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Liu M, Wang J, Umeda I, Wang Z, Kumar S, Zheng Y. Harnessing filamentous fungi and fungal-bacterial co-culture for biological treatment and valorization of hydrothermal liquefaction aqueous phase from corn stover. BIORESOURCE TECHNOLOGY 2024; 409:131240. [PMID: 39122129 DOI: 10.1016/j.biortech.2024.131240] [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: 06/03/2024] [Revised: 07/14/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
To promote the sustainability of hydrothermal liquefaction (HTL) for biofuel production, fungal fermentation was investigated to treat HTL aqueous phase (HTLAP) from corn stover. The most promising fungus, Aspergillus niger demonstrated superior tolerance to HTLAP and capability to produce oxalic acid as a value-added product. The fungal-bacterial co-culture of A. niger and Rhodococcus jostii was beneficial at low COD (chemical oxygen demand) loading of 3800 mg/L in HTLAP, achieving 69% COD removal while producing 0.5 g/L oxalic acid and 11% lipid content in microbial biomass. However, higher COD loading of 4500, 6040, and 7800 mg/L significantly inhibited R. jostii, but promoted A. niger growth with increased oxalic acid production while COD removal remained similar (58-65%). Additionally, most total organic carbon (TOC) in HTLAP was transformed into oxalic acid, representing 46-56% of the consumed TOC. These findings highlighted the potential of fungi for bio-upcycling of HTLAP into value-added products.
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Affiliation(s)
- Meicen Liu
- Department of Grain Science and Industry, Kansas State University, 1980 Kimball Avenue, Manhattan, KS 66506, USA
| | - Jiefu Wang
- Department of Biological Systems Engineering, Virginia Tech, 1230 Washington St. SW, Blacksburg, VA 24060, USA
| | - Isamu Umeda
- Department of Civil and Environmental Engineering, Old Dominion University, Norfolk, VA 23529, USA
| | - Zhiwu Wang
- Department of Biological Systems Engineering, Virginia Tech, 1230 Washington St. SW, Blacksburg, VA 24060, USA
| | - Sandeep Kumar
- Department of Civil and Environmental Engineering, Old Dominion University, Norfolk, VA 23529, USA
| | - Yi Zheng
- Department of Grain Science and Industry, Kansas State University, 1980 Kimball Avenue, Manhattan, KS 66506, USA.
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Chen X, Moran Torres JP, Tedjai SVK, Lugones LG, Wösten HAB. Functional analysis of FlbA-regulated transcription factor genes in Aspergillus niger using a multiplexed CRISPRoff system. Int J Biol Macromol 2024; 277:134326. [PMID: 39089555 DOI: 10.1016/j.ijbiomac.2024.134326] [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: 03/28/2024] [Revised: 05/31/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
FlbA of Aspergillus niger (indirectly) regulates 36 transcription factor (TF) genes. As a result, it promotes sporulation and represses vegetative growth, protein secretion and lysis. In this study, the functions of part of the FlbA-regulated TF genes were studied by using CRISPRoff. This system was recently introduced as an epigenetic tool for modulating gene expression in A. niger. A plasmid encompassing an optimized CRISPRoff system as well as a library of sgRNA genes that target the promoters of the 36 FlbA-regulated TF genes was introduced in A. niger. Out of 24 transformants that exhibited a sporulation phenotype, 12 and 18 strains also showed a biomass and secretion phenotype, respectively. The transforming sgRNAs, and thus the genes responsible for the phenotypes, were identified from five of the transformants. The results show that the genes dofA, dofB, dofC, dofD, and socA are involved in sporulation and extracellular enzyme activity, while dofA and socA also play roles in biomass formation. Overall, this study shows that the multiplexed CRISPRoff system can be effectively used for functional analysis of genes in a fungus.
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Affiliation(s)
- Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Juan P Moran Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - S Vyanjan K Tedjai
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Luis G Lugones
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
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3
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Gonzalez Baez A, Muñoz LP, Timmermans MJ, Garelick H, Purchase D. Molding the future: Optimization of bioleaching of rare earth elements from electronic waste by Penicillium expansum and insights into its mechanism. BIORESOURCE TECHNOLOGY 2024; 402:130750. [PMID: 38685515 DOI: 10.1016/j.biortech.2024.130750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The recovery of rare earth elements (REE) from electronic waste is crucial for ensuring future demand security, as there is a high supply risk for this group of elements, and mitigating the environmental impacts of conventional mining. This research focuses on extracting REE from waste printed circuit boards through bioleaching, addressing the limited attention given to this source. A strain of Penicillium expansum demonstrated efficient bioleaching under optimal conditions of 7.5 initial pH, 0.1 mM phosphate concentration, and excluding a buffering agent. The study achieved significant improvements in La and Tb extraction and enhancements in Pr, Nd, and Gd recovery, approaching 70 % within 24 h. Fungal mechanisms involved in REE extraction included fungal pH control, organic acid biosynthesis, phosphate bioavailability, and potential fungal proton pump involvement. This approach offers a promising solution for sustainable REE recovery from e-waste, contributing to resource security and circular economy.
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Affiliation(s)
- Alejandra Gonzalez Baez
- Middlesex University, Department of Natural Sciences, Faculty of Science and Technology, The Burroughs, NW4 4BT London, UK
| | - Leonardo Pantoja Muñoz
- Middlesex University, Department of Natural Sciences, Faculty of Science and Technology, The Burroughs, NW4 4BT London, UK
| | - Martijn Jtn Timmermans
- Middlesex University, Department of Natural Sciences, Faculty of Science and Technology, The Burroughs, NW4 4BT London, UK
| | - Hemda Garelick
- Middlesex University, Department of Natural Sciences, Faculty of Science and Technology, The Burroughs, NW4 4BT London, UK
| | - Diane Purchase
- Middlesex University, Department of Natural Sciences, Faculty of Science and Technology, The Burroughs, NW4 4BT London, UK.
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Chen X, Moran Torres JP, Jan Vonk P, Damen JMA, Reiding KR, Dijksterhuis J, Lugones LG, Wösten HAB. The pleiotropic phenotype of FlbA of Aspergillus niger is explained in part by the activity of seven of its downstream-regulated transcription factors. Fungal Genet Biol 2024; 172:103894. [PMID: 38657897 DOI: 10.1016/j.fgb.2024.103894] [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: 03/03/2024] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 04/26/2024]
Abstract
Inactivation of flbA in Aspergillus niger results in thinner cell walls, increased cell lysis, abolished sporulation, and an increased secretome complexity. A total of 36 transcription factor (TF) genes are differentially expressed in ΔflbA. Here, seven of these genes (abaA, aslA, aslB, azf1, htfA, nosA, and srbA) were inactivated. Inactivation of each of these genes affected sporulation and, with the exception of abaA, cell wall integrity and protein secretion. The impact on secretion was strongest in the case of ΔaslA and ΔaslB that showed increased pepsin, cellulase, and amylase activity. Biomass was reduced of agar cultures of ΔabaA, ΔaslA, ΔnosA, and ΔsrbA, while biomass was higher in liquid shaken cultures of ΔaslA and ΔaslB. The ΔaslA and ΔhtfA strains showed increased resistance to H2O2, while ΔaslB was more sensitive to this reactive oxygen species. Together, inactivation of the seven TF genes impacted biomass formation, sporulation, protein secretion, and stress resistance, and thereby these genes explain at least part of the pleiotropic phenotype of ΔflbA of A. niger.
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Affiliation(s)
- Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Juan P Moran Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Peter Jan Vonk
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - J Mirjam A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | - Luis G Lugones
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Ashrafi-Saiedlou S, Rasouli-Sadaghiani M, Samadi A, Barin M, Sepehr E. Aspergillus niger as an eco-friendly agent for potassium release from K- bearing minerals: Isolation, screening and culture medium optimization using Plackett-Burman design and response surface methodology. Heliyon 2024; 10:e29117. [PMID: 38623221 PMCID: PMC11016616 DOI: 10.1016/j.heliyon.2024.e29117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
The potential of Aspergillus niger, to enhance non-exchangeable potassium (K+) release from mineral structures were investigated as a cost-effective and environmentally friendly alternative to traditional chemical fertilizers. Optimizing the culture medium for maximum K+ release, alongside identifying potential mechanisms of action of the A. niger including the production of various organic acids and pH reduction in the minerals feldspar and phlogopite, were among the primary objectives of the present study. K+ dissolution from feldspar and phlogopite in the presence of Aspergillus niger were examined through a two-step experiment; impact of different carbon sources (glucose, sucrose, and fructose) on K+ release using the Plackett-Burman design (PBD) with 12 experimental runs and effect of other independent variables including pH (ranging from 5 to 10), carbon concentration (3-12.3 g l-1), and incubation time (5-18 days) on K+ release using the central composite design (CCD). Our results indicated that the PBD demonstrated a strong predictive capacity (RMSE = 0.012-0.018 g l-1 and R2 = 0.85-0.89) for K+ release. According to the CCD model, pH exerted a significant positive influence on increasing soluble K+ release (P < 0.001). The highest levels of K+ release (157.8 and 175.3 mg l-1 in feldspar and phlogopite, respectively) were observed at the central levels (0) of time and carbon source, and at the +α level (+1.68) of pH. Furthermore, based on the CCD model, the optimal conditions for achieving high K+ release from feldspar and phlogopite in a medium were pHs of 10.36 and 10.31, sucrose concentrations of 11.23 and 11.32 g l-1, and incubation times of 15 and 18 days, respectively. The determination coefficients of the CCD model indicated that 89.5% and 92.6% of the changes in soluble K+ for feldspar and phlogopite, could be explained by this model, respectively. In the current study, the production of organic acids and the resulting pH reduction, along with the reduction in mineral particle size in feldspar and phlogopite, were identified as potential mechanisms influencing the enhancement of potassium solubility. The predominant acids in both feldspar and phlogopite were lactic acid (70.9 and 69.15 mg l-1) and citric acid (40.48 and 22.93 mg l-1), although the production levels of organic acids differed in the two minerals. Overall, our findings highlight the potential of A. niger to proficiently release non-exchangeable potassium from mineral matrices, indicating its promising potential in agricultural applications.
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Affiliation(s)
| | | | - Abass Samadi
- Department of Soil Science, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Mohsen Barin
- Department of Soil Science, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Ebrahim Sepehr
- Department of Soil Science, Faculty of Agriculture, Urmia University, Urmia, Iran
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6
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Xu J, Cheng S, Zhang R, Cai F, Zhu Z, Cao J, Wang J, Yu Q. Study on the mechanism of sodium ion inhibiting citric acid fermentation in Aspergillus niger. BIORESOURCE TECHNOLOGY 2024; 394:130245. [PMID: 38145764 DOI: 10.1016/j.biortech.2023.130245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
Excessive sodium significantly inhibits citric acid fermentation by Aspergillus niger during the recycling of citric acid wastewater. This study aimed to elucidate the inhibition mechanism at the interface of physiology and transcriptomics. The results showed that excessive sodium caused a 22.3 % increase in oxalic acid secretion and a 147.6 % increase in H+-ATPase activity at the 4 h fermentation compared to the control. Meanwhile, a 13.1 % reduction in energy charge level and a 15.2 % decline in NADH content were found, which implied the effects on carbon metabolism and redox balance. In addition, transcriptomic analysis revealed that excessive sodium altered the gene expression profiles related to ATPase, hydrolase, and oxidoreductase, as well as pathways like glyoxylate metabolism, and transmembrane transport. These findings gained insights into the metabolic regulation of A. niger response to environmental stress and provided theoretical guidance for the construction of sodium-tolerant A. niger for industrial application.
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Affiliation(s)
- Jian Xu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Sulian Cheng
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Ruijing Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Fengjiao Cai
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Zhengjun Zhu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Jinghua Cao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Jiangbo Wang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Qi Yu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China.
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7
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Książek E. Citric Acid: Properties, Microbial Production, and Applications in Industries. Molecules 2023; 29:22. [PMID: 38202605 PMCID: PMC10779990 DOI: 10.3390/molecules29010022] [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: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Citric acid finds broad applications in various industrial sectors, such as the pharmaceutical, food, chemical, and cosmetic industries. The bioproduction of citric acid uses various microorganisms, but the most commonly employed ones are filamentous fungi such as Aspergillus niger and yeast Yarrowia lipolytica. This article presents a literature review on the properties of citric acid, the microorganisms and substrates used, different fermentation techniques, its industrial utilization, and the global citric acid market. This review emphasizes that there is still much to explore, both in terms of production process techniques and emerging new applications of citric acid.
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Affiliation(s)
- Ewelina Książek
- Department of Agroenginieering and Quality Analysis, Faculty of Production Engineering, Wroclaw University of Economics and Business, Komandorska 118-120, 53-345 Wrocław, Poland
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Liu Z, Fu B, Wang J, Li W, Hu Y, Liu Z, Fu C, Li D, Wang C, Xu N. Transcriptomics Reveals the Effect of Strain Interactions on the Growth of A. Oryzae and Z. Rouxii. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5525-5534. [PMID: 36989392 DOI: 10.1021/acs.jafc.3c00664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The microbial community structure in traditional fermented foods is quite complex, making the relationship between strains unclear. In this regard, the co-culture system can simulate microbial interactions during food fermentation and reveal the morphological changes, metabolic processes, and gene expression of microbial communities. The present study sought to investigate the effects of microbial interactions on the growth of Aspergillus oryzae and Zygosaccharomyces rouxii through omics. After co-cultivation, the pH value and dry weight were consistent with the pure culture of Z. rouxii. Additionally, the consumption of reducing sugar decreased, and the enzymatic activity increased compared with the pure culture of fungus. The analysis of volatile organic compounds (VOCs) and transcriptomics showed that co-culture significantly promoted the effect on Z. rouxii. A total of 6 different VOCs and 2202 differentially expressed genes were identified in the pure and co-culture of Z. rouxii. The differentially expressed genes were mainly related to the endonucleolytic cleavage of rRNA, ribosome biogenesis in eukaryotes, and RNA polymerase metabolic pathways. The study results will provide insights into the effect of microbial interactions on the growth of A. oryzae and Z. rouxii.
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Affiliation(s)
- Zeping Liu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Bin Fu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Jing Wang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Wei Li
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Yong Hu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Zhijie Liu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Caixia Fu
- Hubei Tulaohan Flavouring and Food Co., Ltd., Yichang, Hubei 443000, China
| | - Dongsheng Li
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Chao Wang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Ning Xu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
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Valladares-Diestra KK, Porto de Souza Vandenberghe L, Soccol CR. Integrated xylooligosaccharides production from imidazole-treated sugarcane bagasse with application of in house produced enzymes. BIORESOURCE TECHNOLOGY 2022; 362:127800. [PMID: 36007765 DOI: 10.1016/j.biortech.2022.127800] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
The application of biorefinery concepts to produce different value-added biomolecules such as xylooligosaccharides (XOs) generates economical competitive, sustainable and environmentally friendly processes. The objective of this work was to develop an efficient imidazole-pretreatment process of sugarcane bagasse (SB) and the use of the obtained hemicellulose fraction in the production of XOs with the application of in house produced xylanolytic enzymes using SB as substrate, under a biorefinery approach. SB imidazole pretreatment allowed the recovery of a hemicellulose rich fraction (34%) with 91.2% of delignification. Xylanase production by Aspergillus niger reached 53.1 U·mL-1 at 120 h. The application of produced xylanases in the enzymatic hydrolysis of extracted xylan, allowed the production of 6.06 g·L-1 of XOs, where xylotriose represented >70%. Great perspectives are viewed for the implementation of mixed processes in a sustainable closed cycle to produce biomolecules with concomitant valorization of subproducts from SB chain.
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Affiliation(s)
- Kim Kley Valladares-Diestra
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba-PR 81531-980, Brazil
| | - Luciana Porto de Souza Vandenberghe
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba-PR 81531-980, Brazil.
| | - Carlos Ricardo Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba-PR 81531-980, Brazil
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Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. mSystems 2022; 7:e0023222. [PMID: 35638725 PMCID: PMC9239088 DOI: 10.1128/msystems.00232-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Secondary metabolite clusters (SMCs) encode the machinery for fungal toxin production. However, understanding their function and analyzing their products requires investigation of the developmental and environmental conditions in which they are expressed. Gene expression is often restricted to specific and unexamined stages of the life cycle. Therefore, we applied comparative genomics analyses to identify SMCs in Neurospora crassa and analyzed extensive transcriptomic data spanning nine independent experiments from diverse developmental and environmental conditions to reveal their life cycle-specific gene expression patterns. We reported 20 SMCs comprising 177 genes-a manageable set for investigation of the roles of SMCs across the life cycle of the fungal model N. crassa-as well as gene sets coordinately expressed in 18 predicted SMCs during asexual and sexual growth under three nutritional and two temperature conditions. Divergent activity of SMCs between asexual and sexual development was reported. Of 126 SMC genes that we examined for knockout phenotypes, al-2 and al-3 exhibited phenotypes in asexual growth and conidiation, whereas os-5, poi-2, and pmd-1 exhibited phenotypes in sexual development. SMCs with annotated function in mating and crossing were actively regulated during the switch between asexual and sexual growth. Our discoveries call for attention to roles that SMCs may play in the regulatory switches controlling mode of development, as well as the ecological associations of those developmental stages that may influence expression of SMCs. IMPORTANCE Secondary metabolites (SMs) are low-molecular-weight compounds that often mediate interactions between fungi and their environments. Fungi enriched with SMs are of significant research interest to agriculture and medicine, especially from the aspects of pathogen ecology and environmental epidemiology. However, SM clusters (SMCs) that have been predicted by comparative genomics alone have typically been poorly defined and insufficiently functionally annotated. Therefore, we have investigated coordinate expression in SMCs in the model system N. crassa, and our results suggest that SMCs respond to environmental signals and to stress that are associated with development. This study examined SMC regulation at the level of RNA to integrate observations and knowledge of these genes in various growth and development conditions, supporting combining comparative genomics and inclusive transcriptomics to improve computational annotation of SMCs. Our findings call for detailed study of the function of SMCs during the asexual-sexual switch, a key, often-overlooked developmental stage.
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11
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Li J, Duan Y, Hu Z, Yang F, Wu X, Zhang R. Physiological mechanisms by which gypsum increases the growth and yield of Lentinula edodes. Appl Microbiol Biotechnol 2022; 106:2677-2688. [PMID: 35338385 DOI: 10.1007/s00253-022-11884-4] [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: 09/02/2021] [Revised: 03/05/2022] [Accepted: 03/12/2022] [Indexed: 11/02/2022]
Abstract
Lentinula edodes is one of the most important commercially cultivated edible mushrooms. It is well known that gypsum (CaSO4·2H2O) supplementation in sawdust medium increases the yield of L. edodes, while the physiological mechanisms remain unclear. Our previous study showed that the acidification of the medium to pH 3.5-4.0 was essential for the growth of L. edodes. In this study, it was found that the oxalic acid excreted by L. edodes was responsible for the acidification of the medium. The biosynthesis of oxalic acid was regulated by the ambient pH and buffer capacity of the medium. To acidify the sawdust medium, the concentrations of total and soluble oxalate were 51.1 mmol/kg and 10.8 mmol/kg, respectively. However, when the concentration of soluble oxalate was 8.0 mmol/kg, the mycelial growth rate decreased by 29% compared with the control. Soluble oxalate was toxic to L. edodes, while soluble sulfate was nontoxic. CaSO4 reacted with soluble oxalate to form nontoxic insoluble CaC2O4 and the strong acid H2SO4. When the CaSO4 supplemented in sawdust medium was more than 25 mmol/kg, the soluble oxalate decreased to less than 1 mmol/kg, and the mycelial growth rate increased by 32% compared with the control. In conclusion, gypsum improved the growth and yield by relieving the toxicity of oxalate and facilitating the acidification of sawdust medium. KEY POINTS: • L. edodes excretes oxalic acid to acidify the ambient environment for growth. • Soluble oxalate is toxic to L. edodes. • Gypsum increases growth by reacting with oxalate to relieve its toxicity.
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Affiliation(s)
- Jintao Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yingce Duan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Ziyi Hu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Fan Yang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Xiangli Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Ruiying Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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12
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Jiao W, Liu X, Li Y, Li B, Du Y, Zhang Z, Chen Q, Fu M. Organic acid, a virulence factor for pathogenic fungi, causing postharvest decay in fruits. MOLECULAR PLANT PATHOLOGY 2022; 23:304-312. [PMID: 34820999 PMCID: PMC8743014 DOI: 10.1111/mpp.13159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Decay due to fungal infection is a major cause of postharvest losses in fruits. Acidic fungi may enhance their virulence by locally reducing the pH of the host. Several devastating postharvest fungi, such as Penicillium spp., Botrytis cinerea, and Sclerotinia sclerotiorum, can secrete gluconic acid, oxalic acid, or citric acid. Emerging evidence suggests that organic acids secreted by acidic fungi are important virulence factors. In this review, we summarized the research progress on the biosynthesis of organic acids, the role of the pH signalling transcription factor PacC in regulating organic acid, and the action mechanism of the main organic acid secreted via postharvest pathogenic fungi during infection of host tissues. This paper systematically demonstrates the relationships between tissue acidification and postharvest fungal pathogenicity, which will motivate the study of host-pathogen interactions and provide a better understanding of virulence mechanisms of the pathogens so as to design new technical strategies to prevent postharvest diseases.
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Affiliation(s)
- Wenxiao Jiao
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Xin Liu
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Youyuan Li
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Boqiang Li
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Yamin Du
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Zhanquan Zhang
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Qingmin Chen
- College of Food Science and EngineeringShandong Agricultural and Engineering UniversityJinanChina
| | - Maorun Fu
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
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13
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Soil bacteria protect fungi from phenazines by acting as toxin sponges. Curr Biol 2022; 32:275-288.e5. [PMID: 34813731 PMCID: PMC8792240 DOI: 10.1016/j.cub.2021.11.002] [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: 03/28/2021] [Revised: 08/12/2021] [Accepted: 11/01/2021] [Indexed: 01/26/2023]
Abstract
Many environmentally and clinically important fungi are sensitive to toxic, bacterially produced, redox-active molecules called phenazines. Despite being vulnerable to phenazine assault, fungi inhabit microbial communities that contain phenazine producers. Because many fungi cannot withstand phenazine challenge but some bacterial species can, we hypothesized that bacterial partners may protect fungi in phenazine-replete environments. From a single soil sample, we were able to co-isolate several such physically associated pairings. We discovered the novel species Paraburkholderia edwinii and demonstrated it can protect a co-isolated Aspergillus species from phenazine-1-carboxylic acid (PCA) by sequestering it, acting as a toxin sponge; in turn, it also gains protection. When challenged with PCA, P. edwinii changes its morphology, forming aggregates within the growing fungal colony. Further, the fungal partner triggers P. edwinii to sequester PCA and maintains conditions that limit PCA toxicity by promoting an anoxic and highly reducing environment. A mutagenic screen of P. edwinii revealed this protective program depends on the stress-inducible transcriptional repressor HrcA. We show that one relevant stressor in response to PCA challenge is fungal acidification and that acid stress causes P. edwinii to behave as though the fungus were present. Finally, we reveal this phenomenon as widespread among Paraburkholderia with moderate specificity among bacterial and fungal partners, including plant and human pathogens. Our discovery suggests a common mechanism by which fungi can gain access to phenazine-replete environments and provides a tractable model system for its study. These results have implications for how microbial communities in the rhizosphere as well as in plant and human infection sites negotiate community membership via a chemical dialectic.
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14
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Wu M, Wei H, Ma K, Cui P, Zhu S, Lai D, Ren J, Wang W, Fan A, Lin W, Su H. ThpacC Acts as a Positive Regulator of Homodimericin A Biosynthesis and Antifungal Activities of Trichoderma harzianum 3.9236. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12695-12704. [PMID: 34677054 DOI: 10.1021/acs.jafc.1c04330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Pal/Rim pathway and its key transcription factor PacC play important roles in fungal adaptation to ambient pH regarding growth, secondary metabolism, and virulence. However, the effect of PacC on the secondary metabolism of the important biocontrol fungus Trichoderma harzianum remains elusive. To answer this question, ThpacC deletion (KO-ThpacC) and overexpression (OE-ThpacC) mutants of T. harzianum 3.9236 were constructed. Transcriptomic analysis of T. harzianum and KO-ThpacC suggested that ThpacC acted as both a positive and a negative regulator for secondary metabolite (SM) production. Further investigation revealed that deletion of ThpacC abolished homodimericin A and 8-epi-homodimericin A production. Moreover, ThpacC plays a role in the antagonism of T. harzianum against Sclerotinia sclerotiorum. 8-epi-Homodimericin A demonstrated moderate inhibitory activity against S. sclerotiorum. Our results contribute to a deeper understanding of the ThpacC function on SM production and the antifungal activity of T. harzianum.
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Affiliation(s)
- Mengyue Wu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 15 North Third Ring Road, Chaoyang District, Beijing 100029, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, P. R. China
| | - Huiling Wei
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 15 North Third Ring Road, Chaoyang District, Beijing 100029, P. R. China
| | - Ke Ma
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, P. R. China
| | - Peiqi Cui
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 15 North Third Ring Road, Chaoyang District, Beijing 100029, P. R. China
| | - Shaozhou Zhu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 15 North Third Ring Road, Chaoyang District, Beijing 100029, P. R. China
| | - Daowan Lai
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, P. R. China
| | - Jinwei Ren
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Wenzhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Aili Fan
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 15 North Third Ring Road, Chaoyang District, Beijing 100029, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, P. R. China
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, P. R. China
| | - Haijia Su
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 15 North Third Ring Road, Chaoyang District, Beijing 100029, P. R. China
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15
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Farkas B, Vojtková H, Bujdoš M, Kolenčík M, Šebesta M, Matulová M, Duborská E, Danko M, Kim H, Kučová K, Kisová Z, Matúš P, Urík M. Fungal Mobilization of Selenium in the Presence of Hausmannite and Ferric Oxyhydroxides. J Fungi (Basel) 2021; 7:jof7100810. [PMID: 34682232 PMCID: PMC8539610 DOI: 10.3390/jof7100810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/06/2023] Open
Abstract
Bioleaching of mineral phases plays a crucial role in the mobility and availability of various elements, including selenium. Therefore, the leachability of selenium associated with the surfaces of ferric and manganese oxides and oxyhydroxides, the prevailing components of natural geochemical barriers, has been studied in the presence of filamentous fungus. Both geoactive phases were exposed to selenate and subsequently to growing fungus Aspergillus niger for three weeks. This common soil fungus has shown exceptional ability to alter the distribution and mobility of selenium in the presence of both solid phases. The fungus initiated the extensive bioextraction of selenium from the surfaces of amorphous ferric oxyhydroxides, while the hausmannite (Mn3O4) was highly susceptible to biodeterioration in the presence of selenium. This resulted in specific outcomes regarding the selenium, iron, and manganese uptake by fungus and residual selenium concentrations in mineral phases as well. The adverse effects of bioleaching on fungal growth are also discussed.
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Affiliation(s)
- Bence Farkas
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia; (B.F.); (M.B.); (M.Š.); (M.M.); (E.D.); (P.M.)
| | - Hana Vojtková
- Department of Environmental Engineering, Faculty of Mining and Geology, VŠB–Technical University of Ostrava, 17. Listopadu 15/2172, 708 00 Ostrava, Czech Republic; (H.V.); (K.K.)
| | - Marek Bujdoš
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia; (B.F.); (M.B.); (M.Š.); (M.M.); (E.D.); (P.M.)
| | - Marek Kolenčík
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia;
| | - Martin Šebesta
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia; (B.F.); (M.B.); (M.Š.); (M.M.); (E.D.); (P.M.)
| | - Michaela Matulová
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia; (B.F.); (M.B.); (M.Š.); (M.M.); (E.D.); (P.M.)
| | - Eva Duborská
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia; (B.F.); (M.B.); (M.Š.); (M.M.); (E.D.); (P.M.)
| | - Martin Danko
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia;
| | - Hyunjung Kim
- Department of Mineral Resources and Energy Engineering, Jeonbuk National University, Jeonju 54896, Jeonbuk, Korea;
- Department of Environment and Energy, Jeonbuk National University, Jeonju 54896, Jeonbuk, Korea
| | - Kateřina Kučová
- Department of Environmental Engineering, Faculty of Mining and Geology, VŠB–Technical University of Ostrava, 17. Listopadu 15/2172, 708 00 Ostrava, Czech Republic; (H.V.); (K.K.)
| | - Zuzana Kisová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia;
| | - Peter Matúš
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia; (B.F.); (M.B.); (M.Š.); (M.M.); (E.D.); (P.M.)
| | - Martin Urík
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia; (B.F.); (M.B.); (M.Š.); (M.M.); (E.D.); (P.M.)
- Correspondence:
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16
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Turning Inside Out: Filamentous Fungal Secretion and Its Applications in Biotechnology, Agriculture, and the Clinic. J Fungi (Basel) 2021; 7:jof7070535. [PMID: 34356914 PMCID: PMC8307877 DOI: 10.3390/jof7070535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/25/2021] [Indexed: 12/15/2022] Open
Abstract
Filamentous fungi are found in virtually every marine and terrestrial habitat. Vital to this success is their ability to secrete a diverse range of molecules, including hydrolytic enzymes, organic acids, and small molecular weight natural products. Industrial biotechnologists have successfully harnessed and re-engineered the secretory capacity of dozens of filamentous fungal species to make a diverse portfolio of useful molecules. The study of fungal secretion outside fermenters, e.g., during host infection or in mixed microbial communities, has also led to the development of novel and emerging technological breakthroughs, ranging from ultra-sensitive biosensors of fungal disease to the efficient bioremediation of polluted environments. In this review, we consider filamentous fungal secretion across multiple disciplinary boundaries (e.g., white, green, and red biotechnology) and product classes (protein, organic acid, and secondary metabolite). We summarize the mechanistic understanding for how various molecules are secreted and present numerous applications for extracellular products. Additionally, we discuss how the control of secretory pathways and the polar growth of filamentous hyphae can be utilized in diverse settings, including industrial biotechnology, agriculture, and the clinic.
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17
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Zhou J, Zhuang Y, Xia J. Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions. Microb Cell Fact 2021; 20:125. [PMID: 34193117 PMCID: PMC8247156 DOI: 10.1186/s12934-021-01614-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022] Open
Abstract
Background Genome-scale metabolic model (GSMM) is a powerful tool for the study of cellular metabolic characteristics. With the development of multi-omics measurement techniques in recent years, new methods that integrating multi-omics data into the GSMM show promising effects on the predicted results. It does not only improve the accuracy of phenotype prediction but also enhances the reliability of the model for simulating complex biochemical phenomena, which can promote theoretical breakthroughs for specific gene target identification or better understanding the cell metabolism on the system level. Results Based on the basic GSMM model iHL1210 of Aspergillus niger, we integrated large-scale enzyme kinetics and proteomics data to establish a GSMM based on enzyme constraints, termed a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO). The results show that enzyme constraints effectively improve the model’s phenotype prediction ability, and extended the model’s potential to guide target gene identification through predicting metabolic phenotype changes of A. niger by simulating gene knockout. In addition, enzyme constraints significantly reduced the solution space of the model, i.e., flux variability over 40.10% metabolic reactions were significantly reduced. The new model showed also versatility in other aspects, like estimating large-scale \documentclass[12pt]{minimal}
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\begin{document}$$k_{{cat}}$$\end{document}kcat values, predicting the differential expression of enzymes under different growth conditions. Conclusions This study shows that incorporating enzymes’ abundance information into GSMM is very effective for improving model performance with A. niger. Enzyme-constrained model can be used as a powerful tool for predicting the metabolic phenotype of A. niger by incorporating proteome data. In the foreseeable future, with the fast development of measurement techniques, and more precise and rich proteomics quantitative data being obtained for A. niger, the enzyme-constrained GSMM model will show greater application space on the system level. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01614-2.
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Affiliation(s)
- Jingru Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, 300308, China.
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18
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Laothanachareon T, Bruinsma L, Nijsse B, Schonewille T, Suarez-Diez M, Tamayo-Ramos JA, Martins dos Santos VAP, Schaap PJ. Global Transcriptional Response of Aspergillus niger to Blocked Active Citrate Export through Deletion of the Exporter Gene. J Fungi (Basel) 2021; 7:jof7060409. [PMID: 34071072 PMCID: PMC8224569 DOI: 10.3390/jof7060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Aspergillus niger is the major industrial citrate producer worldwide. Export as well as uptake of citric acid are believed to occur by active, proton-dependent, symport systems. Both are major bottlenecks for industrial citrate production. Therefore, we assessed the consequences of deleting the citT gene encoding the A. niger citrate exporter, effectively blocking active citrate export. We followed the consumption of glucose and citrate as carbon sources, monitored the secretion of organic acids and carried out a thorough transcriptome pathway enrichment analysis. Under controlled cultivation conditions that normally promote citrate secretion, the knock-out strain secreted negligible amounts of citrate. Blocking active citrate export in this way led to a reduced glucose uptake and a reduced expression of high-affinity glucose transporter genes, mstG and mstH. The glyoxylate shunt was strongly activated and an increased expression of the OAH gene was observed, resulting in a more than two-fold higher concentration of oxalate in the medium. Deletion of citT did not affect citrate uptake suggesting that citrate export and citrate uptake are uncoupled from the system.
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Affiliation(s)
- Thanaporn Laothanachareon
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani 12120, Thailand
- Correspondence: (T.L.); (V.A.P.M.d.S.)
| | - Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Tom Schonewille
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Juan Antonio Tamayo-Ramos
- International Research Center in Critical Raw Materials-ICCRAM, University of Burgos, 09001 Burgos, Spain;
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
- LifeGlimmer GmbH, 12163 Berlin, Germany
- Correspondence: (T.L.); (V.A.P.M.d.S.)
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
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19
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Ferrier J, Csetenyi L, Gadd GM. Fungal transformation of natural and synthetic cobalt-bearing manganese oxides and implications for cobalt biogeochemistry. Environ Microbiol 2021; 24:667-677. [PMID: 33955141 DOI: 10.1111/1462-2920.15526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 11/29/2022]
Abstract
Manganese oxide minerals can become enriched in a variety of metals through adsorption and redox processes, and this forms the basis for a close geochemical relationship between Mn oxide phases and Co. Since oxalate-producing fungi can effect geochemical transformation of Mn oxides, an understanding of the fate of Co during such processes could provide new insights on the geochemical behaviour of Co. In this work, the transformation of Mn oxides by Aspergillus niger was investigated using a Co-bearing manganiferous laterite, and a synthetic Co-doped birnessite. A. niger could transform laterite in both fragmented and powder forms, resulting in formation of biomineral crusts that were composed of Mn oxalates hosting Co, Ni and, in transformed laterite fragments, Mg. Total transformation of Co-doped birnessite resulted in precipitation of Co-bearing Mn oxalate. Fungal transformation of the Mn oxide phases included Mn(III,IV) reduction by oxalate, and may also have involved reduction of Co(III) to Co(II). These findings demonstrate that oxalate-producing fungi can influence Co speciation in Mn oxides, with implications for other hosted metals including Al and Fe. This work also provides further understanding of the roles of fungi as geoactive agents which can inform potential applications in metal bioremediation, recycling and biorecovery.
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Affiliation(s)
- John Ferrier
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK
| | - Laszlo Csetenyi
- School of Science and Engineering, Fulton Building, University of Dundee, Dundee, Scotland, DD1 5HN, UK
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK.,State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, College of Chemical Engineering and Environment, China University of Petroleum, 18 Fuxue Road, Changping District, Beijing, 102249, China
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20
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Ghaffarinasab S, Motamedian E. Improving ethanol production by studying the effect of pH using a modified metabolic model and a systemic approach. Biotechnol Bioeng 2021; 118:2934-2946. [PMID: 33913513 DOI: 10.1002/bit.27800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/19/2021] [Accepted: 04/21/2021] [Indexed: 11/06/2022]
Abstract
pH is an important factor affecting the growth and production of microorganisms; especially, its effect on ethanologenic microorganisms. It can change the ionization state of metabolites via the change in the charge of their functional groups that may lead to metabolic alteration. Here, we estimated the ionization state of metabolites and balanced the charge of reactions in genome-scale metabolic models of Saccharomyces cerevisiae, Escherichia coli, and Zymomonas mobilis at pH levels 5, 6, and 7. The robustness analysis was first implemented to anticipate the effect of proton exchange flux on growth rates for the constructed metabolic models at various pH. In accordance with previous experimental reports, the models predict that Z. mobilis is more sensitive to pH rather than S. cerevisiae and the yeast is more regulated by pH rather than E. coli. Then, a systemic approach was proposed to predict the pH effect on metabolic change and to find effective reactions on ethanol production in S. cerevisiae. The correlated reactions with ethanol production at predicted optimal pH in a range of proton exchange rates determined by robustness analysis were identified using the Pearson correlation coefficient. Then, fluxes of these reactions were applied to cluster the various pHs by principal component analysis and to identify the role of these reactions on metabolic differentiation because of pH change. Finally, 12 reactions were selected for up and downregulation to improve ethanol production. Enzyme regulators of the selected reactions were identified using the BRENDA database and 11 selected regulators were screened and optimized via Plackett-Burman and two-level full factorial designs, respectively. The proposed approach has enhanced yields of ethanol from 0.18 to 0.36 mol/mol carbon. Hence, not only a comprehensive approach for understanding the effect of pH on metabolism was proposed in this study, but also it successfully introduced key manipulations for ethanol overproduction.
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Affiliation(s)
- Sajjad Ghaffarinasab
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Motamedian
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
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Yang L, Henriksen MM, Hansen RS, Lübeck M, Vang J, Andersen JE, Bille S, Lübeck PS. Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR-Cas9 system for succinic acid production from renewable biomass. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:206. [PMID: 33317620 PMCID: PMC7737382 DOI: 10.1186/s13068-020-01850-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/04/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Succinic acid has great potential to be a new bio-based building block for deriving a number of value-added chemicals in industry. Bio-based succinic acid production from renewable biomass can provide a feasible approach to partially alleviate the dependence of global manufacturing on petroleum refinery. To improve the economics of biological processes, we attempted to explore possible solutions with a fungal cell platform. In this study, Aspergillus niger, a well-known industrial production organism for bio-based organic acids, was exploited for its potential for succinic acid production. RESULTS With a ribonucleoprotein (RNP)-based CRISPR-Cas9 system, consecutive genetic manipulations were realized in engineering of the citric acid-producing strain A. niger ATCC 1015. Two genes involved in production of two byproducts, gluconic acid and oxalic acid, were disrupted. In addition, an efficient C4-dicarboxylate transporter and a soluble NADH-dependent fumarate reductase were overexpressed. The resulting strain SAP-3 produced 17 g/L succinic acid while there was no succinic acid detected at a measurable level in the wild-type strain using a synthetic substrate. Furthermore, two cultivation parameters, temperature and pH, were investigated for their effects on succinic acid production. The highest amount of succinic acid was obtained at 35 °C after 3 days, and low culture pH had inhibitory effects on succinic acid production. Two types of renewable biomass were explored as substrates for succinic acid production. After 6 days, the SAP-3 strain was capable of producing 23 g/L and 9 g/L succinic acid from sugar beet molasses and wheat straw hydrolysate, respectively. CONCLUSIONS In this study, we have successfully applied the RNP-based CRISPR-Cas9 system in genetic engineering of A. niger and significantly improved the succinic acid production in the engineered strain. The studies on cultivation parameters revealed the impacts of pH and temperature on succinic acid production and the future challenges in strain development. The feasibility of using renewable biomass for succinic acid production by A. niger has been demonstrated with molasses and wheat straw hydrolysate.
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Affiliation(s)
- Lei Yang
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark.
| | - Mikkel Møller Henriksen
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
| | - Rasmus Syrach Hansen
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
| | - Mette Lübeck
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
| | - Jesper Vang
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
- Disease Data Intelligence, Department of Health Technology Bioinformatics, Technical University of Denmark, Bldg. 208, 2800, KemitorvetKgs. Lyngby, Denmark
| | - Julie Egelund Andersen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Signe Bille
- Section of Cell and Neurobiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Peter Stephensen Lübeck
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
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22
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Differences in metabolites production using the Biolog FF Microplate™ system with an emphasis on some organic acids of Aspergillus niger wild type strains. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00521-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Upton DJ, McQueen-Mason SJ, Wood AJ. In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:27. [PMID: 32123544 PMCID: PMC7038614 DOI: 10.1186/s13068-020-01678-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/06/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The fungus Aspergillus niger is an important industrial organism for citric acid fermentation; one of the most efficient biotechnological processes. Previously we introduced a dynamic model that captures this process in the industrially relevant batch fermentation setting, providing a more accurate predictive platform to guide targeted engineering. In this article we exploit this dynamic modelling framework, coupled with a robust genetic algorithm for the in silico evolution of A. niger organic acid production, to provide solutions to complex evolutionary goals involving a multiplicity of targets and beyond the reach of simple Boolean gene deletions. We base this work on the latest metabolic models of the parent citric acid producing strain ATCC1015 dedicated to organic acid production with the required exhaustive genomic coverage needed to perform exploratory in silico evolution. RESULTS With the use of our informed evolutionary framework, we demonstrate targeted changes that induce a complete switch of acid output from citric to numerous different commercially valuable target organic acids including succinic acid. We highlight the key changes in flux patterns that occur in each case, suggesting potentially valuable targets for engineering. We also show that optimum acid productivity is achieved through a balance of organic acid and biomass production, requiring finely tuned flux constraints that give a growth rate optimal for productivity. CONCLUSIONS This study shows how a genome-scale metabolic model can be integrated with dynamic modelling and metaheuristic algorithms to provide solutions to complex metabolic engineering goals of industrial importance. This framework for in silico guided engineering, based on the dynamic batch growth relevant to industrial processes, offers considerable potential for future endeavours focused on the engineering of organisms to produce valuable products.
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Affiliation(s)
- Daniel J. Upton
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | | | - A. Jamie Wood
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
- Department of Mathematics, University of York, Heslington, York, YO10 5DD UK
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Artmann DJ, Vrabl P, Gianordoli R, Burgstaller W. Challenging the charge balance hypothesis: reconsidering buffer effect and reuptake of previously excreted organic acids by Penicillium ochrochloron. FEMS Microbiol Lett 2020; 367:5780226. [PMID: 32129848 PMCID: PMC7150580 DOI: 10.1093/femsle/fnaa039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/03/2020] [Indexed: 01/15/2023] Open
Abstract
Penicillium ochrochloron was used in the past for the leaching of zinc from a zinc oxide containing filter dust via excreted organic acids. Organic acid excretion by P. ochrochloron was stimulated by the addition of an extracellular buffer (2-(N-Morpholino)ethanesulfonic acid, MES; or zinc oxide, ZnO: ZnO + 2 H+ → Zn2+ + H2O). It was tested if the buffer stimulated excretion of organic acid anions is due to the necessity of an anion efflux across the plasma membrane to maintain electroneutrality by balancing the excretion of protons by the H+-ATPase. This charge balance hypothesis was previously postulated for P. ochrochloron. Two strains of P. ochrochloron were studied, which differed in growth parameters and amount of excreted organic acids. From the results, it was concluded that charge balance at the plasma membrane is not the main reason for organic acid excretion in these two strains of P. ochrochloron. Furthermore, the phenomenon of reuptake of excreted organic acids in the presence of about 100 mM of glucose is confirmed. It is suggested that the equilibrium between extracellular and intracellular organic acid anions may be maintained passively by a facilitated diffusion transporter.
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Affiliation(s)
- D J Artmann
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Österreich
| | - P Vrabl
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Österreich
| | - R Gianordoli
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Österreich
| | - W Burgstaller
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Österreich
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Cortesão M, Schütze T, Marx R, Moeller R, Meyer V. Fungal Biotechnology in Space: Why and How? GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_18] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Polák F, Urík M, Bujdoš M, Matúš P. Aspergillus niger enhances oxalate production as a response to phosphate deficiency induced by aluminium(III). J Inorg Biochem 2019; 204:110961. [PMID: 31887612 DOI: 10.1016/j.jinorgbio.2019.110961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/13/2019] [Accepted: 12/10/2019] [Indexed: 10/25/2022]
Abstract
This paper investigates Aspergillus niger's behaviour in the presence of mobile Al3+ species by evaluating the changes in oxalate exudation at various aluminium contents. When the fungus was exposed to Al3+, no significant changes in oxalate production were observed until 100 mg.L-1 aluminium was reached resulting in oxalate production decrease by 18.2%. By stripping the culture medium completely of phosphate, even more prominent decrease by 34.8% and 67.1% at 10 and 100 mg.L-1 aluminium was observed, respectively, indicating the phosphate's significance instead of Al3+ in oxalate production. Our results suggest that the low phosphate bioavailability, which most likely resulted from its interaction with Al3+, stimulated the overproduction of oxalate by A. niger. Furthermore, when the fungus was incubated in aluminium-free media supplemented with 0.1 mM of phosphate, oxalate production increased up to 281.5 μmol.g-1, while at 1.85 mM of available phosphate only 80.7 μmol.g-1 of oxalate was produced. This indicates that oxalic acid is produced by fungus not as a mean to detoxify aluminium, but as an attempt to gain access to additional phosphate.
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Affiliation(s)
- Filip Polák
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 84215 Bratislava, Slovakia; Department of Soil Science and Soil Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcka 129, Prague Suchdol 16500, Czech Republic.
| | - Martin Urík
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Marek Bujdoš
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Peter Matúš
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 84215 Bratislava, Slovakia
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Hossain AH, Hendrikx A, Punt PJ. Identification of novel citramalate biosynthesis pathways in Aspergillus niger. Fungal Biol Biotechnol 2019; 6:19. [PMID: 31827810 PMCID: PMC6862759 DOI: 10.1186/s40694-019-0084-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/04/2019] [Indexed: 11/26/2022] Open
Abstract
Background The filamentous fungus Aspergillus niger is frequently used for industrial production of fermentative products such as enzymes, proteins and biochemicals. Notable examples of industrially produced A. niger fermentation products are glucoamylase and citric acid. Most notably, the industrial production of citric acid achieves high titers, yield and productivities, a feat that has prompted researchers to propose A. niger to serve as heterologous production host for the industrial production of itaconic acid (IA), a promising sustainable chemical building-block for the fabrication of various synthetic resins, coatings, and polymers. Heterologous production of IA in A. niger has resulted in unexpected levels of metabolic rewiring that has led us to the identification of IA biodegradation pathway in A. niger. In this study we have attempted to identify the final product of the IA biodegradation pathway and analyzed the effect of metabolic rewiring on the bioproduction of 9 industrially relevant organic acids. Results IA biodegradation manifests in diminishing titers of IA and the occurrence of an unidentified compound in the HPLC profile. Based on published results on the IA biodegradation pathway, we hypothesized that the final product of IA biodegradation in A. niger may be citramalic acid (CM). Based on detailed HPLC analysis, we concluded that the unidentified compound is indeed CM. Furthermore, by transcriptome analysis we explored the effect of metabolic rewiring on the production of 9 industrially relevant organic acids by transcriptome analysis of IA producing and WT A. niger strains. Interestingly, this analysis led to the identification of a previously unknown biosynthetic cluster that is proposed to be involved in the biosynthesis of CM. Upon overexpression of the putative citramalate synthase and a genomically clustered organic acid transporter, we have observed CM bioproduction by A. niger. Conclusion In this study, we have shown that the end product of IA biodegradation pathway in A. niger is CM. Knock-out of the IA biodegradation pathway results in the cessation of CM production. Furthermore, in this study we have identified a citramalate biosynthesis pathway, which upon overexpression drives citramalate bioproduction in A. niger.
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Affiliation(s)
- Abeer H Hossain
- Dutch DNA Biotech B.V., Padualaan 8, 3584 CH Utrecht, The Netherlands.,2Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Aiko Hendrikx
- Dutch DNA Biotech B.V., Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Peter J Punt
- Dutch DNA Biotech B.V., Padualaan 8, 3584 CH Utrecht, The Netherlands
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Vrabl P, Schinagl CW, Artmann DJ, Heiss B, Burgstaller W. Fungal Growth in Batch Culture - What We Could Benefit If We Start Looking Closer. Front Microbiol 2019; 10:2391. [PMID: 31681243 PMCID: PMC6805767 DOI: 10.3389/fmicb.2019.02391] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/02/2019] [Indexed: 11/17/2022] Open
Abstract
Since filamentous fungi rapidly adjust their metabolic properties to environmental changes, a rigorous standardization and characterization of cultivation conditions is necessary to obtain meaningful and reproducible results. In batch cultures, which are commonly characterized according to the classical growth curve in textbooks (i.e., lag, exponential, stationary, and declining phase), this is of special difficulty. Although various studies in literature report atypically shaped growth curves of filamentous fungi in batch culture, systematic investigations on this topic are scarce and deviations are barely mentioned in textbooks. Summarizing approximately a decade of observations of growth characteristics from bioreactor batch grown filamentous fungi - in particular two strains (CBS123.823 and CBS123.824) of Penicillium ochrochloron - we demonstrate with a series of highly standardized bioreactor batch culture experiments that the classical growth curve failed to describe growth dynamics of the studied fungi in this work. The nature of the first exhausted nutrient was of remarkable importance for the resulting shape of the growth curve. In all experiments, online respirometry proved to be a powerful tool to distinguish growth phases and revealed more physiological states than expected from the mere biomass curve. In this respect we discuss why "atypical" shaped growth curves often remain unrecognized and that they might be the rule rather than the exception. Acknowledging the importance of the correct presentation of this complex topic in textbooks, we also propose a modified growth curve scheme to sensitize students for potential alternative shaped growth curves.
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Affiliation(s)
- Pamela Vrabl
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
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Wang JB, Zhang RJ, Mao ZG, Xue DS, Zhu ZJ, Yu HC, Cai FJ, Cai LY, Bao JW, Xu J. Full recycling of citric acid wastewater through anaerobic digestion, air-stripping and pH control. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 80:1196-1204. [PMID: 31799963 DOI: 10.2166/wst.2019.364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Anaerobic digestion effluent (ADE) from the anaerobic digestion treatment of citric acid wastewater can be reused as a potential substitute for process water in the citric acid fermentation. However, excessive sodium contained in ADE significantly decreases citric acid production. In this paper, the inhibition mechanism of sodium on citric acid fermentation was investigated. We demonstrated that excessive sodium did not increase oxidative stress for Aspergillus niger, but reduced the pH of the medium significantly over the period 4-24 h, which led to lower activities of glucoamylase and isomaltase secreted by A. niger, with a decrease of available sugar concentration and citric acid production. ADE was pretreated by air-stripping prior to recycle and 18 g/L calcium carbonate was added at the start of fermentation to control the pH of the medium. The inhibition caused by ADE was completely alleviated and citric acid production substantially increased from 118.6 g/L to 141.4 g/L, comparable to the fermentation with deionized water (141.2 g/L). This novel process could decrease wastewater discharges and fresh water consumption in the citric acid industry, with benefit to the environment.
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Affiliation(s)
- Jiang-Bo Wang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, China E-mail:
| | - Rui-Jing Zhang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, China E-mail:
| | - Zhong-Gui Mao
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Dong-Sheng Xue
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, China E-mail:
| | - Zheng-Jun Zhu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, China E-mail:
| | - Han-Chao Yu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, China E-mail:
| | - Feng-Jiao Cai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, China E-mail:
| | - Lin-Yang Cai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, China E-mail:
| | - Jia-Wei Bao
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jian Xu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, China E-mail: ; Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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Development of a Cre-loxP-based genetic system in Aspergillus niger ATCC1015 and its application to construction of efficient organic acid-producing cell factories. Appl Microbiol Biotechnol 2019; 103:8105-8114. [DOI: 10.1007/s00253-019-10054-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/08/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
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Brandl J, Aguilar-Pontes MV, Schäpe P, Noerregaard A, Arvas M, Ram AFJ, Meyer V, Tsang A, de Vries RP, Andersen MR. A community-driven reconstruction of the Aspergillus niger metabolic network. Fungal Biol Biotechnol 2018; 5:16. [PMID: 30275963 PMCID: PMC6158834 DOI: 10.1186/s40694-018-0060-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/17/2018] [Indexed: 11/17/2022] Open
Abstract
Background Aspergillus niger is an important fungus used in industrial applications for enzyme and acid production. To enable rational metabolic engineering of the species, available information can be collected and integrated in a genome-scale model to devise strategies for improving its performance as a host organism. Results In this paper, we update an existing model of A. niger metabolism to include the information collected from 876 publications, thereby expanding the coverage of the model by 940 reactions, 777 metabolites and 454 genes. In the presented consensus genome-scale model of A. niger iJB1325 , we integrated experimental data from publications and patents, as well as our own experiments, into a consistent network. This information has been included in a standardized way, allowing for automated testing and continuous improvements in the future. This repository of experimental data allowed the definition of 471 individual test cases, of which the model complies with 373 of them. We further re-analyzed existing transcriptomics and quantitative physiology data to gain new insights on metabolism. Additionally, the model contains 3482 checks on the model structure, thereby representing the best validated genome-scale model on A. niger developed until now. Strain-specific model versions for strains ATCC 1015 and CBS 513.88 have been created containing all data used for model building, thereby allowing users to adopt the models and check the updated version against the experimental data. The resulting model is compliant with the SBML standard and therefore enables users to easily simulate it using their preferred software solution. Conclusion Experimental data on most organisms are scattered across hundreds of publications and several repositories.To allow for a systems level understanding of metabolism, the data must be integrated in a consistent knowledge network. The A. niger iJB1325 model presented here integrates the available data into a highly curated genome-scale model to facilitate the simulation of flux distributions, as well as the interpretation of other genome-scale data by providing the metabolic context. Electronic supplementary material The online version of this article (10.1186/s40694-018-0060-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julian Brandl
- 1Technical University of Denmark, Soeltofts Plads, Building 223, 2800 Kongens Lyngby, Denmark
| | - Maria Victoria Aguilar-Pontes
- 2Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Paul Schäpe
- 6Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Anders Noerregaard
- 1Technical University of Denmark, Soeltofts Plads, Building 223, 2800 Kongens Lyngby, Denmark
| | - Mikko Arvas
- 3VTT Technical Research Centre of Finland, Tietotie 2, 02044 Espoo, Finland.,7Present Address: Finnish Red Cross Blood Service, Helsinki, Finland
| | - Arthur F J Ram
- 5Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Vera Meyer
- 6Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Adrian Tsang
- 4Concordia University, 7141 Sherbrooke Street West, H4B1R6 Montreal, Québec Canada
| | - Ronald P de Vries
- 2Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mikael R Andersen
- 1Technical University of Denmark, Soeltofts Plads, Building 223, 2800 Kongens Lyngby, Denmark
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32
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Zheng X, Yu J, Cairns TC, Zhang L, Zhang Z, Zhang Q, Zheng P, Sun J, Ma Y. Comprehensive Improvement of Sample Preparation Methodologies Facilitates Dynamic Metabolomics of Aspergillus niger. Biotechnol J 2018; 14:e1800315. [PMID: 30144348 DOI: 10.1002/biot.201800315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/27/2018] [Indexed: 12/23/2022]
Abstract
Metabolomics is an essential discipline in industrial biotechnology. Sample preparation approaches dramatically influence data quality and, ultimately, interpretation and conclusions from metabolomic experiments. However, standardized protocols for highly reproducible metabolic datasets are limited, especially for the fungal cell factory Aspergillus niger. Here, an improved liquid chromatography-tandem mass spectrometry-based pipeline for A. niger metabolomics is developed. It is found that fast filtration with liquid nitrogen is more suitable for cell quenching, causing minimal disruption to cell integrity, and improved intracellular metabolite recovery when compared to cold methanol quenching approaches. Seven solutions are evaluated for intracellular metabolite extraction, and found acetonitrile/water (1:1, v/v) at -20 °C, combined with boiling ethanol extraction protocols, showed unbiased metabolite profiling. This improved methodology is applied to unveil the dynamic metabolite profile of one citrate over-producing A. niger isolate under citrate fermentation. Citrate precursors, especially pyruvate, oxaloacetate, and malate, are maintained at a relatively high intracellular level, which can be necessary for high citrate synthesis flux. Glutamine shows a similar trend compared to citrate production, suggesting glutamine may be involved in intracellular pH homeostasis. Taken together, this study delivers a highly standardized and improved metabolomics methodology and paves the way for systems metabolic engineering in biotechnologically important fungi.
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Affiliation(s)
- Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jiandong Yu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Timothy C Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihui Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhidan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Qiongqiong Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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Comparison of Heterotrophic Bioleaching and Ammonium Sulfate Ion Exchange Leaching of Rare Earth Elements from a Madagascan Ion-Adsorption Clay. MINERALS 2018. [DOI: 10.3390/min8060236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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34
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Xie H, Ma Q, Wei DZ, Wang FQ. Transcriptomic analysis of Aspergillus niger strains reveals the mechanism underlying high citric acid productivity. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0208-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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Singh D, Lee CH. Volatiles Mediated Interactions Between Aspergillus oryzae Strains Modulate Morphological Transition and Exometabolomes. Front Microbiol 2018; 9:628. [PMID: 29670599 PMCID: PMC5893800 DOI: 10.3389/fmicb.2018.00628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Notwithstanding its mitosporic nature, an improbable morpho-transformation state i. e., sclerotial development (SD), is vaguely known in Aspergillus oryzae. Nevertheless an intriguing phenomenon governing mold's development and stress response, the effects of exogenous factors engendering SD, especially the volatile organic compounds (VOCs) mediated interactions (VMI) pervasive in microbial niches have largely remained unexplored. Herein, we examined the effects of intra-species VMI on SD in A. oryzae RIB 40, followed by comprehensive analyses of associated growth rates, pH alterations, biochemical phenotypes, and exometabolomes. We cultivated A. oryzae RIB 40 (S1VMI: KACC 44967) opposite a non-SD partner strain, A. oryzae (S2: KCCM 60345), conditioning VMI in a specially designed “twin plate assembly.” Notably, SD in S1VMI was delayed relative to its non-conditioned control (S1) cultivated without partner strain (S2) in twin plate. Selectively evaluating A. oryzae RIB 40 (S1VMI vs. S1) for altered phenotypes concomitant to SD, we observed a marked disparity for corresponding growth rates (S1VMI < S1)7days, media pH (S1VMI > S1)7days, and biochemical characteristics viz., protease (S1VMI > S1)7days, amylase (S1VMI > nS1)3–7days, and antioxidants (S1VMI > S1)7days levels. The partial least squares—discriminant analysis (PLS-DA) of gas chromatography—time of flight—mass spectrometry (GC-TOF-MS) datasets for primary metabolites exhibited a clustered pattern (PLS1, 22.04%; PLS2, 11.36%), with 7 days incubated S1VMI extracts showed higher abundance of amino acids, sugars, and sugar alcohols with lower organic acids and fatty acids levels, relative to S1. Intriguingly, the higher amino acid and sugar alcohol levels were positively correlated with antioxidant activity, likely impeding SD in S1VMI. Further, the PLS-DA (PLS1, 18.11%; PLS2, 15.02%) based on liquid chromatography—mass spectrometry (LC-MS) datasets exhibited a notable disparity for post-SD (9–11 days) sample extracts with higher oxylipins and 13-desoxypaxilline levels in S1VMI relative to S1, intertwining Aspergillus morphogenesis and secondary metabolism. The analysis of VOCs for the 7 days incubated samples displayed considerably higher accumulation of C-8 compounds in the headspace of twin-plate experimental sets (S1VMI:S2) compared to those in non-conditioned controls (S1 and S2—without respective partner strains), potentially triggering altered morpho-transformation and concurring biochemical as well as metabolic states in molds.
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Affiliation(s)
- Digar Singh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
| | - Choong H Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
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36
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Vrabl P, Schinagl CW, Artmann DJ, Krüger A, Ganzera M, Pötsch A, Burgstaller W. The Dynamics of Plasma Membrane, Metabolism and Respiration (PM-M-R) in Penicillium ochrochloron CBS 123824 in Response to Different Nutrient Limitations-A Multi-level Approach to Study Organic Acid Excretion in Filamentous Fungi. Front Microbiol 2017; 8:2475. [PMID: 29312185 PMCID: PMC5732977 DOI: 10.3389/fmicb.2017.02475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/29/2017] [Indexed: 11/23/2022] Open
Abstract
Filamentous fungi are important cell factories. In contrast, we do not understand well even basic physiological behavior in these organisms. This includes the widespread phenomenon of organic acid excretion. One strong hurdle to fully exploit the metabolic capacity of these organisms is the enormous, highly environment sensitive phenotypic plasticity. In this work we explored organic acid excretion in Penicillium ochrochloron from a new point of view by simultaneously investigating three essential metabolic levels: the plasma membrane H+-ATPase (PM); energy metabolism, in particular adenine and pyridine nucleotides (M); and respiration, in particular the alternative oxidase (R). This was done in strictly standardized chemostat culture with different nutrient limitations (glucose, ammonium, nitrate, and phosphate). These different nutrient limitations led to various quantitative phenotypes (as represented by organic acid excretion, oxygen consumption, glucose consumption, and biomass formation). Glucose-limited grown mycelia were used as the reference point (very low organic acid excretion). Both ammonium and phosphate grown mycelia showed increased organic acid excretion, although the patterns of excreted acids were different. In ammonium-limited grown mycelia amount and activity of the plasma membrane H+-ATPase was increased, nucleotide concentrations were decreased, energy charge (EC) and catabolic reduction charge (CRC) were unchanged and alternative respiration was present but not quantifiable. In phosphate-limited grown mycelia (no data on the H+-ATPase) nucleotide concentrations were still lower, EC was slightly decreased, CRC was distinctly decreased and alternative respiration was present and quantifiable. Main conclusions are: (i) the phenotypic plasticity of filamentous fungi demands adaptation of sample preparation and analytical methods at the phenotype level; (ii) each nutrient condition is unique and its metabolic situation must be considered separately; (iii) organic acid excretion is inversely related to nucleotide concentration (but not EC); (iv) excretion of organic acids is the outcome of a simultaneous adjustment of several metabolic levels to nutrient conditions.
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Affiliation(s)
- Pamela Vrabl
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | | | - Anja Krüger
- Institute of Pharmacy/Pharmacognosy, University of Innsbruck, Innsbruck, Austria
| | - Markus Ganzera
- Institute of Pharmacy/Pharmacognosy, University of Innsbruck, Innsbruck, Austria
| | - Ansgar Pötsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, United Kingdom
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37
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Effect of medium pH on chemical selectivity of oxalic acid biosynthesis by Aspergillus niger W78C in submerged batch cultures with sucrose as a carbon source. CHEMICAL PAPERS 2017; 72:1089-1093. [PMID: 29681682 PMCID: PMC5908826 DOI: 10.1007/s11696-017-0354-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023]
Abstract
The pH of the medium is the key environmental parameter of chemical selectivity of oxalic acid biosynthesis by Aspergillus niger. The activity of the enzyme oxaloacetate hydrolase, which is responsible for decomposition of oxaloacetate to oxalate and acetate inside the cell of the fungus, is highest at pH 6. In the present study, the influence of pH in the range of 3–7 on oxalic acid secretion by A. niger W78C from sucrose was investigated. The highest oxalic acid concentration, 64.3 g dm−3, was reached in the medium with pH 6. The chemical selectivity of the process was 58.6% because of the presence of citric and gluconic acids in the cultivation broth in the amount of 15.3 and 30.2 g dm−3, respectively. Both an increase and a decrease of medium pH caused a decrease of oxalic acid concentration. The obtained results confirm that pH 6 of the carbohydrate medium is appropriate for oxalic acid synthesis by A. niger, but the chemical selectivity of the process described in this paper was high in comparison to values reported previously in the literature.
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38
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39
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Polák F, Urík M, Bujdoš M, Uhlík P, Matúš P. Evaluation of aluminium mobilization from its soil mineral pools by simultaneous effect of Aspergillus strains' acidic and chelating exometabolites. J Inorg Biochem 2017; 181:162-168. [PMID: 28927705 DOI: 10.1016/j.jinorgbio.2017.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/18/2017] [Accepted: 09/07/2017] [Indexed: 12/11/2022]
Abstract
This contribution investigates aluminium mobilization from main aluminium pools in soils, phyllosilicates and oxyhydroxides, by acidic and chelating exometabolites of common soil fungi Aspergillus niger and A. clavatus. Their exometabolites' acidity as well as their ability to extract aluminium from solid mineral phases differed significantly during incubation. While both strains are able to mobilize aluminium from boehmite and aluminium oxide mixture to some extent, A. clavatus struggles to mobilize any aluminium from gibbsite. Furthermore, passive and active fungal uptake of aluminium enhances its mobilization from boehmite, especially in later growth phase, with strong linear correlation between aluminium bioaccumulated fraction and increasing culture medium pH. We also provide data on concentrations of oxalate, citrate and gluconate which are synthesized by A. niger and contribute to aluminium mobilization. Compared to boehmite-free treatment, fungus reduces oxalate production significantly in boehmite presence to restrict aluminium extraction efficiency. However, in presence of high phyllosilicates' dosages, aluminium is released to an extent that acetate and citrate is overproduced by fungus. Our results also highlight fungal capability to significantly enhance iron and silicon mobility as these elements are extracted from mineral lattice of phyllosilicates by fungal exometabolites alongside aluminium.
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Affiliation(s)
- Filip Polák
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Martin Urík
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia.
| | - Marek Bujdoš
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Peter Uhlík
- Department of Economic Geology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Peter Matúš
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
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40
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Odoni DI, van Gaal MP, Schonewille T, Tamayo-Ramos JA, Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ. Aspergillus niger Secretes Citrate to Increase Iron Bioavailability. Front Microbiol 2017; 8:1424. [PMID: 28824560 PMCID: PMC5539119 DOI: 10.3389/fmicb.2017.01424] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/13/2017] [Indexed: 11/13/2022] Open
Abstract
Aspergillus niger has an innate ability to secrete various organic acids, including citrate. The conditions required for A. niger citrate overproduction are well described, but the physiological reasons underlying extracellular citrate accumulation are not yet fully understood. One of the less understood culture conditions is the requirement of growth-limiting iron concentrations. While this has been attributed to iron-dependent citrate metabolizing enzymes, this straightforward relationship does not always hold true. Here, we show that an increase in citrate secretion under iron limited conditions is a physiological response consistent with a role of citrate as A. niger iron siderophore. We found that A. niger citrate secretion increases with decreasing amounts of iron added to the culture medium and, in contrast to previous findings, this response is independent of the nitrogen source. Differential transcriptomics analyses of the two A. niger mutants NW305 (gluconate non-producer) and NW186 (gluconate and oxalate non-producer) revealed up-regulation of the citrate biosynthesis gene citA under iron limited conditions compared to iron replete conditions. In addition, we show that A. niger can utilize Fe(III) citrate as iron source. Finally, we discuss our findings in the general context of the pH-dependency of A. niger organic acid production, offering an explanation, besides competition, for why A. niger organic acid production is a sequential process influenced by the external pH of the culture medium.
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Affiliation(s)
- Dorett I Odoni
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Merlijn P van Gaal
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands.,Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
| | - Tom Schonewille
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Juan A Tamayo-Ramos
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands.,LifeGlimmer GmBHBerlin, Germany
| | - Maria Suarez-Diez
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Peter J Schaap
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
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41
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P gas, a Low-pH-Induced Promoter, as a Tool for Dynamic Control of Gene Expression for Metabolic Engineering of Aspergillus niger. Appl Environ Microbiol 2017; 83:AEM.03222-16. [PMID: 28087530 DOI: 10.1128/aem.03222-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/30/2016] [Indexed: 11/20/2022] Open
Abstract
The dynamic control of gene expression is important for adjusting fluxes in order to obtain desired products and achieve appropriate cell growth, particularly when the synthesis of a desired product drains metabolites required for cell growth. For dynamic gene expression, a promoter responsive to a particular environmental stressor is vital. Here, we report a low-pH-inducible promoter, Pgas, which promotes minimal gene expression at pH values above 5.0 but functions efficiently at low pHs, such as pH 2.0. First, we performed a transcriptional analysis of Aspergillus niger, an excellent platform for the production of organic acids, and we found that the promoter Pgas may act efficiently at low pH. Then, a gene for synthetic green fluorescent protein (sGFP) was successfully expressed by Pgas at pH 2.0, verifying the results of the transcriptional analysis. Next, Pgas was used to express the cis-aconitate decarboxylase (cad) gene of Aspergillus terreus in A. niger, allowing the production of itaconic acid at a titer of 4.92 g/liter. Finally, we found that Pgas strength was independent of acid type and acid ion concentration, showing dependence on pH only.IMPORTANCE The promoter Pgas can be used for the dynamic control of gene expression in A. niger for metabolic engineering to produce organic acids. This promoter may also be a candidate tool for genetic engineering.
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42
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Comparative genomics and transcriptome analysis of Aspergillus niger and metabolic engineering for citrate production. Sci Rep 2017; 7:41040. [PMID: 28106122 PMCID: PMC5247736 DOI: 10.1038/srep41040] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023] Open
Abstract
Despite a long and successful history of citrate production in Aspergillus niger, the molecular mechanism of citrate accumulation is only partially understood. In this study, we used comparative genomics and transcriptome analysis of citrate-producing strains—namely, A. niger H915-1 (citrate titer: 157 g L−1), A1 (117 g L−1), and L2 (76 g L−1)—to gain a genome-wide view of the mechanism of citrate accumulation. Compared with A. niger A1 and L2, A. niger H915-1 contained 92 mutated genes, including a succinate-semialdehyde dehydrogenase in the γ-aminobutyric acid shunt pathway and an aconitase family protein involved in citrate synthesis. Furthermore, transcriptome analysis of A. niger H915-1 revealed that the transcription levels of 479 genes changed between the cell growth stage (6 h) and the citrate synthesis stage (12 h, 24 h, 36 h, and 48 h). In the glycolysis pathway, triosephosphate isomerase was up-regulated, whereas pyruvate kinase was down-regulated. Two cytosol ATP-citrate lyases, which take part in the cycle of citrate synthesis, were up-regulated, and may coordinate with the alternative oxidases in the alternative respiratory pathway for energy balance. Finally, deletion of the oxaloacetate acetylhydrolase gene in H915-1 eliminated oxalate formation but neither influence on pH decrease nor difference in citrate production were observed.
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43
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Yang L, Lübeck M, Lübeck PS. Aspergillus as a versatile cell factory for organic acid production. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2016.11.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Upton DJ, McQueen-Mason SJ, Wood AJ. An accurate description of Aspergillus niger organic acid batch fermentation through dynamic metabolic modelling. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:258. [PMID: 29151887 PMCID: PMC5679502 DOI: 10.1186/s13068-017-0950-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/01/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Aspergillus niger fermentation has provided the chief source of industrial citric acid for over 50 years. Traditional strain development of this organism was achieved through random mutagenesis, but advances in genomics have enabled the development of genome-scale metabolic modelling that can be used to make predictive improvements in fermentation performance. The parent citric acid-producing strain of A. niger, ATCC 1015, has been described previously by a genome-scale metabolic model that encapsulates its response to ambient pH. Here, we report the development of a novel double optimisation modelling approach that generates time-dependent citric acid fermentation using dynamic flux balance analysis. RESULTS The output from this model shows a good match with empirical fermentation data. Our studies suggest that citric acid production commences upon a switch to phosphate-limited growth and this is validated by fitting to empirical data, which confirms the diauxic growth behaviour and the role of phosphate storage as polyphosphate. CONCLUSIONS The calibrated time-course model reflects observed metabolic events and generates reliable in silico data for industrially relevant fermentative time series, and for the behaviour of engineered strains suggesting that our approach can be used as a powerful tool for predictive metabolic engineering.
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Affiliation(s)
- Daniel J. Upton
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | | | - A. Jamie Wood
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
- Department of Mathematics, University of York, Heslington, York, YO10 5DD UK
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45
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Guo H, Wan H, Chen H, Fang F, Liu S, Zhou J. Proteomic analysis of the response of α-ketoglutarate-producer Yarrowia lipolytica WSH-Z06 to environmental pH stimuli. Appl Microbiol Biotechnol 2016; 100:8829-41. [PMID: 27535241 DOI: 10.1007/s00253-016-7775-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/25/2016] [Accepted: 08/02/2016] [Indexed: 11/25/2022]
Abstract
During bioproduction of short-chain carboxylates, a shift in pH is a common strategy for enhancing the biosynthesis of target products. Based on two-dimensional gel electrophoresis, comparative proteomics analysis of general and mitochondrial protein samples was used to investigate the cellular responses to environmental pH stimuli in the α-ketoglutarate overproducer Yarrowia lipolytica WSH-Z06. The lower environmental pH stimuli tensioned intracellular acidification and increased the level of reactive oxygen species (ROS). A total of 54 differentially expressed protein spots were detected, and 11 main cellular processes were identified to be involved in the cellular response to environmental pH stimuli. Slight decrease in cytoplasmic pH enhanced the cellular acidogenicity by elevating expression level of key enzymes in tricarboxylic acid cycle (TCA cycle). Enhanced energy biosynthesis, ROS elimination, and membrane potential homeostasis processes were also employed as cellular defense strategies to compete with environmental pH stimuli. Owing to its antioxidant role of α-ketoglutarate, metabolic flux shifted to α-ketoglutarate under lower pH by Y. lipolytica in response to acidic pH stimuli. The identified differentially expressed proteins provide clues for understanding the mechanisms of the cellular responses and for enhancing short-chain carboxylate production through metabolic engineering or process optimization strategies in combination with manipulation of environmental conditions.
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Affiliation(s)
- Hongwei Guo
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biological Chemical Engineering, Huaqiao University, 668 Jimei Road, Amoy, Fujian, 361021, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Hui Wan
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Hongwen Chen
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biological Chemical Engineering, Huaqiao University, 668 Jimei Road, Amoy, Fujian, 361021, China
| | - Fang Fang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Song Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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Hossain AH, Li A, Brickwedde A, Wilms L, Caspers M, Overkamp K, Punt PJ. Rewiring a secondary metabolite pathway towards itaconic acid production in Aspergillus niger. Microb Cell Fact 2016; 15:130. [PMID: 27469970 PMCID: PMC4965889 DOI: 10.1186/s12934-016-0527-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/20/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The industrially relevant filamentous fungus Aspergillus niger is widely used in industry for its secretion capabilities of enzymes and organic acids. Biotechnologically produced organic acids promise to be an attractive alternative for the chemical industry to replace petrochemicals. Itaconic acid (IA) has been identified as one of the top twelve building block chemicals which have high potential to be produced by biotechnological means. The IA biosynthesis cluster (cadA, mttA and mfsA) has been elucidated in its natural producer Aspergillus terreus and transferred to A. niger to enable IA production. Here we report the rewiring of a secondary metabolite pathway towards further improved IA production through the overexpression of a putative cytosolic citrate synthase citB in a A. niger strain carrying the IA biosynthesis cluster. RESULTS We have previously shown that expression of cadA from A. terreus results in itaconic acid production in A. niger AB1.13, albeit at low levels. This low-level production is boosted fivefold by the overexpression of mttA and mfsA in itaconic acid producing AB1.13 CAD background strains. Controlled batch cultivations with AB1.13 CAD + MFS + MTT strains showed increased production of itaconic acid compared with AB1.13 CAD strain. Moreover, preliminary RNA-Seq analysis of an itaconic acid producing AB1.13 CAD strain has led to the identification of the putative cytosolic citrate synthase citB which was induced in an IA producing strain. We have overexpressed citB in a AB1.13 CAD + MFS + MTT strain and by doing so hypothesize to have targeted itaconic acid production to the cytosolic compartment. By overexpressing citB in AB1.13 CAD + MFS + MTT strains in controlled batch cultivations we have achieved highly increased titers of up to 26.2 g/L IA with a productivity of 0.35 g/L/h while no CA was produced. CONCLUSIONS Expression of the IA biosynthesis cluster in Aspergillus niger AB1.13 strain enables IA production. Moreover, in the AB1.13 CAD strain IA production resulted in overexpression of a putative cytosolic citrate synthase citB. Upon overexpression of citB we have achieved titers of up to 26.2 g/L IA with a productivity of 0.35 g/L/h in controlled batch cultivations. By overexpressing citB we have also diminished side product formation and optimized the production pathway towards IA.
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Affiliation(s)
- Abeer H. Hossain
- Dutch DNA Biotech B.V, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - An Li
- Microbiology and Systems Biology, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Anja Brickwedde
- Microbiology and Systems Biology, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Lars Wilms
- Dutch DNA Biotech B.V, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Martien Caspers
- Microbiology and Systems Biology, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Karin Overkamp
- Dutch DNA Biotech B.V, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Peter J. Punt
- Dutch DNA Biotech B.V, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
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Characterizing MttA as a mitochondrial cis-aconitic acid transporter by metabolic engineering. Metab Eng 2016; 35:95-104. [DOI: 10.1016/j.ymben.2016.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/25/2016] [Accepted: 02/03/2016] [Indexed: 01/05/2023]
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Bignell E. The Molecular Basis of pH Sensing, Signaling, and Homeostasis in Fungi. ADVANCES IN APPLIED MICROBIOLOGY 2016; 79:1-18. [PMID: 22569515 DOI: 10.1016/b978-0-12-394318-7.00001-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Fungi mount efficient responses to altered extracellular pH. Characterization of the underlying mechanisms is fundamentally important in terms of understanding the molecular basis of pH homeostasis in higher eukaryotic cells, and for optimizing industrial processes which utilize fungi such as the production of pharmaceutical agents and food-use enzymes. Fungal pH adaptation is also a key requisite for establishment of multiple plant, insect, animal, and human diseases. Due to the differential reliance, respectively, of human and fungal cells upon electroneutral Na(+)-H(+) antiporters and outwardly directed electrogenic proton pumps, fundamental differences in the circuitry of pH homeostasis and adaptation exist, and these might be exploitable from a therapeutic perspective. At the molecular level, fungal pH tolerance is mediated by distinct but complementary homeostatic responses and highly conserved intracellular signaling pathways. Although traditionally studied as independent regulatory entities, the advent of systems biology has fuelled a new awareness of the interconnectivity between these very different modes of regulation. This review focuses upon the most recent advances in molecular understanding of three specific aspects of fungal pH adaptation, namely, sensing, signaling, and homeostasis.
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Affiliation(s)
- Elaine Bignell
- Section of Microbiology, Division of Infectious Diseases, Imperial College London, London, United Kingdom.
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Vesth TC, Brandl J, Andersen MR. FunGeneClusterS: Predicting fungal gene clusters from genome and transcriptome data. Synth Syst Biotechnol 2016; 1:122-129. [PMID: 29062935 PMCID: PMC5640693 DOI: 10.1016/j.synbio.2016.01.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 12/14/2015] [Accepted: 01/05/2016] [Indexed: 12/04/2022] Open
Abstract
Introduction Secondary metabolites of fungi are receiving an increasing amount of interest due to their prolific bioactivities and the fact that fungal biosynthesis of secondary metabolites often occurs from co-regulated and co-located gene clusters. This makes the gene clusters attractive for synthetic biology and industrial biotechnology applications. We have previously published a method for accurate prediction of clusters from genome and transcriptome data, which could also suggest cross-chemistry, however, this method was limited both in the number of parameters which could be adjusted as well as in user-friendliness. Furthermore, sensitivity to the transcriptome data required manual curation of the predictions. In the present work, we have aimed at improving these features. Results FunGeneClusterS is an improved implementation of our previous method with a graphical user interface for off- and on-line use. The new method adds options to adjust the size of the gene cluster(s) being sought as well as an option for the algorithm to be flexible with genes in the cluster which may not seem to be co-regulated with the remainder of the cluster. We have benchmarked the method using data from the well-studied Aspergillus nidulans and found that the method is an improvement over the previous one. In particular, it makes it possible to predict clusters with more than 10 genes more accurately, and allows identification of co-regulated gene clusters irrespective of the function of the genes. It also greatly reduces the need for manual curation of the prediction results. We furthermore applied the method to transcriptome data from A. niger. Using the identified best set of parameters, we were able to identify clusters for 31 out of 76 previously predicted secondary metabolite synthases/synthetases. Furthermore, we identified additional putative secondary metabolite gene clusters. In total, we predicted 432 co-transcribed gene clusters in A. niger (spanning 1.323 genes, 12% of the genome). Some of these had functions related to primary metabolism, e.g. we have identified a cluster for biosynthesis of biotin, as well as several for degradation of aromatic compounds. The data identifies that suggests that larger parts of the fungal genome than previously anticipated operates as gene clusters. This includes both primary and secondary metabolism as well as other cellular maintenance functions. Conclusion We have developed FunGeneClusterS in a graphical implementation and made the method capable of adjustments to different datasets and target clusters. The method is versatile in that it can predict co-regulated clusters not limited to secondary metabolism. Our analysis of data has shown not only the validity of the method, but also strongly suggests that large parts of fungal primary metabolism and cellular functions are both co-regulated and co-located.
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Affiliation(s)
- Tammi C Vesth
- Department of Systems Biology, Technical University of Denmark, Søltofts Plads 223, Denmark
| | - Julian Brandl
- Department of Systems Biology, Technical University of Denmark, Søltofts Plads 223, Denmark
| | - Mikael Rørdam Andersen
- Department of Systems Biology, Technical University of Denmark, Søltofts Plads 223, Denmark
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Characterization of a Newly Isolated Marine Fungus Aspergillus dimorphicus for Optimized Production of the Anti-Tumor Agent Wentilactones. Mar Drugs 2015; 13:7040-54. [PMID: 26610530 PMCID: PMC4663565 DOI: 10.3390/md13117040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/13/2015] [Indexed: 02/08/2023] Open
Abstract
The potential anti-tumor agent wentilactones were produced by a newly isolated marine fungus Aspergillus dimorphicus. This fungus was derived from deep-sea sediment and identified by polyphasic approach, combining phenotypic, molecular, and extrolite profiles. However, wentilactone production was detected only under static cultures with very low yields. In order to improve wentilactone production, culture conditions were optimized using the response surface methodology. Under the optimal static fermentation conditions, the experimental values were closely consistent with the prediction model. The yields of wentilactone A and B were increased about 11-fold to 13.4 and 6.5 mg/L, respectively. The result was further verified by fermentation scale-up for wentilactone production. Moreover, some small-molecule elicitors were found to have capacity of stimulating wentilactone production. To our knowledge, this is first report of optimized production of tetranorlabdane diterpenoids by a deep-sea derived marine fungus. The present study might be valuable for efficient production of wentilactones and fundamental investigation of the anti-tumor mechanism of norditerpenoids.
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