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Deng S, Kim J, Pomraning KR, Gao Y, Evans JE, Hofstad BA, Dai Z, Webb-Robertson BJ, Powell SM, Novikova IV, Munoz N, Kim YM, Swita M, Robles AL, Lemmon T, Duong RD, Nicora C, Burnum-Johnson KE, Magnuson J. Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus. Metab Eng 2023; 80:163-172. [PMID: 37778408 DOI: 10.1016/j.ymben.2023.09.011] [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: 01/31/2023] [Revised: 07/25/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
Aconitic acid is an unsaturated tricarboxylic acid that is attractive for its potential use in manufacturing biodegradable and biocompatible polymers, plasticizers, and surfactants. Previously Aspergillus pseudoterreus was engineered as a platform to produce aconitic acid by deleting the cadA (cis-aconitic acid decarboxylase) gene in the itaconic acid biosynthetic pathway. In this study, the aconitic acid transporter gene (aexA) was identified using comparative global discovery proteomics analysis between the wild-type and cadA deletion strains. The protein AexA belongs to the Major Facilitator Superfamily (MFS). Deletion of aexA almost abolished aconitic acid secretion, while its overexpression led to a significant increase in aconitic acid production. Transportation of aconitic acid across the plasma membrane is a key limiting step in its production. In vitro, proteoliposome transport assay further validated AexA's function and substrate specificity. This research provides new approaches to efficiently pinpoint and characterize exporters of fungal organic acids and accelerate metabolic engineering to improve secretion capability and lower the cost of bioproduction.
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Affiliation(s)
- Shuang Deng
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Joonhoon Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kyle R Pomraning
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Yuqian Gao
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - James E Evans
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Beth A Hofstad
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ziyu Dai
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Bobbie-Jo Webb-Robertson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Samantha M Powell
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Irina V Novikova
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Nathalie Munoz
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Young-Mo Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Marie Swita
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ana L Robles
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Teresa Lemmon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Rylan D Duong
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kristin E Burnum-Johnson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Jon Magnuson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
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2
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Geng C, Jin Z, Gu M, Li J, Tang S, Guo Q, Zhang Y, Zhang W, Li Y, Huang X, Lu X. Microbial production of trans-aconitic acid. Metab Eng 2023; 78:183-191. [PMID: 37315711 DOI: 10.1016/j.ymben.2023.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/22/2023] [Accepted: 06/11/2023] [Indexed: 06/16/2023]
Abstract
Trans-aconitic acid (TAA) is a promising bio-based chemical with the structure of unsaturated tricarboxylic acid, and also has the potential to be a non-toxic nematicide as a potent inhibitor of aconitase. However, TAA has not been commercialized because the traditional production processes of plant extraction and chemical synthesis cannot achieve large-scale production at a low cost. The availability of TAA is a serious obstacle to its widespread application. In this study, we developed an efficient microbial synthesis and fermentation production process for TAA. An engineered Aspergillus terreus strain producing cis-aconitic acid and TAA was constructed by blocking itaconic acid biosynthesis in the industrial itaconic acid-producing strain. Through heterologous expression of exogenous aconitate isomerase, we further designed a more efficient cell factory to specifically produce TAA. Subsequently, the fermentation process was developed and scaled up step-by-step, achieving a TAA titer of 60 g L-1 at the demonstration scale of a 20 m3 fermenter. Finally, the field evaluation of the produced TAA for control of the root-knot nematodes was performed in a field trial, effectively reducing the damage of the root-knot nematode. Our work provides a commercially viable solution for the green manufacturing of TAA, which will significantly facilitate biopesticide development and promote its widespread application as a bio-based chemical.
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Affiliation(s)
- Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
| | - Zhigang Jin
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China; Shandong Lukang Pharmaceutical Co. Ltd., Jining, 272021, Shandong, China
| | - Meng Gu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jibin Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Shen Tang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
| | - Qiang Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Yunpeng Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China.
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3
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Diankristanti PA, Ng IS. Microbial itaconic acid bioproduction towards sustainable development: Insights, challenges, and prospects. BIORESOURCE TECHNOLOGY 2023:129280. [PMID: 37290713 DOI: 10.1016/j.biortech.2023.129280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Microbial biomanufacturing is a promising approach to produce high-value compounds with low-carbon footprint and significant economic benefits. Among twelve "Top Value-Added Chemicals from Biomass", itaconic acid (IA) stands out as a versatile platform chemical with numerous applications. IA is naturally produced by Aspergillus and Ustilago species through a cascade enzymatic reaction between aconitase (EC 4.2.1.3) and cis-aconitic acid decarboxylase (EC 4.1.1.6). Recently, non-native hosts such as Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Yarrowia lipolytica have been genetically engineered to produce IA through the introduction of key enzymes. This review provides an up-to-date summary of the progress made in IA bioproduction, from native to engineered hosts, covers in vivo and in vitro approaches, and highlights the prospects of combination tactics. Current challenges and recent endeavors are also addressed to envision comprehensive strategies for renewable IA production in the future towards sustainable development goals (SDGs).
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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4
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Dai Z, Pomraning KR, Deng S, Kim J, Campbell KB, Robles AL, Hofstad BA, Munoz N, Gao Y, Lemmon T, Swita MS, Zucker JD, Kim YM, Burnum-Johnson KE, Magnuson JK. Metabolic engineering to improve production of 3-hydroxypropionic acid from corn-stover hydrolysate in Aspergillus species. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:53. [PMID: 36991437 DOI: 10.1186/s13068-023-02288-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023]
Abstract
BACKGROUND Fuels and chemicals derived from non-fossil sources are needed to lessen human impacts on the environment while providing a healthy and growing economy. 3-hydroxypropionic acid (3-HP) is an important chemical building block that can be used for many products. Biosynthesis of 3-HP is possible; however, low production is typically observed in those natural systems. Biosynthetic pathways have been designed to produce 3-HP from a variety of feedstocks in different microorganisms. RESULTS In this study, the 3-HP β-alanine pathway consisting of aspartate decarboxylase, β-alanine-pyruvate aminotransferase, and 3-hydroxypropionate dehydrogenase from selected microorganisms were codon optimized for Aspergillus species and placed under the control of constitutive promoters. The pathway was introduced into Aspergillus pseudoterreus and subsequently into Aspergillus niger, and 3-HP production was assessed in both hosts. A. niger produced higher initial 3-HP yields and fewer co-product contaminants and was selected as a suitable host for further engineering. Proteomic and metabolomic analysis of both Aspergillus species during 3-HP production identified genetic targets for improvement of flux toward 3-HP including pyruvate carboxylase, aspartate aminotransferase, malonate semialdehyde dehydrogenase, succinate semialdehyde dehydrogenase, oxaloacetate hydrolase, and a 3-HP transporter. Overexpression of pyruvate carboxylase improved yield in shake-flasks from 0.09 to 0.12 C-mol 3-HP C-mol-1 glucose in the base strain expressing 12 copies of the β-alanine pathway. Deletion or overexpression of individual target genes in the pyruvate carboxylase overexpression strain improved yield to 0.22 C-mol 3-HP C-mol-1 glucose after deletion of the major malonate semialdehyde dehydrogenase. Further incorporation of additional β-alanine pathway genes and optimization of culture conditions (sugars, temperature, nitrogen, phosphate, trace elements) for 3-HP production from deacetylated and mechanically refined corn stover hydrolysate improved yield to 0.48 C-mol 3-HP C-mol-1 sugars and resulted in a final titer of 36.0 g/L 3-HP. CONCLUSIONS The results of this study establish A. niger as a host for 3-HP production from a lignocellulosic feedstock in acidic conditions and demonstrates that 3-HP titer and yield can be improved by a broad metabolic engineering strategy involving identification and modification of genes participated in the synthesis of 3-HP and its precursors, degradation of intermediates, and transport of 3-HP across the plasma membrane.
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Affiliation(s)
- Ziyu Dai
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA.
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kyle R Pomraning
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Shuang Deng
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joonhoon Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristen B Campbell
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ana L Robles
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Beth A Hofstad
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yuqian Gao
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Teresa Lemmon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Marie S Swita
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jeremy D Zucker
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jon K Magnuson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA.
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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5
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Recent Advances on the Production of Itaconic Acid via the Fermentation and Metabolic Engineering. FERMENTATION 2023. [DOI: 10.3390/fermentation9010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Itaconic acid (ITA) is one of the top 12 platform chemicals. The global ITA market is expanding due to the rising demand for bio-based unsaturated polyester resin and its non-toxic qualities. Although bioconversion using microbes is the main approach in the current industrial production of ITA, ecological production of bio-based ITA faces several issues due to: low production efficiency, the difficulty to employ inexpensive raw materials, and high manufacturing costs. As metabolic engineering advances, the engineering of microorganisms offers a novel strategy for the promotion of ITA bio-production. In this review, the most recent developments in the production of ITA through fermentation and metabolic engineering are compiled from a variety of perspectives, including the identification of the ITA synthesis pathway, the metabolic engineering of natural ITA producers, the design and construction of the ITA synthesis pathway in model chassis, and the creation, as well as application, of new metabolic engineering strategies in ITA production. The challenges encountered in the bio-production of ITA in microbial cell factories are discussed, and some suggestions for future study are also proposed, which it is hoped offers insightful views to promote the cost-efficient and sustainable industrial production of ITA.
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Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus. Metab Eng Commun 2022; 15:e00203. [PMID: 36065328 PMCID: PMC9440423 DOI: 10.1016/j.mec.2022.e00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
The global regulator LaeA controls secondary metabolism in diverse Aspergillus species. Here we explored its role in regulation of itaconic acid production in Aspergillus pseudoterreus. To understand its role in regulating metabolism, we deleted and overexpressed laeA, and assessed the transcriptome, proteome, and secreted metabolome prior to and during initiation of phosphate limitation induced itaconic acid production. We found that secondary metabolite clusters, including the itaconic acid biosynthetic gene cluster, are regulated by laeA and that laeA is required for high yield production of itaconic acid. Overexpression of LaeA improves itaconic acid yield at the expense of biomass by increasing the expression of key biosynthetic pathway enzymes and attenuating the expression of genes involved in phosphate acquisition and scavenging. Increased yield was observed in optimized conditions as well as conditions containing excess nutrients that may be present in inexpensive sugar containing feedstocks such as excess phosphate or complex nutrient sources. This suggests that global regulators of metabolism may be useful targets for engineering metabolic flux that is robust to environmental heterogeneity. The Itaconic acid biosynthetic gene cluster is regulated by laeA. LaeA is required for production of itaconic acid. Overexpression of laeA attenuates genes involved in phosphate acquisition. Global regulator engineering increases robustness of itaconic acid production.
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7
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Bruni GO, Klasson KT. Aconitic Acid Recovery from Renewable Feedstock and Review of Chemical and Biological Applications. Foods 2022; 11:foods11040573. [PMID: 35206048 PMCID: PMC8871043 DOI: 10.3390/foods11040573] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 02/05/2023] Open
Abstract
Aconitic acid (propene-1,2,3-tricarboxylic acid) is the most prevalent 6-carbon organic acid that accumulates in sugarcane and sweet sorghum. As a top value-added chemical, aconitic acid may function as a chemical precursor or intermediate for high-value downstream industrial and biological applications. These downstream applications include use as a bio-based plasticizer, cross-linker, and the formation of valuable and multi-functional polyesters that have also been used in tissue engineering. Aconitic acid also plays various biological roles within cells as an intermediate in the tricarboxylic acid cycle and in conferring unique survival advantages to some plants as an antifeedant, antifungal, and means of storing fixed pools of carbon. Aconitic acid has also been reported as a fermentation inhibitor, anti-inflammatory, and a potential nematicide. Since aconitic acid can be sustainably sourced from renewable, inexpensive sources such as sugarcane, molasses, and sweet sorghum syrup, there is enormous potential to provide multiple streams of additional income to the sugar industry through downstream industrial and biological applications that we discuss in this review.
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8
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The Role of Metal Ions in Fungal Organic Acid Accumulation. Microorganisms 2021; 9:microorganisms9061267. [PMID: 34200938 PMCID: PMC8230503 DOI: 10.3390/microorganisms9061267] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/22/2022] Open
Abstract
Organic acid accumulation is probably the best-known example of primary metabolic overflow. Both bacteria and fungi are capable of producing various organic acids in large amounts under certain conditions, but in terms of productivity-and consequently, of commercial importance-fungal platforms are unparalleled. For high product yield, chemical composition of the growth medium is crucial in providing the necessary conditions, of which the concentrations of four of the first-row transition metal elements, manganese (Mn2+), iron (Fe2+), copper (Cu2+) and zinc (Zn2+) stand out. In this paper we critically review the biological roles of these ions, the possible biochemical and physiological consequences of their influence on the accumulation of the most important mono-, di- and tricarboxylic as well as sugar acids by fungi, and the metal ion-related aspects of submerged organic acid fermentations, including the necessary instrumental analytics. Since producing conditions are associated with a cell physiology that differs strongly to what is observed under “standard” growth conditions, here we consider papers and patents only in which organic acid accumulation levels achieved at least 60% of the theoretical maximum yield, and the actual trace metal ion concentrations were verified.
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9
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Pomraning KR, Dai Z, Munoz N, Kim YM, Gao Y, Deng S, Kim J, Hofstad BA, Swita MS, Lemmon T, Collett JR, Panisko EA, Webb-Robertson BJM, Zucker JD, Nicora CD, De Paoli H, Baker SE, Burnum-Johnson KE, Hillson NJ, Magnuson JK. Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus. Front Bioeng Biotechnol 2021; 9:603832. [PMID: 33898398 PMCID: PMC8058442 DOI: 10.3389/fbioe.2021.603832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/16/2021] [Indexed: 11/13/2022] Open
Abstract
Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4 × after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.
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Affiliation(s)
- Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ziyu Dai
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nathalie Munoz
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Shuang Deng
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joonhoon Kim
- Pacific Northwest National Laboratory, Richland, WA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Beth A Hofstad
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marie S Swita
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Teresa Lemmon
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - James R Collett
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ellen A Panisko
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Jeremy D Zucker
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Nathan J Hillson
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jon K Magnuson
- Pacific Northwest National Laboratory, Richland, WA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
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10
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Huang X, Men P, Tang S, Lu X. Aspergillus terreus as an industrial filamentous fungus for pharmaceutical biotechnology. Curr Opin Biotechnol 2021; 69:273-280. [PMID: 33713917 DOI: 10.1016/j.copbio.2021.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022]
Abstract
Aspergillus terreus is an important Aspergillus species, which has been applied in the industrial production of the bio-based chemical itaconic acid and the lipid-lowering drug lovastatin. The excellent fermentation capability has been demonstrated in these industrial applications. The genomic information revealed that the outstanding capacity of natural product synthesis by A. terreus remains to be further explored. With advances of the genome mining strategy, the products of several cryptic biosynthetic gene clusters have been discovered recently. In addition, a series of metabolic engineering studies have been performed in the industrial strains of lovastatin and itaconic acid to further improve the production processes. This review presents the current progress and the future outlook in the field of A. terreus biotechnology.
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Affiliation(s)
- Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, No. 189 Songling Road, Qingdao 266101, China
| | - Ping Men
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shen Tang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, No. 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Wenhai Rd 1, Aoshanwei, Qingdao, China.
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