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Yoshioka I, Kirimura K. Generation of citric acid-hyperproducers independent of methanol effect by high-level expression of cexA encoding citrate exporter in Aspergillus tubingensis. Biosci Biotechnol Biochem 2024; 88:1203-1211. [PMID: 39089868 DOI: 10.1093/bbb/zbae099] [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: 12/01/2023] [Accepted: 07/05/2024] [Indexed: 08/04/2024]
Abstract
Methanol reportedly stimulates citric acid (CA) production by Aspergillus niger and A. tubingensis; however, the underlying mechanisms remain unclear. Here, we elucidated the molecular functions of the citrate exporter gene cexA in relation to CA production by A. tubingensis WU-2223L. Methanol addition to the medium containing glucose as a carbon source markedly increased CA production by strain WU-2223L by 3.38-fold, resulting in a maximum yield of 65.5 g/L, with enhanced cexA expression. Conversely, the cexA-complementing strain with the constitutive expression promoter Ptef1 (strain LhC-1) produced 68.3 or 66.7 g/L of CA when cultivated without or with methanol, respectively. Additionally, strain LhC-2 harboring two copies of the cexA expression cassette produced 80.7 g/L of CA without methanol addition. Overall, we showed that cexA is a target gene for methanol in CA hyperproduction by A. tubingensis WU-2223L. Based on these findings, methanol-independent CA-hyperproducing strains, LhC-1 and LhC-2, were successfully generated.
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Affiliation(s)
- Isato Yoshioka
- R esearch Institute for Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
- Medical Mycology Research Center, Chiba University, Chiba, Chiba, Japan
| | - Kohtaro Kirimura
- R esearch Institute for Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
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Zhang R, Chen Y, Wang W, Chen J, Liu D, Zhang L, Xiang Q, Zhao K, Ma M, Yu X, Chen Q, Penttinen P, Gu Y. Combined transcriptomic and metabolomic analysis revealed that pH changes affected the expression of carbohydrate and ribosome biogenesis-related genes in Aspergillus niger SICU-33. Front Microbiol 2024; 15:1389268. [PMID: 38962137 PMCID: PMC11220263 DOI: 10.3389/fmicb.2024.1389268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024] Open
Abstract
The process of carbohydrate metabolism and genetic information transfer is an important part of the study on the effects of the external environment on microbial growth and development. As one of the most significant environmental parameters, pH has an important effect on mycelial growth. In this study, the effects of environmental pH on the growth and nutrient composition of Aspergillus niger (A. niger) filaments were determined. The pH values of the medium were 5, 7, and 9, respectively, and the molecular mechanism was further investigated by transcriptomics and metabolomics methods. The results showed that pH 5 and 9 significantly inhibited filament growth and polysaccharide accumulation of A. niger. Further, the mycelium biomass of A. niger and the crude polysaccharide content was higher when the medium's pH was 7. The DEGs related to ribosome biogenesis were the most abundant, and the downregulated expression of genes encoding XRN1, RRM, and RIO1 affected protein translation, modification, and carbohydrate metabolism in fungi. The dynamic changes of pargyline and choline were in response to the oxidative metabolism of A. niger SICU-33. The ribophorin_I enzymes and DL-lactate may be important substances related to pH changes during carbohydrate metabolism of A.niger SICU-33. The results of this study provide useful transcriptomic and metabolomic information for further analyzing the bioinformatic characteristics of A. niger and improving the application in ecological agricultural fermentation.
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Affiliation(s)
- Runji Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yulan Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wenxian Wang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Juan Chen
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Dongyang Liu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Lingzi Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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Kaushal M, Upton DJ, Gupta JK, Wood AJ, Srivastava S. Reconstruction of a genome-scale metabolic model and in-silico flux analysis of Aspergillus tubingensis: a non-mycotoxinogenic citric acid-producing fungus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:70. [PMID: 38807234 PMCID: PMC11134751 DOI: 10.1186/s13068-024-02506-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/20/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Aspergillus tubingensis is a citric acid-producing fungus that can utilize sugars in hydrolysate of lignocellulosic biomass such as sugarcane bagasse and, unlike A. niger, does not produce mycotoxins. To date, no attempt has been made to model its metabolism at genome scale. RESULTS Here, we utilized the whole-genome sequence (34.96 Mb length) and the measured biomass composition to reconstruct a genome-scale metabolic model (GSMM) of A. tubingensis DJU120 strain. The model, named iMK1652, consists of 1652 genes, 1657 metabolites and 2039 reactions distributed over four cellular compartments. The model has been extensively curated manually. This included removal of dead-end metabolites and generic reactions, addition of secondary metabolite pathways and several transporters. Several mycotoxin synthesis pathways were either absent or incomplete in the genome, providing a genomic basis for the non-toxinogenic nature of this species. The model was further refined based on the experimental phenotypic microarray (Biolog) data. The model closely captured DJU120 fermentative data on glucose, xylose, and phosphate consumption, as well as citric acid and biomass production, showing its applicability to capture citric acid fermentation of lignocellulosic biomass hydrolysate. CONCLUSIONS The model offers a framework to conduct metabolic systems biology investigations and can act as a scaffold for integrative modelling of A. tubingensis.
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Affiliation(s)
- Mehak Kaushal
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Perfect Day India Pvt. Ltd., Bangalore, India
| | - Daniel J Upton
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Jai K Gupta
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
- JKG: Zero Cow Factory, Surat, India
| | - A Jamie Wood
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
| | - Shireesh Srivastava
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Nishitani A, Hiramatsu K, Kadooka C, Hiroshima K, Sawada K, Okutsu K, Yoshizaki Y, Takamine K, Goto M, Tamaki H, Futagami T. Overexpression of the DHA1 family, ChlH and ChlK, leads to enhanced dicarboxylic acids production in koji fungi, Aspergillus luchuensis mut. kawachii and Aspergillus oryzae. J Biosci Bioeng 2024; 137:281-289. [PMID: 38331655 DOI: 10.1016/j.jbiosc.2024.01.010] [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: 09/26/2023] [Revised: 01/09/2024] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
The white koji fungus Aspergillus luchuensis mut. kawachii secretes substantial amounts of citric acid through the expression of the citric acid exporter CexA, a member of the DHA1 family. In this study, we aimed to characterize 11 CexA homologs (Chl proteins) encoded in the genome of A. luchuensis mut. kawachii to identify novel transporters useful for organic acid production. We constructed overexpression strains of chl genes using a cexA disruptant of the A. luchuensis mut. kawachii as the host strain, which prevented excessive secretion of citric acid into the culture supernatant. Subsequently, we evaluated the effects of overexpression of chl on producing organic acids by analyzing the culture supernatant. All overexpression strains did not exhibit significant citric acid accumulation in the culture supernatant, indicating that Chl proteins are not responsible for citric acid export. Furthermore, the ChlH overexpression strain displayed an accumulation of 2-oxoglutaric and fumaric acids in the culture supernatant, while the ChlK overexpression strain exhibited the accumulation of 2-oxoglutaric, malic and succinic acids. Notably, the ChlH and ChlK overexpression led to a substantial increase in the production of 2-oxoglutaric acid, reaching approximately 25 mM and 50 mM, respectively. Furthermore, ChlH and ChlK overexpression also significantly increased the secretory production of dicarboxylic acids, including 2-oxoglutaric acid, in the yellow koji fungus, Aspergillus oryzae. Our study demonstrates that overexpression of DHA1 family gene results in enhanced secretion of organic acids in koji fungi of the genus Aspergillus.
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Affiliation(s)
- Atsushi Nishitani
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Center for Advanced Science Research and Promotion, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kentaro Hiramatsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
| | - Chihiro Kadooka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto 860-0082, Japan
| | - Kyoka Hiroshima
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
| | | | - Kayu Okutsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Yumiko Yoshizaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kazunori Takamine
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Masatoshi Goto
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Hisanori Tamaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
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Islamova R, Yanshin N, Zamyatkina E, Gulk E, Zuy E, Billig S, Birkemeyer C, Tarakhovskaya E. Metabolic Adjustment of High Intertidal Alga Pelvetia canaliculata to the Tidal Cycle Includes Oscillations of Soluble Carbohydrates, Phlorotannins, and Citric Acid Content. Int J Mol Sci 2023; 24:10626. [PMID: 37445801 PMCID: PMC10341635 DOI: 10.3390/ijms241310626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The brown alga Pelvetia canaliculata is one of the species successfully adapted to intertidal conditions. Inhabiting the high intertidal zone, Pelvetia spends most of its life exposed to air, where it is subjected to desiccation, light, and temperature stresses. However, the physiological and biochemical mechanisms allowing this alga to tolerate such extreme conditions are still largely unknown. The objective of our study is to compare the biochemical composition of Pelvetia during the different phases of the tidal cycle. To our knowledge, this study is the first attempt to draft a detailed biochemical network underneath the complex physiological processes, conferring the successful survival of this organism in the harsh conditions of the high intertidal zone of the polar seas. We considered the tide-induced changes in relative water content, stress markers, titratable acidity, pigment, and phlorotannin content, as well as the low molecular weight metabolite profiles (GC-MS-based approach) in Pelvetia thalli. Thallus desiccation was not accompanied by considerable increase in reactive oxygen species content. Metabolic adjustment of P. canaliculata to emersion included accumulation of soluble carbohydrates, various phenolic compounds, including intracellular phlorotannins, and fatty acids. Changes in titratable acidity accompanied by the oscillations of citric acid content imply that some processes related to the crassulacean acid metabolism (CAM) may be involved in Pelvetia adaptation to the tidal cycle.
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Affiliation(s)
- Renata Islamova
- Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034 Saint Petersburg, Russia; (R.I.)
| | - Nikolay Yanshin
- Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034 Saint Petersburg, Russia; (R.I.)
| | - Elizaveta Zamyatkina
- Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034 Saint Petersburg, Russia; (R.I.)
| | - Ekaterina Gulk
- Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034 Saint Petersburg, Russia; (R.I.)
| | - Ekaterina Zuy
- Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034 Saint Petersburg, Russia; (R.I.)
| | - Susan Billig
- Faculty of Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany (C.B.)
| | - Claudia Birkemeyer
- Faculty of Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany (C.B.)
- German Center for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, 04103 Leipzig, Germany
| | - Elena Tarakhovskaya
- Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034 Saint Petersburg, Russia; (R.I.)
- Vavilov Institute of General Genetics, Saint Petersburg Branch, Russian Academy of Science, Universitetskaya Nab., 7/9, 199034 Saint Petersburg, Russia
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Li K, Burton-Pimentel KJ, Brouwer-Brolsma EM, Blaser C, Badertscher R, Pimentel G, Portmann R, Feskens EJM, Vergères G. Identifying Plasma and Urinary Biomarkers of Fermented Food Intake and Their Associations with Cardiometabolic Health in a Dutch Observational Cohort. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4426-4439. [PMID: 36853956 PMCID: PMC10021015 DOI: 10.1021/acs.jafc.2c05669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Identification of food intake biomarkers (FIBs) for fermented foods could help improve their dietary assessment and clarify their associations with cardiometabolic health. We aimed to identify novel FIBs for fermented foods in the plasma and urine metabolomes of 246 free-living Dutch adults using nontargeted LC-MS and GC-MS. Furthermore, associations between identified metabolites and several cardiometabolic risk factors were explored. In total, 37 metabolites were identified corresponding to the intakes of coffee, wine, and beer (none were identified for cocoa, bread, cheese, or yoghurt intake). While some of these metabolites appeared to originate from raw food (e.g., niacin and trigonelline for coffee), others overlapped different fermented foods (e.g., 4-hydroxybenzeneacetic acid for both wine and beer). In addition, several fermentation-dependent metabolites were identified (erythritol and citramalate). Associations between these identified metabolites with cardiometabolic parameters were weak and inconclusive. Further evaluation is warranted to confirm their relationships with cardiometabolic disease risk.
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Affiliation(s)
- Katherine
J. Li
- Division
of Human Nutrition and Health, Department of Agrotechnology and Food
Science, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
- Agroscope, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland
| | | | - Elske M. Brouwer-Brolsma
- Division
of Human Nutrition and Health, Department of Agrotechnology and Food
Science, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Carola Blaser
- Agroscope, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland
| | | | | | - Reto Portmann
- Agroscope, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland
| | - Edith J. M. Feskens
- Division
of Human Nutrition and Health, Department of Agrotechnology and Food
Science, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Guy Vergères
- Agroscope, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland
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Analyzing Citramalic Acid Enantiomers in Apples and Commercial Fruit Juice by Liquid Chromatography-Tandem Mass Spectrometry with Pre-Column Derivatization. Molecules 2023; 28:molecules28041556. [PMID: 36838544 PMCID: PMC9959191 DOI: 10.3390/molecules28041556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Optically active citramalic acid (CMA) is naturally present as an acidic taste component in fruits, such as apples. The absolute configuration of CMA in such fruits was investigated by high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) following pre-column derivatization with a chiral reagent, benzyl 5-(2-aminoethyl)-3-methyl-4-oxoimidazolidine-1-carboxylate. The developed LC-MS/MS method successfully separated the enantiomers of CMA using an octadecylsilica column with a resolution and separation factor of 2.19 and 1.09, respectively. Consequently, the R-form of CMA was detected in the peel and fruit of three kinds of apple at concentrations in the 1.24-37.8 and 0.138-1.033 mg/wet 100 g ranges, respectively. In addition, R- CMA was present in commercial apple juice, whereas no quantity was detected in commercial blueberry, perilla, or Japanese apricot juice.
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Wang Y, Guo Y, Cao W, Liu H. Synergistic effects on itaconic acid production in engineered Aspergillus niger expressing the two distinct biosynthesis clusters from Aspergillus terreus and Ustilago maydis. Microb Cell Fact 2022; 21:158. [PMID: 35953829 PMCID: PMC9367143 DOI: 10.1186/s12934-022-01881-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Itaconic acid (IA) is a versatile platform chemical widely used for the synthesis of various polymers and current methods for IA production based on Aspergillus terreus fermentation are limited in terms of process efficiency and productivity. To construct more efficient IA production strains, A. niger was used as a chassis for engineering IA production by assembling the key components of IA biosynthesis pathways from both A. terreus and Ustilago maydis. RESULTS Recombinant A. niger S1596 overexpressing the A. terreus IA biosynthesis genes cadA, mttA, mfsA produced IA of 4.32 g/L, while A. niger S2120 overexpressing the U. maydis IA gene cluster adi1, tad1, mtt1, itp1 achieved IA of 3.02 g/L. Integration of the two IA production pathways led to the construction of A. niger S2083 with IA titers of 5.58 g/L. Increasing cadA copy number in strain S2083 created strain S2209 with titers of 7.99 g/L and deleting ictA to block IA degradation in S2209 created strain S2288 with IA titers of 8.70 g/L. Overexpressing acoA to enhance the supply of IA precursor in strain S2288 generated strain S2444 with IA titers of 9.08 g/L in shake flask. CONCLUSION Recombinant A. niger overexpressing the U. maydis IA biosynthesis pathway was capable of IA accumulation. Combined expression of the two IA biosynthesis pathways from A. terreus and U. maydis in A. niger resulted in much higher IA titers. Furthermore, increasing cadA copy number, deleting ictA to block IA degradation and overexpressing acoA to enhance IA precursor supply all showed beneficial effects on IA accumulation.
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Affiliation(s)
- Yaqi Wang
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Yufei Guo
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, People's Republic of China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China. .,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, People's Republic of China.
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Metabolic Profiling of Organic Acids Reveals the Involvement of HuIPMS2 in Citramalic Acid Synthesis in Pitaya. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pitayas are rich in organic acids, especially citramalic acid, which is significantly higher than the plants. However, the mechanism of citramalic acid biosynthesis remains to be fully elucidated. In this study, organic acid compositions and contents, as well as expression patterns of key genes related to organic acid metabolism were analyzed during fruit maturation of four different pitaya cultivars i.e., ‘Guanhuabai’ (GHB), ‘Guanhuahong’ (GHH), ‘Wucihuanglong’ (WCHL), and ‘Youcihuanglong’ (YCHL). The total organic acid contents increased first and then declined during fruit maturation. The main organic acids were citramalic acid during the early stages of GHB, GHH, and WCHL pitayas, and dominated by malic acid as fruit maturation. In comparison, citric acid and malic acid were main organic acid for ‘YCHL’ pitaya. Citramalate synthase (IPMS) was involved in the synthesis of citramalic acid, and three types of HuIPMS i.e., HuIPMS1, HuIPMS2, and HuIPMS3, were obtained in our study. Highest expression levels of HuIPMS1 were detected in sepals, while HuIPMS2 and HuIPMS3 exhibited preferential expression in tender stems and ovaries. The expression levels of HuIPMS2 and HuIPMS3 were positively correlated with the content of citramalic acid in the four pitaya cultivars. HuIPMS2 was a chloroplast-localized protein, while HuIPMS3 presented a cytoplasmic-like and nuclear subcellular localization. These findings provide an important basis for further understanding of the molecular mechanism that leads to citramalic acid metabolism during pitaya fruit maturation.
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Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways. Microbiol Spectr 2021; 9:e0089821. [PMID: 34523946 PMCID: PMC8557879 DOI: 10.1128/spectrum.00898-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Fungal secondary metabolites are widely used as therapeutics and are vital components of drug discovery programs. A major challenge hindering discovery of novel secondary metabolites is that the underlying pathways involved in their biosynthesis are transcriptionally silent under typical laboratory growth conditions, making it difficult to identify the transcriptional networks that they are embedded in. Furthermore, while the genes participating in secondary metabolic pathways are typically found in contiguous clusters on the genome, known as biosynthetic gene clusters (BGCs), this is not always the case, especially for global and pathway-specific regulators of pathways’ activities. To address these challenges, we used 283 genome-wide gene expression data sets of the ascomycete cell factory Aspergillus niger generated during growth under 155 different conditions to construct two gene coexpression networks based on Spearman’s correlation coefficients (SCCs) and on mutual rank-transformed Pearson’s correlation coefficients (MR-PCCs). By mining these networks, we predicted six transcription factors, named MjkA to MjkF, to regulate secondary metabolism in A. niger. Overexpression of each transcription factor using the Tet-On cassette modulated the production of multiple secondary metabolites. We found that the SCC and MR-PCC approaches complemented each other, enabling the delineation of putative global (SCC) and pathway-specific (MR-PCC) transcription factors. These results highlight the potential of coexpression network approaches to identify and activate fungal secondary metabolic pathways and their products. More broadly, we argue that drug discovery programs in fungi should move beyond the BGC paradigm and focus on understanding the global regulatory networks in which secondary metabolic pathways are embedded. IMPORTANCE There is an urgent need for novel bioactive molecules in both agriculture and medicine. The genomes of fungi are thought to contain vast numbers of metabolic pathways involved in the biosynthesis of secondary metabolites with diverse bioactivities. Because these metabolites are biosynthesized only under specific conditions, the vast majority of the fungal pharmacopeia awaits discovery. To discover the genetic networks that regulate the activity of secondary metabolites, we examined the genome-wide profiles of gene activity of the cell factory Aspergillus niger across hundreds of conditions. By constructing global networks that link genes with similar activities across conditions, we identified six putative global and pathway-specific regulators of secondary metabolite biosynthesis. Our study shows that elucidating the behavior of the genetic networks of fungi under diverse conditions harbors enormous promise for understanding fungal secondary metabolism, which ultimately may lead to novel drug candidates.
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Polozsányi Z, Kaliňák M, Babjak M, Šimkovič M, Varečka Ľ. How to enter the state of dormancy? A suggestion by Trichoderma atroviride conidia. Fungal Biol 2021; 125:934-949. [PMID: 34649680 DOI: 10.1016/j.funbio.2021.07.001] [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: 07/18/2020] [Revised: 06/12/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
It is generally accepted that conidia, propagules of filamentous fungi, exist in the state of dormancy. This state is defined mostly phenomenologically, e.g., by germination requirements. Its molecular characteristics are scarce and are concentrated on the water or osmolyte content, and/or respiration. However, a question of whether conidia are metabolic or ametabolic forms of life cannot be answered on the basis of available experimental data. In other words, are mature conidia open thermodynamic systems as are mycelia, or do they become closed upon the transition to the dormant state? In this article, we present observations which may help to define the transition of freshly formed conidia to the putative dormant forms using measurements of selected enzyme activities, 1H- and 13C-NMR and LC-MS-metabolomes, and 14C-bicarbonate or 45Ca2+ inward transport. We have found that Trichoderma atroviride and Aspergillus niger conidia arrest the 45Ca2+ uptake during the development stopping thereby the cyclic (i.e., bidirectional) Ca2+ flow existing in vegetative mycelia and conidia of T. atroviride across the cytoplasmic membrane. Furthermore, we have found that the activity of α-ketoglutarate dehydrogenase was rendered completely inactive after 3 weeks from the conidia formation unlike of other central carbon metabolism enzymes. This may explain the loss of conidial respiration. Finally, we found that conidia take up the H14CO3- and convert it into few stable compounds within 80 d of maturation, with minor quantitative differences in the extent of this process. The uptake of H13CO3- confirmed these observation and demonstrated the incorporation of H13CO3- even in the absence of exogenous substrates. These results suggest that T. atroviride conidia remain metabolically active during first ten weeks of maturation. Under these circumstances, their metabolism displays features similar to those of chemoautotrophic microorganisms. However, the Ca2+ homeostasis changed from the open to the closed thermodynamic state during the early period of conidial maturation. These results may be helpful for studying the conidial ageing and/or maturation, and for defining the conidial dormant state in biochemical terms.
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Affiliation(s)
- Zoltán Polozsányi
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Michal Kaliňák
- Central Laboratories, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Matej Babjak
- Department of Organic Chemistry, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Martin Šimkovič
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia.
| | - Ľudovít Varečka
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
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Brisson VL, Zhuang WQ, Alvarez-Cohen L. Metabolomic Analysis Reveals Contributions of Citric and Citramalic Acids to Rare Earth Bioleaching by a Paecilomyces Fungus. Front Microbiol 2020; 10:3008. [PMID: 31993037 PMCID: PMC6971059 DOI: 10.3389/fmicb.2019.03008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/26/2022] Open
Abstract
Conventional methods for extracting rare earth elements from monazite ore require high energy inputs and produce environmentally damaging waste streams. Bioleaching offers a potentially more environmentally friendly alternative extraction process. In order to better understand bioleaching mechanisms, we conducted an exo-metabolomic analysis of a previously isolated rare earth bioleaching fungus from the genus Paecilomyces (GenBank accession numbers KM874779 and KM 874781) to identify contributions of compounds exuded by this fungus to bioleaching activity. Exuded compounds were compared under two growth conditions: growth with monazite ore as the only phosphate source, and growth with a soluble phosphate source (K2HPO4) added. Overall metabolite profiling, in combination with glucose consumption and biomass accumulation data, reflected a lag in growth when this organism was grown with only monazite. We analyzed the relationships between metabolite concentrations, rare earth solubilization, and growth conditions, and identified several metabolites potentially associated with bioleaching. Further investigation using laboratory prepared solutions of 17 of these metabolites indicated statistically significant leaching contributions from both citric and citramalic acids. These contributions (16.4 and 15.0 mg/L total rare earths solubilized) accounted for a portion, but not all, of the leaching achieved with direct bioleaching (42 ± 15 mg/L final rare earth concentration). Additionally, citramalic acid released significantly less of the radioactive element thorium than did citric acid (0.25 ± 0.01 mg/L compared to 1.18 ± 0.01 mg/L), suggesting that citramalic acid may have preferable leaching properties for a monazite bioleaching process.
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Affiliation(s)
- Vanessa L Brisson
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States.,Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei-Qin Zhuang
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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