-replicative, recyclable AMA1-based plasmid which allows unlimited number of genomic modifications without the limitation of integrative selection markers. As test case, we successfully targeted the wetA gene, which encodes a regulator of conidiophore development. Finally, CRISPR/Cas9-derived ΔwetA strains were analyzed. Mutants showed reduced axenic growth, differential pathogenicity and altered conidiogenesis and germination. Additionally, P. digitatum and P. expansum ΔwetA mutants showed distinct sensitivity to fungal antifungal proteins (AFPs), which are small, cationic, cysteine-rich proteins that have become interesting antifungals to be applied in agriculture, medicine and in the food industry. With this work, we demonstrate the feasibility of the CRISPR/Cas9 system, expanding the repertoire of genetic engineering tools available for these two important postharvest pathogens and open up the possibility to adapt them to other economically relevant phytopathogenic fungi, for which toolkits for genetic modifications are often limited.
Collapse
|
35
|
Lian LD, Shi LY, Zhu J, Liu R, Shi L, Ren A, Yu HS, Zhao MW. GlSwi6 Positively Regulates Cellulase and Xylanase Activities through Intracellular Ca2+ Signaling in Ganoderma lucidum. J Fungi (Basel) 2022; 8:jof8020187. [PMID: 35205940 PMCID: PMC8877461 DOI: 10.3390/jof8020187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/23/2022] Open
Abstract
Ganoderma lucidum is a white-rot fungus that produces a range of lignocellulolytic enzymes to decompose lignin and cellulose. The mitogen-activated protein kinase (MAPK) pathway has been implicated in xylanases and cellulases production. As the downstream transcription factor of Slt2-MAPK, the function of Swi6 in G. lucidum has not been fully studied. In this study, the transcription factor GlSwi6 in G. lucidum was characterized and shown to significantly positively regulate cellulases and xylanases production. Knockdown of the GlSwi6 gene decreased the activities of cellulases and xylanases by approximately 31%~38% and 54%~60% compared with those of the wild-type (WT) strain, respectively. Besides, GlSwi6 can be alternatively spliced into two isoforms, GlSwi6A and GlSwi6B, and overexpression of GlSwi6B increased the activities of cellulase and xylanase by approximately 50% and 60%, respectively. Further study indicates that the existence of GlSwi6B significantly increased the concentration of cytosolic Ca2+. Our study indicated that GlSwi6 promotes the activities of cellulase and xylanase by regulating the Ca2+ signaling. These results connected the GlSwi6 and Ca2+ signaling in the regulation of cellulose degradation, and provide an insight for further improvement of cellulase or xylanase activities in G. lucidum as well as other fungi.
Collapse
|
36
|
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
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Zhang Z, Xiang B, Zhao S, Yang L, Chen Y, Hu Y, Hu S. Construction of a novel filamentous fungal protein expression system based on redesigning of regulatory elements. Appl Microbiol Biotechnol 2022; 106:647-661. [PMID: 35019997 DOI: 10.1007/s00253-022-11761-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/26/2021] [Accepted: 01/05/2022] [Indexed: 12/20/2022]
Abstract
Filamentous fungi are extensively used as an important expression host for the production of a variety of essential industrial proteins. They have significant promise as an expression system for protein synthesis due to their inherent superior secretory capabilities. The purpose of this study was to develop a novel expression system by utilizing a Penicillium oxalicum strain that possesses a high capacity for protein secretion. The expression of glycoside hydrolases in P. oxalicum was evaluated in a cleaner extracellular background where the formation of two major amylases was inhibited. Four glycoside hydrolases (CBHI, Amy15B, BGL1, and Cel12A) were expressed under the highly constitutive promoter PubiD. It was found that the proteins exhibited high purity in the culture supernatant after cultivation with starch. Two inducible promoters, Pamy15A and PempA, under the activation of the transcription factor AmyR were used as elements in the construction of versatile vectors. When using the cellobiohydrolase CBHI as the extracellular quantitative reporter, the empA promoter screened from the AmyR-overexpressing strain was shown to be superior to the amy15A promoter based on RNA-sequencing data. Therefore, we designed an expression system consisting of a cleaner background host strain and an adjustable promoter. This system enables rapid and high-throughput evaluation of glycoside hydrolases from filamentous fungi.Key points• A new protein expression system derived from Penicillium oxalicum has been developed.• The expression platform is capable of secreting recombinant proteins with high purity.• The adjustable promoter may allow for further optimization of recombinant protein synthesis.
Collapse
Affiliation(s)
- Zhe Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Boyu Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengfang Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Le Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Yu Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Yibo Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China.
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| |
Collapse
|
39
|
Feng X, Yao Y, Xu N, Jia H, Li X, Zhao J, Chen S, Qu Y. Pretreatment Affects Profits From Xylanase During Enzymatic Saccharification of Corn Stover Through Changing the Interaction Between Lignin and Xylanase Protein. Front Microbiol 2022; 12:754593. [PMID: 35002999 PMCID: PMC8739958 DOI: 10.3389/fmicb.2021.754593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022] Open
Abstract
Effective pretreatment is vital to improve the biomass conversion efficiency, which often requires the addition of xylanase as an accessory enzyme to enhance enzymatic saccharification of corn stover. In this study, we investigated the effect of two sophisticated pretreatment methods including ammonium sulfite (AS) and steam explosion (SE) on the xylanase profits involved in enzymatic hydrolysis of corn stover. We further explored the interactions between lignin and xylanase Xyn10A protein. Our results showed that the conversion rates of glucan and xylan in corn stover by AS pretreatment were higher by Xyn10A supplementation than that by SE pretreatment. Compared with the lignin from SE pretreated corn stover, the lignin from AS pretreated corn stover had a lower Xyn10A initial adsorption velocity (13.56 vs. 10.89 mg g−1 min−1) and adsorption capacity (49.46 vs. 27.42 mg g−1 of lignin) and weakened binding strength (310.6 vs. 215.9 L g−1). Our study demonstrated the low absolute zeta potential and strong hydrophilicity of the lignin may partly account for relative weak interaction between xylanase protein and lignin from AS pretreated corn stover. In conclusion, our results suggested that AS pretreatment weakened the inhibition of lignin to enzyme, promoted the enzymatic hydrolysis of corn stover, and decreased the cost of enzyme in bioconversion.
Collapse
Affiliation(s)
- Xiaoting Feng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yini Yao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Nuo Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hexue Jia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shicheng Chen
- Department of Clinical and Diagnostic Sciences, School of Health Sciences, Oakland University, Rochester, MI, United States
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| |
Collapse
|
40
|
Madhavan A, Arun KB, Sindhu R, Alphonsa Jose A, Pugazhendhi A, Binod P, Sirohi R, Reshmy R, Kumar Awasthi M. Engineering interventions in industrial filamentous fungal cell factories for biomass valorization. BIORESOURCE TECHNOLOGY 2022; 344:126209. [PMID: 34715339 DOI: 10.1016/j.biortech.2021.126209] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 05/15/2023]
Abstract
Filamentous fungi possess versatile capabilities for synthesizing a variety of valuable bio compounds, including enzymes, organic acids and small molecule secondary metabolites. The advancements of genetic and metabolic engineering techniques and the availability of sequenced genomes discovered their potential as expression hosts for recombinant protein production. Remarkably, plant-biomass degrading filamentous fungi show the unique capability to decompose lignocellulose, an extremely recalcitrant biopolymer. The basic biochemical approaches have motivated several industrial processes for lignocellulose biomass valorisation into fermentable sugars and other biochemical for biofuels, biomolecules, and biomaterials. The review gives insight into current trends in engineering filamentous fungi for enzymes, fuels, and chemicals from lignocellulose biomass. This review describes the variety of enzymes and compounds that filamentous fungi produce, engineering of filamentous fungi for biomass valorisation with a special focus on lignocellulolytic enzymes and other bulk chemicals.
Collapse
Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India.
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Anju Alphonsa Jose
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | | | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea; Centre for Energy & Environmental Sustainability, Lucknow 226001. Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, PR China
| |
Collapse
|
41
|
Hu Y, Li M, Liu Z, Song X, Qu Y, Qin Y. Carbon catabolite repression involves physical interaction of the transcription factor CRE1/CreA and the Tup1-Cyc8 complex in Penicillium oxalicum and Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:244. [PMID: 34952627 PMCID: PMC8710005 DOI: 10.1186/s13068-021-02092-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 12/04/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cellulolytic enzyme production in filamentous fungi requires a release from carbon catabolite repression (CCR). The protein CRE1/CreA (CRE = catabolite responsive element) is a key transcription factor (TF) that is involved in CCR and represses cellulolytic gene expression. CRE1/CreA represents the functional equivalent of Mig1p, an important Saccharomyces cerevisiae TF in CCR that exerts its repressive effect by recruiting a corepressor complex Tup1p-Cyc8p. Although it is known from S. cerevisiae that CRE1/CreA might repress gene expression via interacting with the corepressor complex Tup1-Cyc8, this mechanism is unconfirmed in other filamentous fungi, since the physical interaction has not yet been verified in these organisms. The precise mechanism on how CRE1/CreA achieves transcriptional repression after DNA binding remains unknown. RESULTS The results from tandem affinity purification and bimolecular fluorescence complementation revealed a direct physical interaction between the TF CRE1/CreA and the complex Tup1-Cyc8 in the nucleus of cellulolytic fungus Trichoderma reesei and Penicillium oxalicum. Both fungi have the ability to secrete a complex arsenal of enzymes to synergistically degrade lignocellulosic materials. In P. oxalicum, the protein PoCyc8, a subunit of complex Tup1-Cyc8, interacts directly with TF PoCreA and histone H3 lysine 36 (H3K36) methyltransferase PoSet2 in the nucleus. The di-methylation level of H3K36 in the promoter of prominent cellulolytic genes (cellobiohydrolase-encoding gene Pocbh1/cel7A and endoglucanase-encoding gene Poegl1/cel7B) is positively correlated with the expression levels of TF PoCreA. Since the methylation of H3K36 was also demonstrated to be a repression marker of cellulolytic gene expression, it appears feasible that the cellulolytic genes are repressed via PoCreA-Tup1-Cyc8-Set2-mediated transcriptional repression. CONCLUSION This study verifies the long-standing conjecture that the TF CRE1/CreA represses gene expression by interacting with the corepressor complex Tup1-Cyc8 in filamentous fungi. A reasonable explanation is proposed that PoCreA represses gene expression by recruiting complex PoTup1-Cyc8. Histone methyltransferase Set2, which methylates H3K36, is also involved in the regulatory network by interacting with PoCyc8. The findings contribute to the understanding of CCR mechanism in filamentous fungi and could aid in biotechnologically relevant enzyme production.
Collapse
Affiliation(s)
- Yueyan Hu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Mengxue Li
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Zhongjiao Liu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Xin Song
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Yinbo Qu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Yuqi Qin
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| |
Collapse
|
42
|
Ptitsyn LR, Yampolskaya TA, Kutukova EA, Altman IB. Identification of Core Cellulolytic Enzymes from the Talaromyces cellulolyticus Strains Y-94 and S6-25. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
43
|
Kislitsin VY, Chulkin AM, Zorov IN, Shashkov IA, Satrutdinov AD, Sinitsyn AP, Rozhkova AM. Influence of Mono- and Oligosaccharides on cbh1 Gene Transcription in the Filamentous Fungus Penicillium verruculosum. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821090040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
44
|
Zhang T, Mai RM, Fang QQ, Ou JF, Mo LX, Tian D, Li CX, Gu LS, Luo XM, Feng JX, Zhao S. Regulatory function of the novel transcription factor CxrC in Penicillium oxalicum. Mol Microbiol 2021; 116:1512-1532. [PMID: 34797006 DOI: 10.1111/mmi.14843] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 10/24/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
Numerous transcription factors (TFs) in ascomycete fungi play crucial roles in cellular processes; however, how most of them function is poorly understood. Here, we identified and characterized a novel TF, CxrC (POX01387), acting downstream of the key TF CxrA, which is essential for plant-biomass-degrading-enzyme (PBDE) production in Penicillium oxalicum. Deletion of cxrC in P. oxalicum significantly affected the production of PBDEs, as well as mycelial growth and conidiospore production. CxrA directly repressed the expression of cxrC after about 12 hr following switch to Avicel culture. CxrC bound the promoters of major PBDE genes and genes involved in conidiospore development. CxrC was found to bind the TSSGTYR core sequence (S: C and G; Y: T and C; R: G and A) of the important cellulase genes cbh1 and eg1. Both N- and C-terminal peptides of CxrC and the CxrC phosphorylation were found to mediate its homodimerization. The conserved motif LPSVRSLLTP (65-74) in CxrC was found to be required for regulating cellulase production. This study reveals novel mechanisms of TF-mediated regulation of the expression of PBDE genes and genes involved in cellular processes in an ascomycete fungus.
Collapse
Affiliation(s)
- 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, People's Republic of China
| | - Rong-Ming Mai
- 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
| | - Qi-Qi Fang
- 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
| | - 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
| | - 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, Nanning, People's Republic of China
| | - Cheng-Xi 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
| | - Li-Sha Gu
- 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
| | - 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
| |
Collapse
|
45
|
Fan C, Zhang W, Su X, Ji W, Luo H, Zhang Y, Liu B, Yao B, Huang H, Xu X. CRISPR/Cas9-mediated genome editing directed by a 5S rRNA-tRNA Gly hybrid promoter in the thermophilic filamentous fungus Humicola insolens. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:206. [PMID: 34688310 PMCID: PMC8542335 DOI: 10.1186/s13068-021-02057-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Humicola insolens is a filamentous fungus with high potential of producing neutral and heat- and alkali-resistant cellulase. However, the genetic engineering tools, particularly the genome-editing tool, are scarce, hindering the study of cellulase expression regulation in this organism. RESULTS Herein, a CRISPR/Cas9 genome-editing system was established in H. insolens based on a hybrid 5S rRNA-tRNAGly promoter. This system is superior to the HDV (hepatitis delta virus) system in genome editing, allowing highly efficient single gene destruction in H. insolens with rates of deletion up to 84.1% (37/44). With this system, a putative pigment synthesis gene pks and the transcription factor xyr1 gene were disrupted with high efficiency. Moreover, the extracellular protein concentration and cellulase activity largely decreased when xyr1 was deleted, demonstrating for the first time that Xyr1 plays an important role in cellulase expression regulation. CONCLUSIONS The established CRISPR/Cas9 system is a powerful genetic operation tool for H. insolens, which will accelerate studies on the regulation mechanism of cellulase expression and engineering of H. insolens for higher cellulase production.
Collapse
Affiliation(s)
- Chao Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Xiaoyun Su
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China
| | - Wangli Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Huiying Luo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Bo Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China
| | - Huoqing Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China.
| | - Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China.
| |
Collapse
|
46
|
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.
Collapse
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
| |
Collapse
|
47
|
Gabriel R, Mueller R, Floerl L, Hopson C, Harth S, Schuerg T, Fleissner A, Singer SW. CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:169. [PMID: 34384463 PMCID: PMC8359064 DOI: 10.1186/s13068-021-02018-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Filamentous fungi are excellent lignocellulose degraders, which they achieve through producing carbohydrate active enzymes (CAZymes). CAZyme production is highly orchestrated and gene expression analysis has greatly expanded understanding of this important biotechnological process. The thermophilic fungus Thermoascus aurantiacus secretes highly active thermostable enzymes that enable saccharifications at higher temperatures; however, the genome-wide measurements of gene expression in response to CAZyme induction are not understood. RESULTS A fed-batch system with plant biomass-derived sugars D-xylose, L-arabinose and cellobiose established that these sugars induce CAZyme expression in T. aurantiacus. The C5 sugars induced both cellulases and hemicellulases, while cellobiose specifically induced cellulases. A minimal medium formulation was developed to enable gene expression studies of T. aurantiacus with these inducers. It was found that d-xylose and L-arabinose strongly induced a wide variety of CAZymes, auxiliary activity (AA) enzymes and carbohydrate esterases (CEs), while cellobiose facilitated lower expression of mostly cellulase genes. Furthermore, putative orthologues of different unfolded protein response genes were up-regulated during the C5 sugar feeding together with genes in the C5 sugar assimilation pathways. CONCLUSION This work has identified two additional CAZyme inducers for T. aurantiacus, L-arabinose and cellobiose, along with D-xylose. A combination of biochemical assays and RNA-seq measurements established that C5 sugars induce a suite of cellulases and hemicellulases, providing paths to produce broad spectrum thermotolerant enzymatic mixtures.
Collapse
Affiliation(s)
- Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Rebecca Mueller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Lena Floerl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Cynthia Hopson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Chemical Engineering and Materials, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28040, Madrid, Spain
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Frankfurt Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Andre Fleissner
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106, Braunschweig, Germany
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
| |
Collapse
|
48
|
The F-box protein gene exo- 1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi. Proc Natl Acad Sci U S A 2021; 118:2025689118. [PMID: 34168079 DOI: 10.1073/pnas.2025689118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbohydrate active enzymes (CAZymes) are vital for the lignocellulose-based biorefinery. The development of hypersecreting fungal protein production hosts is therefore a major aim for both academia and industry. However, despite advances in our understanding of their regulation, the number of promising candidate genes for targeted strain engineering remains limited. Here, we resequenced the genome of the classical hypersecreting Neurospora crassa mutant exo-1 and identified the causative point of mutation to reside in the F-box protein-encoding gene, NCU09899. The corresponding deletion strain displayed amylase and invertase activities exceeding those of the carbon catabolite derepressed strain Δcre-1, while glucose repression was still mostly functional in Δexo-1 Surprisingly, RNA sequencing revealed that while plant cell wall degradation genes are broadly misexpressed in Δexo-1, only a small fraction of CAZyme genes and sugar transporters are up-regulated, indicating that EXO-1 affects specific regulatory factors. Aiming to elucidate the underlying mechanism of enzyme hypersecretion, we found the high secretion of amylases and invertase in Δexo-1 to be completely dependent on the transcriptional regulator COL-26. Furthermore, misregulation of COL-26, CRE-1, and cellular carbon and nitrogen metabolism was confirmed by proteomics. Finally, we successfully transferred the hypersecretion trait of the exo-1 disruption by reverse engineering into the industrially deployed fungus Myceliophthora thermophila using CRISPR-Cas9. Our identification of an important F-box protein demonstrates the strength of classical mutants combined with next-generation sequencing to uncover unanticipated candidates for engineering. These data contribute to a more complete understanding of CAZyme regulation and will facilitate targeted engineering of hypersecretion in further organisms of interest.
Collapse
|
49
|
Guo H, Xu G, Wu R, Li Z, Yan M, Jia Z, Li Z, Chen M, Bao X, Qu Y. A Homeodomain-Containing Transcriptional Factor PoHtf1 Regulated the Development and Cellulase Expression in Penicillium oxalicum. Front Microbiol 2021; 12:671089. [PMID: 34177850 PMCID: PMC8222722 DOI: 10.3389/fmicb.2021.671089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
Homeodomain-containing transcription factors (Htfs) play important roles in animals, fungi, and plants during some developmental processes. Here, a homeodomain-containing transcription factor PoHtf1 was functionally characterized in the cellulase-producing fungi Penicillium oxalicum 114-2. PoHtf1 was shown to participate in colony growth and conidiation through regulating the expression of its downstream transcription factor BrlA, the key regulator of conidiation in P. oxalicum 114-2. Additionally, PoHtf1 inhibited the expression of the major cellulase genes by coordinated regulation of cellulolytic regulators CreA, AmyR, ClrB, and XlnR. Furthermore, transcriptome analysis showed that PoHtf1 participated in the secondary metabolism including the pathway synthesizing conidial yellow pigment. These data show that PoHtf1 mediates the complex transcriptional-regulatory network cascade between developmental processes and cellulolytic gene expression in P. oxalicum 114-2. Our results should assist the development of strategies for the metabolic engineering of mutants for applications in the enzymatic hydrolysis for biochemical production.
Collapse
Affiliation(s)
- Hao Guo
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Gen Xu
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Ruimei Wu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhigang Li
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Mengdi Yan
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Zhilei Jia
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Zhonghai Li
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Mei Chen
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, School of Life Sciences, National Glycoengineering Research Center, Shandong University, Qingdao, China
| |
Collapse
|
50
|
Pang XM, Tian D, Zhang T, Liao LS, Li CX, Luo XM, Feng JX, Zhao S. G protein γ subunit modulates expression of plant-biomass-degrading enzyme genes and mycelial-development-related genes in Penicillium oxalicum. Appl Microbiol Biotechnol 2021; 105:4675-4691. [PMID: 34076714 DOI: 10.1007/s00253-021-11370-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/05/2021] [Accepted: 05/26/2021] [Indexed: 01/24/2023]
Abstract
Heterotrimeric-G-protein-mediated signaling pathways modulate the expression of the essential genes in many fundamental cellular processes in fungi at the transcription level. However, these processes remain unclear in Penicillium oxalicum. In this study, we generated knockout and knockout-complemented strains of gng-1 (POX07071) encoding the Gγ protein and found that GNG-1 modulated the expression of genes encoding plant-biomass-degrading enzymes (PBDEs) and sporulation-related activators. Interestingly, GNG-1 affected expression of the cxrB that encodes a known transcription factor required for the expression of major cellulase and xylanase genes. Constitutive overexpression of cxrB in ∆gng-1 circumvented the dependence of PBDE production on GNG-1. Further evidence indicated that CxrB indirectly regulated the transcription levels of key amylase genes by controlling the expression of the regulatory gene amyR. These data extended the diversity of Gγ protein functions and provided new insight into the signal transduction and regulation of PBDE gene expression in filamentous fungi. KEY POINTS: • GNG-1 modulates the expression of PBDE genes and sporulation-related genes. • GNG-1 controls expression of the key regulatory gene cxrB. • Overexpression of cxrB circumvents dependence of PBDE production on GNG-1.
Collapse
Affiliation(s)
- Xiao-Ming Pang
- 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
| | - 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, 100 Daxue Road, Nanning, Guangxi, 530004, 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, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Cheng-Xi 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, 100 Daxue Road, Nanning, Guangxi, 530004, 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, 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
| | - 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.
| |
Collapse
|