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Wang R, Su Y, Yang W, Zhang H, Wang J, Gao W. Enhanced precision and efficiency in metabolic regulation: Compartmentalized metabolic engineering. BIORESOURCE TECHNOLOGY 2024; 402:130786. [PMID: 38703958 DOI: 10.1016/j.biortech.2024.130786] [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: 02/27/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Metabolic engineering has witnessed remarkable advancements, enabling successful large-scale, cost-effective and efficient production of numerous compounds. However, the predominant expression of heterologous genes in the cytoplasm poses limitations, such as low substrate concentration, metabolic competition and product toxicity. To overcome these challenges, compartmentalized metabolic engineering allows the spatial separation of metabolic pathways for the efficient and precise production of target compounds. Compartmentalized metabolic engineering and its common strategies are comprehensively described in this study, where various membranous compartments and membraneless compartments have been used for compartmentalization and constructive progress has been made. Additionally, the challenges and future directions are discussed in depth. This review is dedicated to providing compartmentalized, precise and efficient methods for metabolic production, and provides valuable guidance for further development in the field of metabolic engineering.
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Affiliation(s)
- Rubing Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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Xie CY, Su RR, Wu B, Sun ZY, Tang YQ. Response mechanisms of different Saccharomyces cerevisiae strains to succinic acid. BMC Microbiol 2024; 24:158. [PMID: 38720268 PMCID: PMC11077785 DOI: 10.1186/s12866-024-03314-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The production of succinic acid (SA) from biomass has attracted worldwide interest. Saccharomyces cerevisiae is preferred for SA production due to its strong tolerance to low pH conditions, ease of genetic manipulation, and extensive application in industrial processes. However, when compared with bacterial producers, the SA titers and productivities achieved by engineered S. cerevisiae strains were relatively low. To develop efficient SA-producing strains, it's necessary to clearly understand how S. cerevisiae cells respond to SA. RESULTS In this study, we cultivated five S. cerevisiae strains with different genetic backgrounds under different concentrations of SA. Among them, KF7 and NBRC1958 demonstrated high tolerance to SA, whereas NBRC2018 displayed the least tolerance. Therefore, these three strains were chosen to study how S. cerevisiae responds to SA. Under a concentration of 20 g/L SA, only a few differentially expressed genes were observed in three strains. At the higher concentration of 60 g/L SA, the response mechanisms of the three strains diverged notably. For KF7, genes involved in the glyoxylate cycle were significantly downregulated, whereas genes involved in gluconeogenesis, the pentose phosphate pathway, protein folding, and meiosis were significantly upregulated. For NBRC1958, genes related to the biosynthesis of vitamin B6, thiamin, and purine were significantly downregulated, whereas genes related to protein folding, toxin efflux, and cell wall remodeling were significantly upregulated. For NBRC2018, there was a significant upregulation of genes connected to the pentose phosphate pathway, gluconeogenesis, fatty acid utilization, and protein folding, except for the small heat shock protein gene HSP26. Overexpression of HSP26 and HSP42 notably enhanced the cell growth of NBRC1958 both in the presence and absence of SA. CONCLUSIONS The inherent activities of small heat shock proteins, the levels of acetyl-CoA and the strains' potential capacity to consume SA all seem to affect the responses and tolerances of S. cerevisiae strains to SA. These factors should be taken into consideration when choosing host strains for SA production. This study provides a theoretical basis and identifies potential host strains for the development of robust and efficient SA-producing strains.
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Affiliation(s)
- Cai-Yun Xie
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Ran-Ran Su
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture, Renmin Rd. 4-13, Chengdu, 610041, Sichuan, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
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Morales-Palomo S, Navarrete C, Martínez JL, González-Fernández C, Tomás-Pejó E. Transcriptomic profiling of an evolved Yarrowia lipolytica strain: tackling hexanoic acid fermentation to increase lipid production from short-chain fatty acids. Microb Cell Fact 2024; 23:101. [PMID: 38566056 PMCID: PMC10988856 DOI: 10.1186/s12934-024-02367-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Short-chain fatty acids (SCFAs) are cost-effective carbon sources for an affordable production of lipids. Hexanoic acid, the acid with the longest carbon chain in the SCFAs pool, is produced in anaerobic fermentation of organic residues and its use is very challenging, even inhibiting oleaginous yeasts growth. RESULTS In this investigation, an adaptive laboratory evolution (ALE) was performed to improve Yarrowia lipolytica ACA DC 50109 tolerance to high hexanoic acid concentrations. Following ALE, the transcriptomic analysis revealed several genetic adaptations that improved the assimilation of this carbon source in the evolved strain compared to the wild type (WT). Indeed, the evolved strain presented a high expression of the up-regulated gene YALI0 E16016g, which codes for FAT1 and is related to lipid droplets formation and responsible for mobilizing long-chain acids within the cell. Strikingly, acetic acid and other carbohydrate transporters were over-expressed in the WT strain. CONCLUSIONS A more tolerant yeast strain able to attain higher lipid content under the presence of high concentrations of hexanoic acid has been obtained. Results provided novel information regarding the assimilation of hexanoic acid in yeasts.
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Affiliation(s)
| | - Clara Navarrete
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - José Luis Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Cristina González-Fernández
- Biotechnological Processes Unit, IMDEA Energy, Móstoles (Madrid), Spain
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Valladolid, 47011, Spain
- Institute of Sustainable Processes, Valladolid, 47011, Spain
| | - Elia Tomás-Pejó
- Biotechnological Processes Unit, IMDEA Energy, Móstoles (Madrid), Spain.
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Ye C, Hong H, Gao J, Li M, Gou Y, Gao D, Dong C, Huang L, Xu Z, Lian J. Characterization and engineering of peroxisome targeting sequences for compartmentalization engineering in Pichia pastoris. Biotechnol Bioeng 2024. [PMID: 38568751 DOI: 10.1002/bit.28706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
Peroxisomal compartmentalization has emerged as a highly promising strategy for reconstituting intricate metabolic pathways. In recent years, significant progress has been made in the peroxisomes through harnessing precursor pools, circumventing metabolic crosstalk, and minimizing the cytotoxicity of exogenous pathways. However, it is important to note that in methylotrophic yeasts (e.g. Pichia pastoris), the abundance and protein composition of peroxisomes are highly variable, particularly when peroxisome proliferation is induced by specific carbon sources. The intricate subcellular localization of native proteins, the variability of peroxisomal metabolic pathways, and the lack of systematic characterization of peroxisome targeting signals have limited the applications of peroxisomal compartmentalization in P. pastoris. Accordingly, this study established a high-throughput screening method based on β-carotene biosynthetic pathway to evaluate the targeting efficiency of PTS1s (Peroxisome Targeting Signal Type 1) in P. pastoris. First, 25 putative endogenous PTS1s were characterized and 3 PTS1s with high targeting efficiency were identified. Then, directed evolution of PTS1s was performed by constructing two PTS1 mutant libraries, and a total of 51 PTS1s (29 classical and 22 noncanonical PTS1s) with presumably higher peroxisomal targeting efficiency were identified, part of which were further characterized via confocal microscope. Finally, the newly identified PTS1s were employed for peroxisomal compartmentalization of the geraniol biosynthetic pathway, resulting in more than 30% increase in the titer of monoterpene compared with when the pathway was localized to the cytosol. The present study expands the synthetic biology toolkit and lays a solid foundation for peroxisomal compartmentalization in P. pastoris.
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Affiliation(s)
- Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Haosen Hong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
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Fu X, Zhu X. Key homeobox transcription factors regulate the development of the firefly's adult light organ and bioluminescence. Nat Commun 2024; 15:1736. [PMID: 38443352 PMCID: PMC10914744 DOI: 10.1038/s41467-024-45559-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 01/26/2024] [Indexed: 03/07/2024] Open
Abstract
Adult fireflies exhibit unique flashing courtship signals, emitted by specialized light organs, which develop mostly independently from larval light organs during the pupal stage. The mechanisms of adult light organ development have not been thoroughly studied until now. Here we show that key homeobox transcription factors AlABD-B and AlUNC-4 regulate the development of adult light organs and bioluminescence in the firefly Aquatica leii. Interference with the expression of AlAbd-B and AlUnc-4 genes results in undeveloped or non-luminescent adult light organs. AlABD-B regulates AlUnc-4, and they interact with each other. AlABD-B and AlUNC-4 activate the expression of the luciferase gene AlLuc1 and some peroxins. Four peroxins are involved in the import of AlLUC1 into peroxisomes. Our study provides key insights into the development of adult light organs and flash signal control in fireflies.
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Affiliation(s)
- Xinhua Fu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xinlei Zhu
- Firefly Conservation Research Centre, Wuhan, 430070, China
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Song S, Ye C, Jin Y, Dai H, Hu J, Lian J, Pan R. Peroxisome-based metabolic engineering for biomanufacturing and agriculture. Trends Biotechnol 2024:S0167-7799(24)00034-9. [PMID: 38423802 DOI: 10.1016/j.tibtech.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Subcellular compartmentalization of metabolic pathways plays a crucial role in metabolic engineering. The peroxisome has emerged as a highly valuable and promising compartment for organelle engineering, particularly in the fields of biological manufacturing and agriculture. In this review, we summarize the remarkable achievements in peroxisome engineering in yeast, the industrially popular biomanufacturing chassis host, to produce various biocompounds. We also review progress in plant peroxisome engineering, a field that has already exhibited high potential in both biomanufacturing and agriculture. Moreover, we outline various experimentally validated strategies to improve the efficiency of engineered pathways in peroxisomes, as well as prospects of peroxisome engineering.
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Affiliation(s)
- Shuyan Song
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Cuifang Ye
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Yijun Jin
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Huaxin Dai
- Beijing Life Science Academy, Changping 102209, Beijing, China
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Jiazhang Lian
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China.
| | - Ronghui Pan
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China.
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Ma Y, Shang Y, Stephanopoulos G. Engineering peroxisomal biosynthetic pathways for maximization of triterpene production in Yarrowia lipolytica. Proc Natl Acad Sci U S A 2024; 121:e2314798121. [PMID: 38261612 PMCID: PMC10835042 DOI: 10.1073/pnas.2314798121] [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: 08/25/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Constructing efficient cell factories for product synthesis is frequently hampered by competing pathways and/or insufficient precursor supply. This is particularly evident in the case of triterpenoid biosynthesis in Yarrowia lipolytica, where squalene biosynthesis is tightly coupled to cytosolic biosynthesis of sterols essential for cell viability. Here, we addressed this problem by reconstructing the complete squalene biosynthetic pathway, starting from acetyl-CoA, in the peroxisome, thus harnessing peroxisomal acetyl-CoA pool and sequestering squalene synthesis in this organelle from competing cytosolic reactions. This strategy led to increasing the squalene levels by 1,300-fold relatively to native cytosolic synthesis. Subsequent enhancement of the peroxisomal acetyl-CoA supply by two independent approaches, 1) converting cellular lipid pool to peroxisomal acetyl-CoA and 2) establishing an orthogonal acetyl-CoA shortcut from CO2-derived acetate in the peroxisome, further significantly improved local squalene accumulation. Using these approaches, we constructed squalene-producing strains capable of yielding 32.8 g/L from glucose, and 31.6 g/L from acetate by employing a cofeeding strategy, in bioreactor fermentations. Our findings provide a feasible strategy for protecting intermediate metabolites that can be claimed by multiple reactions by engineering peroxisomes in Y. lipolytica as microfactories for the production of such intermediates and in particular acetyl-CoA-derived metabolites.
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Affiliation(s)
- Yongshuo Ma
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, Chinese Academy of Agricultural Sciences (CAAS)-Yunnan Normal University (YNNU)-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming650500, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy (Ministry of Education), Yunnan Normal University, Kunming650500, China
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
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Vasylyshyn R, Dmytruk O, Sybirnyy A, Ruchała J. Engineering of Ogataea polymorpha strains with ability for high-temperature alcoholic fermentation of cellobiose. FEMS Yeast Res 2024; 24:foae007. [PMID: 38400543 DOI: 10.1093/femsyr/foae007] [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: 08/31/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 02/25/2024] Open
Abstract
Successful conversion of cellulosic biomass into biofuels requires organisms capable of efficiently utilizing xylose as well as cellodextrins and glucose. Ogataea (Hansenula) polymorpha is the natural xylose-metabolizing organism and is one of the most thermotolerant yeasts known, with a maximum growth temperature above 50°C. Cellobiose-fermenting strains, derivatives of an improved ethanol producer from xylose O. polymorpha BEP/cat8∆, were constructed in this work by the introduction of heterologous genes encoding cellodextrin transporters (CDTs) and intracellular enzymes (β-glucosidase or cellobiose phosphorylase) that hydrolyze cellobiose. For this purpose, the genes gh1-1 of β-glucosidase, CDT-1m and CDT-2m of cellodextrin transporters from Neurospora crassa and the CBP gene coding for cellobiose phosphorylase from Saccharophagus degradans, were successfully expressed in O. polymorpha. Through metabolic engineering and mutagenesis, strains BEP/cat8∆/gh1-1/CDT-1m and BEP/cat8∆/CBP-1/CDT-2mAM were developed, showing improved parameters for high-temperature alcoholic fermentation of cellobiose. The study highlights the need for further optimization to enhance ethanol yields and elucidate cellobiose metabolism intricacies in O. polymorpha yeast. This is the first report of the successful development of stable methylotrophic thermotolerant strains of O. polymorpha capable of coutilizing cellobiose, glucose, and xylose under high-temperature alcoholic fermentation conditions at 45°C.
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Affiliation(s)
- Roksolana Vasylyshyn
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Olena Dmytruk
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Andriy Sybirnyy
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Justyna Ruchała
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
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Brechting PJ, Shah C, Rakotondraibe L, Shen Q, Rappleye CA. Histoplasma capsulatum requires peroxisomes for multiple virulence functions including siderophore biosynthesis. mBio 2023; 14:e0328422. [PMID: 37432032 PMCID: PMC10470777 DOI: 10.1128/mbio.03284-22] [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: 11/30/2022] [Accepted: 05/30/2023] [Indexed: 07/12/2023] Open
Abstract
Peroxisomes are versatile eukaryotic organelles essential for many functions in fungi, including fatty acid metabolism, reactive oxygen species detoxification, and secondary metabolite biosynthesis. A suite of Pex proteins (peroxins) maintains peroxisomes, while peroxisomal matrix enzymes execute peroxisome functions. Insertional mutagenesis identified peroxin genes as essential components supporting the intraphagosomal growth of the fungal pathogen Histoplasma capsulatum. Disruption of the peroxins Pex5, Pex10, or Pex33 in H. capsulatum prevented peroxisome import of proteins targeted to the organelle via the PTS1 pathway. This loss of peroxisome protein import limited H. capsulatum intracellular growth in macrophages and attenuated virulence in an acute histoplasmosis infection model. Interruption of the alternate PTS2 import pathway also attenuated H. capsulatum virulence, although only at later time points of infection. The Sid1 and Sid3 siderophore biosynthesis proteins contain a PTS1 peroxisome import signal and localize to the H. capsulatum peroxisome. Loss of either the PTS1 or PTS2 peroxisome import pathway impaired siderophore production and iron acquisition in H. capsulatum, demonstrating compartmentalization of at least some biosynthetic steps for hydroxamate siderophore biosynthesis. However, the loss of PTS1-based peroxisome import caused earlier virulence attenuation than either the loss of PTS2-based protein import or the loss of siderophore biosynthesis, indicating additional PTS1-dependent peroxisomal functions are important for H. capsulatum virulence. Furthermore, disruption of the Pex11 peroxin also attenuated H. capsulatum virulence independently of peroxisomal protein import and siderophore biosynthesis. These findings demonstrate peroxisomes contribute to H. capsulatum pathogenesis by facilitating siderophore biosynthesis and another unidentified role(s) for the organelle during fungal virulence. IMPORTANCE The fungal pathogen Histoplasma capsulatum infects host phagocytes and establishes a replication-permissive niche within the cells. To do so, H. capsulatum overcomes and subverts antifungal defense mechanisms which include the limitation of essential micronutrients. H. capsulatum replication within host cells requires multiple distinct functions of the fungal peroxisome organelle. These peroxisomal functions contribute to H. capsulatum pathogenesis at different times during infection and include peroxisome-dependent biosynthesis of iron-scavenging siderophores to enable fungal proliferation, particularly after activation of cell-mediated immunity. The multiple essential roles of fungal peroxisomes reveal this organelle as a potential but untapped target for the development of therapeutics.
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Affiliation(s)
| | - Chandan Shah
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Liva Rakotondraibe
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, Columbus, Ohio, USA
| | - Qian Shen
- Department of Biology, Rhodes College, Memphis, Tennessee, USA
| | - Chad A. Rappleye
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
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Dmytruk KV, Ruchala J, Fayura LR, Chrzanowski G, Dmytruk OV, Tsyrulnyk AO, Andreieva YA, Fedorovych DV, Motyka OI, Mattanovich D, Marx H, Sibirny AA. Efficient production of bacterial antibiotics aminoriboflavin and roseoflavin in eukaryotic microorganisms, yeasts. Microb Cell Fact 2023; 22:132. [PMID: 37474952 PMCID: PMC10357625 DOI: 10.1186/s12934-023-02129-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Actinomycetes Streptomyces davaonensis and Streptomyces cinnabarinus synthesize a promising broad-spectrum antibiotic roseoflavin, with its synthesis starting from flavin mononucleotide and proceeding through an immediate precursor, aminoriboflavin, that also has antibiotic properties. Roseoflavin accumulation by the natural producers is rather low, whereas aminoriboflavin accumulation is negligible. Yeasts have many advantages as biotechnological producers relative to bacteria, however, no recombinant producers of bacterial antibiotics in yeasts are known. RESULTS Roseoflavin biosynthesis genes have been expressed in riboflavin- or FMN-overproducing yeast strains of Candida famata and Komagataella phaffii. Both these strains accumulated aminoriboflavin, whereas only the latter produced roseoflavin. Aminoriboflavin isolated from the culture liquid of C. famata strain inhibited the growth of Staphylococcus aureus (including MRSA) and Listeria monocytogenes. Maximal accumulation of aminoriboflavin in shake-flasks reached 1.5 mg L- 1 (C. famata), and that of roseoflavin was 5 mg L- 1 (K. phaffii). Accumulation of aminoriboflavin and roseoflavin by K. phaffii recombinant strain in a bioreactor reached 22 and 130 mg L- 1, respectively. For comparison, recombinant strains of the native bacterial producer S. davaonensis accumulated near one-order less of roseoflavin while no recombinant producers of aminoriboflavin was reported at all. CONCLUSIONS Yeast recombinant producers of bacterial antibiotics aminoriboflavin and roseoflavin were constructed and evaluated.
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Affiliation(s)
- Kostyantyn V Dmytruk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Justyna Ruchala
- University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland
| | - Liubov R Fayura
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | | | - Olena V Dmytruk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Andriy O Tsyrulnyk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Yuliia A Andreieva
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Daria V Fedorovych
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Olena I Motyka
- Research Institute of Epidemiology and Hygiene of the Danylo Halytsky Lviv National Medical University, Zelena St, 12, Lviv, 79005, Ukraine
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Vienna, 1190, Austria
| | - Hans Marx
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Vienna, 1190, Austria
| | - Andriy A Sibirny
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine.
- University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland.
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11
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Transcriptional Response of Multi-Stress-Tolerant Saccharomyces cerevisiae to Sequential Stresses. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
During the fermentation process, yeast cells face different stresses, and their survival and fermentation efficiency depend on their adaptation to these challenging conditions. Yeast cells must tolerate not only a single stress but also multiple simultaneous and sequential stresses. However, the adaptation and cellular response when cells are sequentially stressed are not completely understood. To explore this, we exposed a multi-stress-tolerant strain (BT0510) to different consecutive stresses to globally explore a common response, focusing on the genes induced in both stresses. Gene Ontology, pathway analyses, and common transcription factor motifs identified many processes linked to this common response. A metabolic shift to the pentose phosphate pathway, peroxisome activity, and the oxidative stress response were some of the processes found. The SYM1, STF2, and HSP genes and the transcription factors Adr1 and Usv1 may play a role in this response. This study presents a global view of the transcriptome of a multi-resistance yeast and provides new insights into the response to sequential stresses. The identified response genes can indicate future directions for the genetic engineering of yeast strains, which could improve many fermentation processes, such as those used for bioethanol production and beverages.
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12
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Chen L, Xiao W, Yao M, Wang Y, Yuan Y. Compartmentalization engineering of yeasts to overcome precursor limitations and cytotoxicity in terpenoid production. Front Bioeng Biotechnol 2023; 11:1132244. [PMID: 36911190 PMCID: PMC9997727 DOI: 10.3389/fbioe.2023.1132244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Metabolic engineering strategies for terpenoid production have mainly focused on bottlenecks in the supply of precursor molecules and cytotoxicity to terpenoids. In recent years, the strategies involving compartmentalization in eukaryotic cells has rapidly developed and have provided several advantages in the supply of precursors, cofactors and a suitable physiochemical environment for product storage. In this review, we provide a comprehensive analysis of organelle compartmentalization for terpenoid production, which can guide the rewiring of subcellular metabolism to make full use of precursors, reduce metabolite toxicity, as well as provide suitable storage capacity and environment. Additionally, the strategies that can enhance the efficiency of a relocated pathway by increasing the number and size of organelles, expanding the cell membrane and targeting metabolic pathways in several organelles are also discussed. Finally, the challenges and future perspectives of this approach for the terpenoid biosynthesis are also discussed.
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Affiliation(s)
- Lifei Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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13
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Juhas M. The World of Microorganisms. BRIEF LESSONS IN MICROBIOLOGY 2023:1-16. [DOI: 10.1007/978-3-031-29544-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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14
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Ciamponi FE, Procópio DP, Murad NF, Franco TT, Basso TO, Brandão MM. Multi-omics network model reveals key genes associated with p-coumaric acid stress response in an industrial yeast strain. Sci Rep 2022; 12:22466. [PMID: 36577778 PMCID: PMC9797568 DOI: 10.1038/s41598-022-26843-2] [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: 09/28/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
The production of ethanol from lignocellulosic sources presents increasingly difficult issues for the global biofuel scenario, leading to increased production costs of current second-generation (2G) ethanol when compared to first-generation (1G) plants. Among the setbacks encountered in industrial processes, the presence of chemical inhibitors from pre-treatment processes severely hinders the potential of yeasts in producing ethanol at peak efficiency. However, some industrial yeast strains have, either naturally or artificially, higher tolerance levels to these compounds. Such is the case of S. cerevisiae SA-1, a Brazilian fuel ethanol industrial strain that has shown high resistance to inhibitors produced by the pre-treatment of cellulosic complexes. Our study focuses on the characterization of the transcriptomic and physiological impact of an inhibitor of this type, p-coumaric acid (pCA), on this strain under chemostat cultivation via RNAseq and quantitative physiological data. It was found that strain SA-1 tend to increase ethanol yield and production rate while decreasing biomass yield when exposed to pCA, in contrast to pCA-susceptible strains, which tend to decrease their ethanol yield and fermentation efficiency when exposed to this substance. This suggests increased metabolic activity linked to mitochondrial and peroxisomal processes. The transcriptomic analysis also revealed a plethora of differentially expressed genes located in co-expressed clusters that are associated with changes in biological pathways linked to biosynthetic and energetical processes. Furthermore, it was also identified 20 genes that act as interaction hubs for these clusters, while also having association with altered pathways and changes in metabolic outputs, potentially leading to the discovery of novel targets for metabolic engineering toward a more robust industrial yeast strain.
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Affiliation(s)
- F. E. Ciamponi
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
| | - D. P. Procópio
- grid.11899.380000 0004 1937 0722Department of Chemical Engineering, University of São Paulo (USP), Av. Prof. Luciano Gualberto, 380, São Paulo, SP 05508-010 Brazil
| | - N. F. Murad
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
| | - T. T. Franco
- grid.411087.b0000 0001 0723 2494School of Chemical Engineering (FEQ), State University of Campinas (Unicamp), Av. Albert Einstein, 500, Campinas, SP 13083-852 Brazil
| | - T. O. Basso
- grid.11899.380000 0004 1937 0722Department of Chemical Engineering, University of São Paulo (USP), Av. Prof. Luciano Gualberto, 380, São Paulo, SP 05508-010 Brazil
| | - M. M. Brandão
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
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15
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A Transcriptomic Analysis of Higher-Order Ecological Interactions in a Eukaryotic Model Microbial Ecosystem. mSphere 2022; 7:e0043622. [PMID: 36259715 PMCID: PMC9769528 DOI: 10.1128/msphere.00436-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Nonlinear ecological interactions within microbial ecosystems and their contribution to ecosystem functioning remain largely unexplored. Higher-order interactions, or interactions in systems comprised of more than two members that cannot be explained by cumulative pairwise interactions, are particularly understudied, especially in eukaryotic microorganisms. The wine fermentation ecosystem presents an ideal model to study yeast ecosystem establishment and functioning. Some pairwise ecological interactions between wine yeast species have been characterized, but very little is known about how more complex, multispecies systems function. Here, we evaluated nonlinear ecosystem properties by determining the transcriptomic response of Saccharomyces cerevisiae to pairwise versus tri-species culture. The transcriptome revealed that genes expressed during pairwise coculture were enriched in the tri-species data set but also that just under half of the data set comprised unique genes attributed to a higher-order response. Through interactive protein-association network visualizations, a holistic cell-wide view of the gene expression data was generated, which highlighted known stress response and metabolic adaptation mechanisms which were specifically activated during tri-species growth. Further, extracellular metabolite data corroborated that the observed differences were a result of a biotic stress response. This provides exciting new evidence showing the presence of higher-order interactions within a model microbial ecosystem. IMPORTANCE Higher-order interactions are one of the major blind spots in our understanding of microbial ecosystems. These systems remain largely unpredictable and are characterized by nonlinear dynamics, in particular when the system is comprised of more than two entities. By evaluating the transcriptomic response of S. cerevisiae to an increase in culture complexity from a single species to two- and three-species systems, we were able to confirm the presence of a unique response in the more complex setting that could not be explained by the responses observed at the pairwise level. This is the first data set that provides molecular targets for further analysis to explain unpredictable ecosystem dynamics in yeast.
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16
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Feng P, Skowyra ML, Rapoport TA. Structure and function of the peroxisomal ubiquitin ligase complex. Biochem Soc Trans 2022; 50:1921-1930. [PMID: 36421406 PMCID: PMC9788354 DOI: 10.1042/bst20221393] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 09/26/2023]
Abstract
Peroxisomes are membrane-bounded organelles that exist in most eukaryotic cells and are involved in the oxidation of fatty acids and the destruction of reactive oxygen species. Depending on the organism, they house additional metabolic reactions that range from glycolysis in parasitic protozoa to the production of ether lipids in animals and antibiotics in fungi. The importance of peroxisomes for human health is revealed by various disorders - notably the Zellweger spectrum - that are caused by defects in peroxisome biogenesis and are often fatal. Most peroxisomal metabolic enzymes reside in the lumen, but are synthesized in the cytosol and imported into the organelle by mobile receptors. The receptors accompany cargo all the way into the lumen and must return to the cytosol to start a new import cycle. Recycling requires receptor monoubiquitination by a membrane-embedded ubiquitin ligase complex composed of three RING finger (RF) domain-containing proteins: PEX2, PEX10, and PEX12. A recent cryo-electron microscopy (cryo-EM) structure of the complex reveals its function as a retro-translocation channel for peroxisomal import receptors. Each subunit of the complex contributes five transmembrane segments that assemble into an open channel. The N terminus of a receptor likely inserts into the pore from the lumenal side, and is then monoubiquitinated by one of the RFs to enable extraction into the cytosol. If recycling is compromised, receptors are polyubiquitinated by the concerted action of the other two RFs and ultimately degraded. The new data provide mechanistic insight into a crucial step of peroxisomal protein import.
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Affiliation(s)
- Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
| | - Michael L. Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
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17
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Anteghini M, Haja A, Martins dos Santos VA, Schomaker L, Saccenti E. OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection. Comput Struct Biotechnol J 2022; 21:128-133. [PMID: 36544474 PMCID: PMC9747352 DOI: 10.1016/j.csbj.2022.11.058] [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: 07/20/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
We present the OrganelX e-Science Web Server that provides a user-friendly implementation of the In-Pero and In-Mito classifiers for sub-peroxisomal and sub-mitochondrial localization of peroxisomal and mitochondrial proteins and the Is-PTS1 algorithm for detecting and validating potential peroxisomal proteins carrying a PTS1 signal sequence. The OrganelX e-Science Web Server is available at https://organelx.hpc.rug.nl/fasta/.
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Affiliation(s)
- Marco Anteghini
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands,LifeGlimmer GmbH, Berlin, Germany,Corresponding author at: Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands (M. Anteghini).
| | - Asmaa Haja
- Bernoulli Institute, University of Groningen, Groningen, The Netherlands
| | - Vitor A.P. Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany,Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands
| | - Lambert Schomaker
- Bernoulli Institute, University of Groningen, Groningen, The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands,Corresponding author at: Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands (M. Anteghini).
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18
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Sibirny AA. Metabolic engineering of non-conventional yeasts for construction of the advanced producers of biofuels and high-value chemicals. BBA ADVANCES 2022; 3:100071. [PMID: 37082251 PMCID: PMC10074886 DOI: 10.1016/j.bbadva.2022.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Non-conventional yeasts, i.e. yeasts different from Saccharomyces cerevisiae, represent heterogenous group of unicellular fungi consisting of near 1500 species. Some of these species have interesting and sometimes unique properties like ability to grow on methanol, n-alkanes, ferment pentose sugars xylose and l-arabinose, grow at high temperatures (50°С and more), overproduce riboflavin (vitamin B2) and others. These unique properties are important for development of basic science; moreover, some of them possess also significant applied interest for elaboration of new biotechnologies. Current paper represents review of the recent own results and of those of other authors in the field of non-conventional yeast study for construction of the advanced producers of biofuels (ethanol, isobutanol) from lignocellulosic sugars glucose and xylose or crude glycerol (Ogataea polymorpha, Magnusiomyces magnusii) and vitamin B2 (riboflavin) from glucose and cheese whey (Candida famata).
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Affiliation(s)
- Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, Lviv 79005 Ukraine
- University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601 Poland
- Corresponding author at: Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, Lviv 79005 Ukraine.
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19
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Mukherjee M, Blair RH, Wang ZQ. Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production. Metab Eng 2022; 74:139-149. [DOI: 10.1016/j.ymben.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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20
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Hidalgo-Vico S, Casas J, García C, Lillo MP, Alonso-Monge R, Román E, Pla J. Overexpression of the White Opaque Switching Master Regulator Wor1 Alters Lipid Metabolism and Mitochondrial Function in Candida albicans. J Fungi (Basel) 2022; 8:1028. [PMID: 36294593 PMCID: PMC9604646 DOI: 10.3390/jof8101028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 02/26/2024] Open
Abstract
Candida albicans is a commensal yeast that inhabits the gastrointestinal tract of humans; increased colonization of this yeast in this niche has implicated the master regulator of the white-opaque transition, Wor1, by mechanisms not completely understood. We have addressed the role that this transcription factor has on commensalism by the characterization of strains overexpressing this gene. We show that WOR1 overexpression causes an alteration of the total lipid content of the fungal cell and significantly alters the composition of structural and reserve molecular species lipids as determined by lipidomic analysis. These cells are hypersensitive to membrane-disturbing agents such as SDS, have increased tolerance to azoles, an augmented number of peroxisomes, and increased phospholipase activity. WOR1 overexpression also decreases mitochondrial activity and results in altered susceptibility to certain oxidants. All together, these changes reflect drastic alterations in the cellular physiology that facilitate adaptation to the gastrointestinal tract environment.
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Affiliation(s)
- Susana Hidalgo-Vico
- Departamento de Microbiología y Parasitología-IRYCIS, Facultad de Farmacia, Universidad Complutense de Madrid, Avda. Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Josefina Casas
- Research Unit on BioActive Molecules (RUBAM), Department of Biological Chemistry, Instituto de Química Avanzada de Cataluña, Jordi Girona 18–26, 08034 Barcelona, Spain
| | - Carolina García
- Departamento de Química Física Biológica, Instituto Química Física “Rocasolano”, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - M. Pilar Lillo
- Departamento de Química Física Biológica, Instituto Química Física “Rocasolano”, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Rebeca Alonso-Monge
- Departamento de Microbiología y Parasitología-IRYCIS, Facultad de Farmacia, Universidad Complutense de Madrid, Avda. Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Elvira Román
- Departamento de Microbiología y Parasitología-IRYCIS, Facultad de Farmacia, Universidad Complutense de Madrid, Avda. Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Jesús Pla
- Departamento de Microbiología y Parasitología-IRYCIS, Facultad de Farmacia, Universidad Complutense de Madrid, Avda. Ramón y Cajal s/n, 28040 Madrid, Spain
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21
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Li N, Hua B, Chen Q, Teng F, Ruan M, Zhu M, Zhang L, Huo Y, Liu H, Zhuang M, Shen H, Zhu H. A sphingolipid-mTORC1 nutrient-sensing pathway regulates animal development by an intestinal peroxisome relocation-based gut-brain crosstalk. Cell Rep 2022; 40:111140. [PMID: 35905721 DOI: 10.1016/j.celrep.2022.111140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 05/23/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022] Open
Abstract
The mTOR-dependent nutrient-sensing and response machinery is the central hub for animals to regulate their cellular and developmental programs. However, equivalently pivotal nutrient and metabolite signals upstream of mTOR and developmental-regulatory signals downstream of mTOR are not clear, especially at the organism level. We previously showed glucosylceramide (GlcCer) acts as a critical nutrient and metabolite signal for overall amino acid levels to promote development by activating the intestinal mTORC1 signaling pathway. Here, through a large-scale genetic screen, we find that the intestinal peroxisome is critical for antagonizing the GlcCer-mTORC1-mediated nutrient signal. Mechanistically, GlcCer deficiency, inactive mTORC1, or prolonged starvation relocates intestinal peroxisomes closer to the apical region in a kinesin- and microtubule-dependent manner. Those apical accumulated peroxisomes further release peroxisomal-β-oxidation-derived glycolipid hormones that target chemosensory neurons and downstream nuclear hormone receptor DAF-12 to arrest the animal development. Our data illustrate a sophisticated gut-brain axis that predominantly orchestrates nutrient-sensing-dependent development in animals.
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Affiliation(s)
- Na Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Beilei Hua
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fukang Teng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Meiyu Ruan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengnan Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Li Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yinbo Huo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Hongqin Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Min Zhuang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Huali Shen
- Institutes of Biomedical Sciences, Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Huanhu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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22
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Bacterial Infection Induces Ultrastructural and Transcriptional Changes in the King Oyster Mushroom ( Pleurotus eryngii). Microbiol Spectr 2022; 10:e0144522. [PMID: 35616396 PMCID: PMC9241817 DOI: 10.1128/spectrum.01445-22] [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] [Indexed: 11/20/2022] Open
Abstract
Pleurotus eryngii (king oyster mushroom) is a commercially important mushroom with high nutritional and economic value. However, soft rot disease, caused by the pathogenic bacterium Erwinia beijingensis, poses a threat to its quality and production. Morphological and ultrastructural observations of P. eryngii were conducted at early, middle, and late stages of infection. At 2 days postinoculation (dpi), small yellow spots on the fruiting body were observed. The infected tissue displayed hyphal deformations and breaks at 5 dpi. At 9 dpi, damage to cell wall integrity and absence of intact cellular organelles were observed and the diseased fruiting bodies were unable to grow normally. Transcriptome analysis identified 4,296 differentially expressed genes in the fruiting body following infection. In fact, broad transcriptional reprogramming was observed in infected fruiting bodies compared to controls. The affected pathways included antioxidant systems, peroxisome biogenesis, autophagy, and oxidation-reduction. More specifically, pex genes were downregulated during infection, indicating impaired peroxisome homeostasis and redox balance. Additionally, genes encoding chitinase, β-1,3-glucanase, and proteases associated with cell wall degradation were upregulated in infected P. eryngii. This study provides insights into the responses of P. eryngii during soft rot disease and facilitates the understanding of the pathogenic process of bacteriosis in mushrooms. IMPORTANCEPleurotus eryngii (king oyster mushroom) is a popular and economically valuable edible mushroom; however, it suffers from various bacterial diseases, including soft rot disease caused by the bacterium Erwinia beijingensis. Here, we examined bacterial infection of the mushroom through morphological and ultrastructural observations as well as transcriptome analysis. Pathogen attack damaged the cell structure of P. eryngii, including the cell wall, and also induced high levels of reactive oxygen species. These results were reflected in differential gene expression in P. eryngii as a response to the pathogenic bacteria, including genes involved in antioxidant systems, peroxisome biogenesis, autophagy, oxidation-reduction, ribosome biogenesis, and cell-wall degradation, among others. This study provides insights into the structural and molecular responses of P. eryngii during soft rot disease, improving our understanding and the potential control of the pathogenic process of bacteriosis in mushrooms.
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23
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Jin K, Xia H, Liu Y, Li J, Du G, Lv X, Liu L. Compartmentalization and transporter engineering strategies for terpenoid synthesis. Microb Cell Fact 2022; 21:92. [PMID: 35599322 PMCID: PMC9125818 DOI: 10.1186/s12934-022-01819-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial cell factories for terpenoid synthesis form a less expensive and more environment-friendly approach than chemical synthesis and extraction, and are thus being regarded as mainstream research recently. Organelle compartmentalization for terpenoid synthesis has received much attention from researchers owing to the diverse physiochemical characteristics of organelles. In this review, we first systematically summarized various compartmentalization strategies utilized in terpenoid production, mainly plant terpenoids, which can provide catalytic reactions with sufficient intermediates and a suitable environment, while bypassing competing metabolic pathways. In addition, because of the limited storage capacity of cells, strategies used for the expansion of specific organelle membranes were discussed. Next, transporter engineering strategies to overcome the cytotoxic effects of terpenoid accumulation were analyzed. Finally, we discussed the future perspectives of compartmentalization and transporter engineering strategies, with the hope of providing theoretical guidance for designing and constructing cell factories for the purpose of terpenoid production.
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24
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Mattila H, Österman-Udd J, Mali T, Lundell T. Basidiomycota Fungi and ROS: Genomic Perspective on Key Enzymes Involved in Generation and Mitigation of Reactive Oxygen Species. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:837605. [PMID: 37746164 PMCID: PMC10512322 DOI: 10.3389/ffunb.2022.837605] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/21/2022] [Indexed: 09/26/2023]
Abstract
Our review includes a genomic survey of a multitude of reactive oxygen species (ROS) related intra- and extracellular enzymes and proteins among fungi of Basidiomycota, following their taxonomic classification within the systematic classes and orders, and focusing on different fungal lifestyles (saprobic, symbiotic, pathogenic). Intra- and extracellular ROS metabolism-involved enzymes (49 different protein families, summing 4170 protein models) were searched as protein encoding genes among 63 genomes selected according to current taxonomy. Extracellular and intracellular ROS metabolism and mechanisms in Basidiomycota are illustrated in detail. In brief, it may be concluded that differences between the set of extracellular enzymes activated by ROS, especially by H2O2, and involved in generation of H2O2, follow the differences in fungal lifestyles. The wood and plant biomass degrading white-rot fungi and the litter-decomposing species of Agaricomycetes contain the highest counts for genes encoding various extracellular peroxidases, mono- and peroxygenases, and oxidases. These findings further confirm the necessity of the multigene families of various extracellular oxidoreductases for efficient and complete degradation of wood lignocelluloses by fungi. High variations in the sizes of the extracellular ROS-involved gene families were found, however, among species with mycorrhizal symbiotic lifestyle. In addition, there are some differences among the sets of intracellular thiol-mediation involving proteins, and existence of enzyme mechanisms for quenching of intracellular H2O2 and ROS. In animal- and plant-pathogenic species, extracellular ROS enzymes are absent or rare. In these fungi, intracellular peroxidases are seemingly in minor role than in the independent saprobic, filamentous species of Basidiomycota. Noteworthy is that our genomic survey and review of the literature point to that there are differences both in generation of extracellular ROS as well as in mechanisms of response to oxidative stress and mitigation of ROS between fungi of Basidiomycota and Ascomycota.
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Affiliation(s)
| | | | | | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, Helsinki, Finland
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Choi BH, Kang HJ, Kim SC, Lee PC. Organelle Engineering in Yeast: Enhanced Production of Protopanaxadiol through Manipulation of Peroxisome Proliferation in Saccharomyces cerevisiae. Microorganisms 2022; 10:microorganisms10030650. [PMID: 35336225 PMCID: PMC8950469 DOI: 10.3390/microorganisms10030650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may consequently reduce the desired yield of the target isoprenoid. As a strategy to overcome this suggested limitation, we selected peroxisome membranes as depots for the additional storage of biosynthesized isoprenoids to facilitate increased isoprenoid production in Saccharomyces cerevisiae. To maximize the peroxisome membrane storage capacity of S.cerevisiae, the copy number and size of peroxisomes were increased through genetic engineering of the expression of three peroxisome biogenesis-related peroxins (Pex11p, Pex34p, and Atg36p). The genetically enlarged and high copied peroxisomes in S.cerevisiae were stably maintained under a bioreactor fermentation condition. The peroxisome-engineered S.cerevisiae strains were then utilized as host strains for metabolic engineering of heterologous protopanaxadiol pathway. The yields of protopanaxadiol from the engineered peroxisome strains were ca 78% higher than those of the parent strain, which strongly supports the rationale for harnessing the storage capacity of the peroxisome membrane to accommodate the biosynthesized compounds. Consequently, this study presents in-depth knowledge on peroxisome biogenesis engineering in S.cerevisiae and could serve as basic information for improvement in ginsenosides production and as a potential platform to be utilized for other isoprenoids.
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Affiliation(s)
- Bo Hyun Choi
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Hyun Joon Kang
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea;
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
- Correspondence: ; Tel.: +82-31-219-2461
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Berguson HP, Caulfield LW, Price MS. Influence of Pathogen Carbon Metabolism on Interactions With Host Immunity. Front Cell Infect Microbiol 2022; 12:861405. [PMID: 35372116 PMCID: PMC8968422 DOI: 10.3389/fcimb.2022.861405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/24/2022] [Indexed: 11/22/2022] Open
Abstract
Cryptococcus neoformans is a ubiquitous opportunistic fungal pathogen typically causing disease in immunocompromised individuals and is globally responsible for about 15% of AIDS-related deaths annually. C. neoformans first causes pulmonary infection in the host and then disseminates to the brain, causing meningoencephalitis. The yeast must obtain and metabolize carbon within the host in order to survive in the central nervous system and cause disease. Communication between pathogen and host involves recognition of multiple carbon-containing compounds on the yeast surface: polysaccharide capsule, fungal cell wall, and glycosylated proteins comprising the major immune modulators. The structure and function of polysaccharide capsule has been studied for the past 70 years, emphasizing its role in virulence. While protected by the capsule, fungal cell wall has likewise been a focus of study for several decades for its role in cell integrity and host recognition. Associated with both of these major structures are glycosylated proteins, which exhibit known immunomodulatory effects. While many studies have investigated the role of carbon metabolism on virulence and survival within the host, the precise mechanism(s) affecting host-pathogen communication remain ill-defined. This review summarizes the current knowledge on mutants in carbon metabolism and their effect on the host immune response that leads to changes in pathogen recognition and virulence. Understanding these critical interactions will provide fresh perspectives on potential treatments and the natural history of cryptococcal disease.
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Affiliation(s)
- Hannah P. Berguson
- Department of Anatomical Sciences, Liberty University College of Osteopathic Medicine, Lynchburg, VA, United States
| | - Lauren W. Caulfield
- Department of Biology and Chemistry, Liberty University, Lynchburg, VA, United States
| | - Michael S. Price
- Department of Molecular and Cellular Sciences, Liberty University College of Osteopathic Medicine, Lynchburg, VA, United States
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
- *Correspondence: Michael S. Price,
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Mycobacterium tuberculosis Acetyltransferase Suppresses Oxidative Stress by Inducing Peroxisome Formation in Macrophages. Int J Mol Sci 2022; 23:ijms23052584. [PMID: 35269727 PMCID: PMC8909987 DOI: 10.3390/ijms23052584] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 02/01/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) inhibits host oxidative stress responses facilitating its survival in macrophages; however, the underlying molecular mechanisms are poorly understood. Here, we identified a Mtb acetyltransferase (Rv3034c) as a novel counter actor of macrophage oxidative stress responses by inducing peroxisome formation. An inducible Rv3034c deletion mutant of Mtb failed to induce peroxisome biogenesis, expression of the peroxisomal β-oxidation pathway intermediates (ACOX1, ACAA1, MFP2) in macrophages, resulting in reduced intracellular survival compared to the parental strain. This reduced virulence phenotype was rescued by repletion of Rv3034c. Peroxisome induction depended on the interaction between Rv3034c and the macrophage mannose receptor (MR). Interaction between Rv3034c and MR induced expression of the peroxisomal biogenesis proteins PEX5p, PEX13p, PEX14p, PEX11β, PEX19p, the peroxisomal membrane lipid transporter ABCD3, and catalase. Expression of PEX14p and ABCD3 was also enhanced in lungs from Mtb aerosol-infected mice. This is the first report that peroxisome-mediated control of ROS balance is essential for innate immune responses to Mtb but can be counteracted by the mycobacterial acetyltransferase Rv3034c. Thus, peroxisomes represent interesting targets for host-directed therapeutics to tuberculosis.
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Pex7 selectively imports PTS2 target proteins to peroxisomes and is required for anthracnose disease development in Colletotrichum scovillei. Fungal Genet Biol 2021; 157:103636. [PMID: 34742890 DOI: 10.1016/j.fgb.2021.103636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/22/2022]
Abstract
Pex7 is a shuttling receptor that imports matrix proteins with a type 2 peroxisomal targeting signal (PTS2) to peroxisomes. The Pex7-mediated PTS2 protein import contributes to crucial metabolic processes such as the fatty acid β-oxidation and glucose metabolism in a number of fungi, but cellular roles of Pex7 between the import of PTS2 target proteins and metabolic processes have not been fully understood. In this study, we investigated the functional roles of CsPex7, a homolog of the yeast Pex7, by targeted gene deletion in the pepper anthracnose fungus Colletotrichum scovillei. CsPex7 was required for carbon source utilization, scavenging of reactive oxygen species, conidial production, and disease development in C. scovillei. The expression of fluorescently tagged PTS2 signal of hexokinases and 3-ketoacyl-CoA thiolases showed that peroxisomal localization of the hexokinase CsGlk1 PTS2 is dependent on CsPex7, but those of the 3-ketoacyl-CoA thiolases are independent on CsPex7. In addition, GFP-tagged CsPex7 proteins were intensely localized to the peroxisomes on glucose-containing media, indicating a role of CsPex7 in glucose utilization. Collectively, these findings indicate that CsPex7 selectively recognizes specific PTS2 signal for import of PTS2-containing proteins to peroxisomes, thereby mediating peroxisomal targeting efficiency of PTS2-containing proteins in C. scovillei. On pepper fruits, the ΔCspex7 mutant exhibited significantly reduced virulence, in which excessive accumulation of hydrogen peroxide was observed in the pepper cells. We think the reduced virulence results from the abnormality in hydrogen peroxide metabolism of the ΔCspex7 mutant. Our findings provide insight into the cellular roles of CsPex7 in PTS2 protein import system.
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Infant T, Deb R, Ghose S, Nagotu S. Post-translational modifications of proteins associated with yeast peroxisome membrane: An essential mode of regulatory mechanism. Genes Cells 2021; 26:843-860. [PMID: 34472666 PMCID: PMC9291962 DOI: 10.1111/gtc.12892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022]
Abstract
Peroxisomes are single membrane‐bound organelles important for the optimum functioning of eukaryotic cells. Seminal discoveries in the field of peroxisomes are made using yeast as a model. Several proteins required for the biogenesis and function of peroxisomes are identified to date. As with proteins involved in other major cellular pathways, peroxisomal proteins are also subjected to regulatory post‐translational modifications. Identification, characterization and mapping of these modifications to specific amino acid residues on proteins are critical toward understanding their functional significance. Several studies have tried to identify post‐translational modifications of peroxisomal proteins and determine their impact on peroxisome structure and function. In this manuscript, we provide an overview of the various post‐translational modifications that govern the peroxisome dynamics in yeast.
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Affiliation(s)
- Terence Infant
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Rachayeeta Deb
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Suchetana Ghose
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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Lin NX, He RZ, Xu Y, Yu XW. Augmented peroxisomal ROS buffering capacity renders oxidative and thermal stress cross-tolerance in yeast. Microb Cell Fact 2021; 20:131. [PMID: 34247591 PMCID: PMC8273976 DOI: 10.1186/s12934-021-01623-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
Background Thermotolerant yeast has outstanding potential in industrial applications. Komagataella phaffii (Pichia pastoris) is a common cell factory for industrial production of heterologous proteins. Results Herein, we obtained a thermotolerant K. phaffii mutant G14 by mutagenesis and adaptive evolution. G14 exhibited oxidative and thermal stress cross-tolerance and high heterologous protein production efficiency. The reactive oxygen species (ROS) level and lipid peroxidation in G14 were reduced compared to the parent. Oxidative stress response (OSR) and heat shock response (HSR) are two major responses to thermal stress, but the activation of them was different in G14 and its parent. Compared with the parent, G14 acquired the better performance owing to its stronger OSR. Peroxisomes, as the main cellular site for cellular ROS generation and detoxification, had larger volume in G14 than the parent. And, the peroxisomal catalase activity and expression level in G14 was also higher than that of the parent. Excitingly, the gene knockdown of CAT encoding peroxisomal catalase by dCas9 severely reduced the oxidative and thermal stress cross-tolerance of G14. These results suggested that the augmented OSR was responsible for the oxidative and thermal stress cross-tolerance of G14. Nevertheless, OSR was not strong enough to protect the parent from thermal stress, even when HSR was initiated. Therefore, the parent cannot recover, thereby inducing the autophagy pathway and resulting in severe cell death. Conclusions Our findings indicate the importance of peroxisome and the significance of redox balance in thermotolerance of yeasts. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01623-1.
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Affiliation(s)
- Nai-Xin Lin
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, People's Republic of China
| | - Rui-Zhen He
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, People's Republic of China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, People's Republic of China
| | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, People's Republic of China.
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Wu PC, Chen YK, Yago JI, Chung KR. Peroxisomes Implicated in the Biosynthesis of Siderophores and Biotin, Cell Wall Integrity, Autophagy, and Response to Hydrogen Peroxide in the Citrus Pathogenic Fungus Alternaria alternata. Front Microbiol 2021; 12:645792. [PMID: 34262533 PMCID: PMC8273606 DOI: 10.3389/fmicb.2021.645792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Little is known about the roles of peroxisomes in the necrotrophic fungal plant pathogens. In the present study, a Pex6 gene encoding an ATPase-associated protein was characterized by analysis of functional mutations in the tangerine pathotype of Alternaria alternata, which produces a host-selective toxin. Peroxisomes were observed in fungal cells by expressing a mCherry fluorescent protein tagging with conserved tripeptides serine-lysing-leucine and transmission electron microscopy. The results indicated that Pex6 plays no roles in peroxisomal biogenesis but impacts protein import into peroxisomes. The number of peroxisomes was affected by nutritional conditions and H2O2, and their degradation was mediated by an autophagy-related machinery termed pexophagy. Pex6 was shown to be required for the formation of Woronin bodies, the biosynthesis of biotin, siderophores, and toxin, the uptake and accumulation of H2O2, growth, and virulence, as well as the Slt2 MAP kinase-mediated maintenance of cell wall integrity. Adding biotin, oleate, and iron in combination fully restored the growth of the pex6-deficient mutant (Δpex6), but failed to restore Δpex6 virulence to citrus. Adding purified toxin could only partially restore Δpex6 virulence even in the presence of biotin, oleate, and iron. Sensitivity assays revealed that Pex6 plays no roles in resistance to H2O2 and superoxide, but plays a negative role in resistance to 2-chloro-5-hydroxypyridine (a hydroxyl radical-generating compound), eosin Y and rose Bengal (singlet oxygen-generating compounds), and 2,3,5-triiodobenzoic acid (an auxin transport inhibitor). The diverse functions of Pex6 underscore the importance of peroxisomes in physiology, pathogenesis, and development in A. alternata.
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Affiliation(s)
- Pei-Ching Wu
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Kun Chen
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Jonar I Yago
- Plant Science Department, College of Agriculture, Nueva Vizcaya State University, Bayombong, Philippines
| | - Kuang-Ren Chung
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
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Kurylenko O, Ruchala J, Kruk B, Vasylyshyn R, Szczepaniak J, Dmytruk K, Sibirny A. The role of Mig1, Mig2, Tup1 and Hap4 transcription factors in regulation of xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha. FEMS Yeast Res 2021; 21:6275188. [PMID: 33983391 DOI: 10.1093/femsyr/foab029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 05/07/2021] [Indexed: 01/20/2023] Open
Abstract
Glucose is a preferred carbon source for most living organisms. The metabolism and regulation of glucose utilization are well studied mostly for Saccharomyces cerevisiae. Xylose is the main pentose sugar released from the lignocellulosic biomass, which has a high potential as a renewable feedstock for bioethanol production. The thermotolerant yeast Ogataea (Hansenula) polymorpha, in contrast to S. cerevisiae, is able to metabolize and ferment not only glucose but also xylose. However, in non-conventional yeasts, the regulation of glucose and xylose metabolism remains poorly understood. In this study, we characterize the role of transcriptional factors Mig1, Mig2, Tup1 and Hap4 in the natural xylose-fermenting yeast O. polymorpha. The deletion of MIG1 had no significant influence on ethanol production either from xylose or glucose, however the deletion of both MIG1 and MIG2 reduced the amount of ethanol produced from these sugars. The deletion of HAP4-A and TUP1 genes resulted in increased ethanol production from xylose. Inversely, the overexpression of HAP4-A and TUP1 genes reduced ethanol production during xylose alcoholic fermentation. Thus, HAP4-A and TUP1 are involved in repression of xylose metabolism and fermentation in yeast O. polymorpha and their deletion could be a viable strategy to improve ethanol production from this pentose.
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Affiliation(s)
- Olena Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Justyna Ruchala
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine.,Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Barbara Kruk
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Roksolana Vasylyshyn
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Justyna Szczepaniak
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Kostyantyn Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine.,Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
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Kulagina N, Besseau S, Papon N, Courdavault V. Peroxisomes: A New Hub for Metabolic Engineering in Yeast. Front Bioeng Biotechnol 2021; 9:659431. [PMID: 33898407 PMCID: PMC8058402 DOI: 10.3389/fbioe.2021.659431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/01/2021] [Indexed: 01/09/2023] Open
Affiliation(s)
- Natalja Kulagina
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Sébastien Besseau
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Nicolas Papon
- Université d'Angers, EA3142 "Groupe d'Etude des Interactions Hôte-Pathogène", Angers, France
| | - Vincent Courdavault
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
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Yocum HC, Pham A, Da Silva NA. Successful Enzyme Colocalization Strategies in Yeast for Increased Synthesis of Non-native Products. Front Bioeng Biotechnol 2021; 9:606795. [PMID: 33634084 PMCID: PMC7901933 DOI: 10.3389/fbioe.2021.606795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Yeast cell factories, particularly Saccharomyces cerevisiae, have proven valuable for the synthesis of non-native compounds, ranging from commodity chemicals to complex natural products. One significant challenge has been ensuring sufficient carbon flux to the desired product. Traditionally, this has been addressed by strategies involving "pushing" and "pulling" the carbon flux toward the products by overexpression while "blocking" competing pathways via downregulation or gene deletion. Colocalization of enzymes is an alternate and complementary metabolic engineering strategy to control flux and increase pathway efficiency toward the synthesis of non-native products. Spatially controlling the pathway enzymes of interest, and thus positioning them in close proximity, increases the likelihood of reaction along that pathway. This mini-review focuses on the recent developments and applications of colocalization strategies, including enzyme scaffolding, construction of synthetic organelles, and organelle targeting, in both S. cerevisiae and non-conventional yeast hosts. Challenges with these techniques and future directions will also be discussed.
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Affiliation(s)
- Hannah C Yocum
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Anhuy Pham
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Nancy A Da Silva
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
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Wang Z, Feng J, Jiang Y, Xu X, Xu L, Zhou Q, Huang B. MrPEX33 is involved in infection-related morphogenesis and pathogenicity of Metarhizium robertsii. Appl Microbiol Biotechnol 2021; 105:1079-1090. [PMID: 33443633 DOI: 10.1007/s00253-020-11071-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/03/2020] [Accepted: 12/17/2020] [Indexed: 11/30/2022]
Abstract
Peroxisomes, being indispensable organelles, play an important role in different biological processes in eukaryotes. PEX33, a filamentous fungus-specific peroxin of the docking machinery of peroxisomes, is involved in the virulence and development of other fungal pathogens. However, it is not clear whether PEX33 is necessary for the pathogenicity and development of an insect pathogenic fungus. In the present study, we report the presence of homologs of PEX33, namely MrPEX33 (MAA_05331), in the entomopathogenic fungus, Metarhizium robertsii. An M. robertsii transgenic strain expressing the fusion protein with MrPEX33-GFP and mCherry-PTS1 showed that MrPEX33 localizes to peroxisomes. The results also demonstrated that MrPEX33 is involved in the peroxisomal import pathway by peroxisomal targeting signals. Targeted gene deletion of MrPEX33 led to a significant decline in the asexual sporulation capacity, which was accompanied by downregulation of several conidiation-associated genes, such as wetA, abaA, and brlA. More importantly, our bioassay results showed that the virulence of ∆MrPEX33 mutants, against Galleria mellonella through cuticle infection, was greatly reduced. This was further accompanied by a significant drop in appressorium formation and cuticle penetration. Additionally, ∆MrPEX33 mutants showed a significant decrease in tolerance to cell wall integrity and oxidative stress. Taken together, our results suggest that MrPEX33 is involved in the cuticle infection-related morphogenesis and pathogenicity. KEY POINTS: • MrPEX33 is a specific peroxin of the docking machinery of peroxisomes. • MrPEX33 localizes to peroxisomes and is involved in the import of matrix proteins. • MrPEX33 is involved in the pathogenicity associated with cuticle infections.
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Affiliation(s)
- Zhangxun Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Jianyu Feng
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Yuanyuan Jiang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Xiuzhen Xu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Liuyi Xu
- Key Laboratory of State Forestry Administration on Prevention and Control of Pine Wood Nematode Disease, Anhui Academy of Forestry, Hefei, 230088, China
| | - Quan Zhou
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.
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Siedlik MJ, Yang Z, Kadam PS, Eberwine J, Issadore D. Micro- and Nano-Devices for Studying Subcellular Biology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005793. [PMID: 33345457 PMCID: PMC8258219 DOI: 10.1002/smll.202005793] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Indexed: 05/27/2023]
Abstract
Cells are complex machines whose behaviors arise from their internal collection of dynamically interacting organelles, supramolecular complexes, and cytoplasmic chemicals. The current understanding of the nature by which subcellular biology produces cell-level behaviors is limited by the technological hurdle of measuring the large number (>103 ) of small-sized (<1 μm) heterogeneous organelles and subcellular structures found within each cell. In this review, the emergence of a suite of micro- and nano-technologies for studying intracellular biology on the scale of organelles is described. Devices that use microfluidic and microelectronic components for 1) extracting and isolating subcellular structures from cells and lysate; 2) analyzing the physiology of individual organelles; and 3) recreating subcellular assembly and functions in vitro, are described. The authors envision that the continued development of single organelle technologies and analyses will serve as a foundation for organelle systems biology and will allow new insight into fundamental and clinically relevant biological questions.
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Affiliation(s)
- Michael J Siedlik
- Department of Bioengineering, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Zijian Yang
- Department of Mechanical Engineering and Applied Science, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Parnika S Kadam
- Systems Pharmacology and Translational Therapeutics, 38 John Morgan Building, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - James Eberwine
- Systems Pharmacology and Translational Therapeutics, 38 John Morgan Building, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - David Issadore
- Department of Bioengineering, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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38
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Transforming yeast peroxisomes into microfactories for the efficient production of high-value isoprenoids. Proc Natl Acad Sci U S A 2020; 117:31789-31799. [PMID: 33268495 DOI: 10.1073/pnas.2013968117] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Current approaches for the production of high-value compounds in microorganisms mostly use the cytosol as a general reaction vessel. However, competing pathways and metabolic cross-talk frequently prevent efficient synthesis of target compounds in the cytosol. Eukaryotic cells control the complexity of their metabolism by harnessing organelles to insulate biochemical pathways. Inspired by this concept, herein we transform yeast peroxisomes into microfactories for geranyl diphosphate-derived compounds, focusing on monoterpenoids, monoterpene indole alkaloids, and cannabinoids. We introduce a complete mevalonate pathway in the peroxisome to convert acetyl-CoA to several commercially important monoterpenes and achieve up to 125-fold increase over cytosolic production. Furthermore, peroxisomal production improves subsequent decoration by cytochrome P450s, supporting efficient conversion of (S)-(-)-limonene to the menthol precursor trans-isopiperitenol. We also establish synthesis of 8-hydroxygeraniol, the precursor of monoterpene indole alkaloids, and cannabigerolic acid, the cannabinoid precursor. Our findings establish peroxisomal engineering as an efficient strategy for the production of isoprenoids.
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39
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Chovanová K, Böhmer M, Poljovka A, Budiš J, Harichová J, Szemeš T, Zámocký M. Parallel Molecular Evolution of Catalases and Superoxide Dismutases-Focus on Thermophilic Fungal Genomes. Antioxidants (Basel) 2020; 9:antiox9111047. [PMID: 33120873 PMCID: PMC7712995 DOI: 10.3390/antiox9111047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022] Open
Abstract
Catalases (CAT) and superoxide dismutases (SOD) represent two main groups of enzymatic antioxidants that are present in almost all aerobic organisms and even in certain anaerobes. They are closely interconnected in the catabolism of reactive oxygen species because one product of SOD reaction (hydrogen peroxide) is the main substrate of CAT reaction finally leading to harmless products (i.e., molecular oxygen and water). It is therefore interesting to compare the molecular evolution of corresponding gene families. We have used a phylogenomic approach to elucidate the evolutionary relationships among these two main enzymatic antioxidants with a focus on the genomes of thermophilic fungi. Distinct gene families coding for CuZnSODs, FeMnSODs, and heme catalases are very abundant in thermophilic Ascomycota. Here, the presented results demonstrate that whereas superoxide dismutase genes remained rather constant during long-term evolution, the total count of heme catalase genes was reduced in thermophilic fungi in comparison with their mesophilic counterparts. We demonstrate here, for the newly discovered ascomycetous genes coding for thermophilic superoxide dismutases and catalases (originating from our sequencing project), the expression patterns of corresponding mRNA transcripts and further analyze translated protein sequences. Our results provide important implications for the physiology of reactive oxygen species metabolism in eukaryotic cells at elevated temperatures.
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Affiliation(s)
- Katarína Chovanová
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; (K.C.); (A.P.); (J.H.)
| | - Miroslav Böhmer
- Department of Molecular Biology, Faculty of Nat. Sciences, Science Park of Comenius University, Comenius University, Ilkovičova 8, SK-84104 Bratislava, Slovakia; (M.B.); (J.B.); (T.S.)
| | - Andrej Poljovka
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; (K.C.); (A.P.); (J.H.)
| | - Jaroslav Budiš
- Department of Molecular Biology, Faculty of Nat. Sciences, Science Park of Comenius University, Comenius University, Ilkovičova 8, SK-84104 Bratislava, Slovakia; (M.B.); (J.B.); (T.S.)
| | - Jana Harichová
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; (K.C.); (A.P.); (J.H.)
| | - Tomáš Szemeš
- Department of Molecular Biology, Faculty of Nat. Sciences, Science Park of Comenius University, Comenius University, Ilkovičova 8, SK-84104 Bratislava, Slovakia; (M.B.); (J.B.); (T.S.)
| | - Marcel Zámocký
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; (K.C.); (A.P.); (J.H.)
- Department of Chemistry, Institute of Biochemistry, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Correspondence:
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Dmytruk OV, Bulbotka NV, Sibirny AA. Degradation of Methanol Catabolism Enzymes of Formaldehyde Dehydrogenase and Formate Dehydrogenase in Methylotrophic Yeast Komagataella phaffii. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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González-Robles A, González-Lázaro M, Lagunes-Guillén AE, Omaña-Molina M, Lares-Jiménez LF, Lares-Villa F, Martínez-Palomo A. Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans. Genome Biol Evol 2020; 12:1734-1750. [PMID: 32602891 PMCID: PMC7549135 DOI: 10.1093/gbe/evaa129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Peroxisomes perform various metabolic processes that are primarily related to the elimination of reactive oxygen species and oxidative lipid metabolism. These organelles are present in all major eukaryotic lineages, nevertheless, information regarding the presence of peroxisomes in opportunistic parasitic protozoa is scarce and in many cases it is still unknown whether these organisms have peroxisomes at all. Here, we performed ultrastructural, cytochemical, and bioinformatic studies to investigate the presence of peroxisomes in three genera of free-living amoebae from two different taxonomic groups that are known to cause fatal infections in humans. By transmission electron microscopy, round structures with a granular content limited by a single membrane were observed in Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba polyphaga, Acanthamoeba royreba, Balamuthia mandrillaris (Amoebozoa), and Naegleria fowleri (Heterolobosea). Further confirmation for the presence of peroxisomes was obtained by treating trophozoites in situ with diaminobenzidine and hydrogen peroxide, which showed positive reaction products for the presence of catalase. We then performed comparative genomic analyses to identify predicted peroxin homologues in these organisms. Our results demonstrate that a complete set of peroxins-which are essential for peroxisome biogenesis, proliferation, and protein import-are present in all of these amoebae. Likewise, our in silico analyses allowed us to identify a complete set of peroxins in Naegleria lovaniensis and three novel peroxin homologues in Naegleria gruberi. Thus, our results indicate that peroxisomes are present in these three genera of free-living amoebae and that they have a similar peroxin complement despite belonging to different evolutionary lineages.
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Affiliation(s)
- Arturo González-Robles
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Mónica González-Lázaro
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Anel Edith Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Maritza Omaña-Molina
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlanepantla, Estado de México, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Adolfo Martínez-Palomo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
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Gerke J, Frauendorf H, Schneider D, Wintergoller M, Hofmeister T, Poehlein A, Zebec Z, Takano E, Scrutton NS, Braus GH. Production of the Fragrance Geraniol in Peroxisomes of a Product-Tolerant Baker's Yeast. Front Bioeng Biotechnol 2020; 8:582052. [PMID: 33102464 PMCID: PMC7546902 DOI: 10.3389/fbioe.2020.582052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/27/2020] [Indexed: 12/18/2022] Open
Abstract
Monoterpenoids, such as the plant metabolite geraniol, are of high industrial relevance since they are important fragrance materials for perfumes, cosmetics, and household products. Chemical synthesis or extraction from plant material for industry purposes are complex, environmentally harmful or expensive and depend on seasonal variations. Heterologous microbial production offers a cost-efficient and sustainable alternative but suffers from low metabolic flux of the precursors and toxicity of the monoterpenoid to the cells. In this study, we evaluated two approaches to counteract both issues by compartmentalizing the biosynthetic enzymes for geraniol to the peroxisomes of Saccharomyces cerevisiae as production sites and by improving the geraniol tolerance of the yeast cells. The combination of both approaches led to an 80% increase in the geraniol titers. In the future, the inclusion of product tolerance and peroxisomal compartmentalization into the general chassis engineering toolbox for monoterpenoids or other host-damaging, industrially relevant metabolites may lead to an efficient, low-cost, and eco-friendly microbial production for industrial purposes.
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Affiliation(s)
- Jennifer Gerke
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Holm Frauendorf
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Maxim Wintergoller
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | | | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ziga Zebec
- Molecular Enzymology, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Eriko Takano
- Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Molecular Enzymology, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom.,Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
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43
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Cao X, Yang S, Cao C, Zhou YJ. Harnessing sub-organelle metabolism for biosynthesis of isoprenoids in yeast. Synth Syst Biotechnol 2020; 5:179-186. [PMID: 32637671 PMCID: PMC7332497 DOI: 10.1016/j.synbio.2020.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 11/25/2022] Open
Abstract
Current yeast metabolic engineering in isoprenoids production mainly focuses on rewiring of cytosolic metabolic pathway. However, the precursors, cofactors and the enzymes are distributed in various sub-cellular compartments, which may hamper isoprenoid biosynthesis. On the other side, pathway compartmentalization provides several advantages for improving metabolic flux toward target products. We here summarize the recent advances on harnessing sub-organelle for isoprenoids biosynthesis in yeast, and analyze the knowledge about the localization of enzymes, cofactors and metabolites for guiding the rewiring of the sub-organelle metabolism. This review may provide some insights for constructing efficient yeast cell factories for production of isoprenoids and even other natural products.
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Affiliation(s)
- Xuan Cao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Shan Yang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chunyang Cao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China.,School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
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44
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Dzanaeva L, Kruk B, Ruchala J, Nielsen J, Sibirny A, Dmytruk K. The role of peroxisomes in xylose alcoholic fermentation in the engineered
Saccharomyces cerevisiae. Cell Biol Int 2020; 44:1606-1615. [DOI: 10.1002/cbin.11353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 02/02/2020] [Accepted: 03/19/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Ljubov Dzanaeva
- Department of Molecular Genetics and Biotechnology, Institute of Cell BiologyNAS of UkraineLviv Ukraine
| | - Barbara Kruk
- Department of Biotechnology and MicrobiologyUniversity of RzeszowRzeszow Poland
| | - Justyna Ruchala
- Department of Biotechnology and MicrobiologyUniversity of RzeszowRzeszow Poland
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg Sweden
| | - Andriy Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell BiologyNAS of UkraineLviv Ukraine
- Department of Biotechnology and MicrobiologyUniversity of RzeszowRzeszow Poland
| | - Kostyantyn Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell BiologyNAS of UkraineLviv Ukraine
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45
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Dmytruk O, Bulbotka N, Zazulya A, Semkiv M, Dmytruk K, Sibirny A. Fructose-1,6-bisphosphatase degradation in the methylotrophic yeast Komagataella phaffii occurs in autophagy pathway. Cell Biol Int 2020; 45:528-535. [PMID: 31903651 DOI: 10.1002/cbin.11304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/04/2020] [Indexed: 11/11/2022]
Abstract
Many enzymes of methanol metabolism of methylotrophic yeasts are located in peroxisomes whereas some of them have the cytosolic localization. After shift of methanol-grown cells of methylotrophic yeasts to glucose medium, a decrease in the activity of cytosolic (formaldehyde dehydrogenase, formate dehydrogenase, and fructose-1,6-bisphosphatase [FBP]) along with peroxisomal enzymes of methanol metabolism is observed. Mechanisms of inactivation of cytosolic enzymes remain unknown. To study the mechanism of FBP inactivation, the changes in its specific activity of the wild type strain GS200, the strain with the deletion of the GSS1 hexose sensor gene and strain defected in autophagy pathway SMD1163 of Komagataella phaffii with or without the addition of the MG132 (proteasome degradation inhibitor) were investigated after shift of methanol-grown cells in glucose medium. Western blot analysis showed that inactivation of FBP in GS200 occurred due to protein degradation whereas inactivation in the strains SMD1163 and gss1Δ was negligible in such conditions. The effect of the proteasome inhibitor MG132 on FBP inactivation was insignificant. To confirm FBP degradation pathway, the recombinant strains with GFP-labeled Fbp1 of K. phaffii and red fluorescent protein-labeled peroxisomes were constructed on the background of GS200 and SMD1163. The fluorescent microscopy analysis of the constructed strains was performed using the vacuolar membrane dye FM4-64. Microscopic data confirmed that Fbp1 degrades by autophagy pathway in K. phaffii. K. phaffii transformants, which express heterologous β-galactosidase under FLD promoter, have been constructed.
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Affiliation(s)
- Olena Dmytruk
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Nina Bulbotka
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Anastasya Zazulya
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Marta Semkiv
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Kostyantyn Dmytruk
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Andriy Sibirny
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine.,Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
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46
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Ortega-Martínez M, Gutiérrez-Dávila V, Niderhauser-García A, Salazar-Aranda R, Solís-Soto JM, Montes-de-Oca-Luna R, Jaramillo-Rangel G. Peroxisomicine A1, a potential antineoplastic agent, causes micropexophagy in addition to macropexophagy. Cell Biol Int 2020; 44:918-923. [PMID: 31814220 DOI: 10.1002/cbin.11280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022]
Abstract
Peroxisomicine A1 (PA1) is a potential antineoplastic agent with high and selective toxicity toward peroxisomes of tumor cells. Pexophagy is a selective autophagy process that degrades damaged peroxisomes; this process has been studied mainly in methylotrophic yeasts. There are two main modes of pexophagy in yeast: macropexophagy and micropexophagy. Previous studies showed that peroxisomes damaged by a prolonged exposition to PA1 are eliminated by macropexophagy. In this work, Candida boidinii was grown in methanol-containing media, and PA1 was added to the cultures at 2 µg/mL after they reached the mid-exponential growth phase. Samples were taken at 5, 10, 15, 20, and 25 min after the addition of PA1 and processed for ultrastructural analysis. Typical morphological characteristics of micropexophagy were observed: the direct engulfment of peroxisomes by the vacuolar membrane and the presence of the micropexophagic membrane apparatus (MIPA), which mediates the fusion between the opposing tips of the vacuole to complete sequestration of peroxisomes from the cytosol. In conclusion, here we report that, in addition to macropexophagy, peroxisomes damaged by PA1 can be eliminated by micropexophagy. This information is useful to deepen the knowledge of the mechanism of action of PA1 and of that of pexophagy per se.
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Affiliation(s)
- Marta Ortega-Martínez
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Vanessa Gutiérrez-Dávila
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Alberto Niderhauser-García
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Ricardo Salazar-Aranda
- Department of Analytical Chemistry, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Juan M Solís-Soto
- Department of Physiology, School of Dentistry, Autonomous University of Nuevo Leon, Dr. Eduardo Aguirre P. y Silao, Monterrey, Nuevo León, 64460, Mexico
| | - Roberto Montes-de-Oca-Luna
- Department of Histology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Gilberto Jaramillo-Rangel
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
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47
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Germain K, Kim PK. Pexophagy: A Model for Selective Autophagy. Int J Mol Sci 2020; 21:ijms21020578. [PMID: 31963200 PMCID: PMC7013971 DOI: 10.3390/ijms21020578] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 01/03/2023] Open
Abstract
The removal of damaged or superfluous organelles from the cytosol by selective autophagy is required to maintain organelle function, quality control and overall cellular homeostasis. Precisely how substrate selectivity is achieved, and how individual substrates are degraded during selective autophagy in response to both extracellular and intracellular cues is not well understood. The aim of this review is to highlight pexophagy, the autophagic degradation of peroxisomes, as a model for selective autophagy. Peroxisomes are dynamic organelles whose abundance is rapidly modulated in response to metabolic demands. Peroxisomes are routinely turned over by pexophagy for organelle quality control yet can also be degraded by pexophagy in response to external stimuli such as amino acid starvation or hypoxia. This review discusses the molecular machinery and regulatory mechanisms governing substrate selectivity during both quality-control pexophagy and pexophagy in response to external stimuli, in yeast and mammalian systems. We draw lessons from pexophagy to infer how the cell may coordinate the degradation of individual substrates by selective autophagy across different cellular cues.
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Affiliation(s)
- Kyla Germain
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peter K. Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Correspondence: ; Tel.: +1-416-813-5983
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Kong X, Zhang H, Wang X, van der Lee T, Waalwijk C, van Diepeningen A, Brankovics B, Xu J, Xu J, Chen W, Feng J. FgPex3, a Peroxisome Biogenesis Factor, Is Involved in Regulating Vegetative Growth, Conidiation, Sexual Development, and Virulence in Fusarium graminearum. Front Microbiol 2019; 10:2088. [PMID: 31616386 PMCID: PMC6764106 DOI: 10.3389/fmicb.2019.02088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/23/2019] [Indexed: 12/28/2022] Open
Abstract
Peroxisomes are involved in a wide range of important cellular functions. Here, the role of the peroxisomal membrane protein PEX3 in the plant-pathogen and mycotoxin producer Fusarium graminearum was studied using knock-out and complemented strains. To fluorescently label peroxisomes’ punctate structures, GFP and RFP fusions with the PTS1 and PTS2 localization signal were transformed into the wild type PH-1 and ΔFgPex3 knock-out strains. The GFP and RFP transformants in the ΔFgPex3 background showed a diffuse fluorescence pattern across the cytoplasm suggesting the absence of mature peroxisomes. The ΔFgPex3 strain showed a minor, non-significant reduction in growth on various sugar carbon sources. In contrast, deletion of FgPex3 affected fatty acid β-oxidation in F. graminearum and significantly reduced the utilization of fatty acids. Furthermore, the ΔFgPex3 mutant was sensitive to osmotic stressors as well as to cell wall-damaging agents. Reactive oxygen species (ROS) levels in the mutant had increased significantly, which may be linked to the reduced longevity of cultured strains. The mutant also showed reduced production of conidiospores, while sexual reproduction was completely impaired. The pathogenicity of ΔFgPex3, especially during the process of systemic infection, was strongly reduced on both tomato and on wheat, while to production of deoxynivalenol (DON), an important factor for virulence, appeared to be unaffected.
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Affiliation(s)
- Xiangjiu Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xiaoliang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Theo van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Cees Waalwijk
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Anne van Diepeningen
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Balazs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Jin Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Jingsheng Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
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Scheckhuber CQ. Characterization of survival and stress resistance in S. cerevisiae mutants affected in peroxisome inheritance and proliferation, Δinp1 and Δpex11. Folia Microbiol (Praha) 2019; 65:423-429. [PMID: 31273644 DOI: 10.1007/s12223-019-00724-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
Abstract
Baker's yeast is a valuable model system for the study of biological aging as it can be utilized for the measurement of replicative and chronological life spans in response to interventions. Whereas replicative aging in Saccharomyces cerevisiae mirrors dividing mammalian cells, chronological aging is seen in non-dividing cells. Aging is strongly influenced by the cellular organelles, especially by mitochondria which house essential functions like oxidative phosphorylation. Additionally, peroxisomes were shown to modulate the aging process, mainly by their turnover of reactive oxygen species. There is a fundamental interest in understanding how mitochondria and peroxisomes contribute to cellular aging. This work analyzes chronological aging in yeast mutants that are affected in peroxisomal proliferation and inheritance. Deletion of INP1 (retention of peroxisomes in the mother cell) or PEX11 (division of peroxisomes) leads to clearly reduced life spans compared to the wild-type control under conditions which depend on peroxisomal metabolism. Δinp1 cells are long-lived in contrast to the wild type and Δpex11 when assayed under conditions that not necessitate peroxisome function. Neither treatment affects the index of respiratory capacity, indicating fully functional mitochondria. Evaluation of stress resistances reveals that Δinp1 has significantly higher resistance to the apoptosis elicitor acetic acid. Old Δpex11 cells from an oleate culture are more susceptible to hydrogen peroxide treatment compared to Δinp1 and the wild type. Finally, aged cells are hyper-sensitive to heat shock treatment in contrast to young cells.
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Affiliation(s)
- Christian Q Scheckhuber
- Centro de Investigación y de Estudios Avanzados del IPN - Unidad Monterrey, Parque de Investigación e Innovación Tecnológica, CP 66600, Apodaca, Nuevo León, Mexico.
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50
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Teixeira LDL, Dörr F, Dias CT, Pinto E, Lajolo FM, Villas-Bôas SG, Hassimotto NM. Human urine metabolomic signature after ingestion of polyphenol-rich juice of purple grumixama (Eugenia brasiliensis Lam.). Food Res Int 2019; 120:544-552. [DOI: 10.1016/j.foodres.2018.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/26/2018] [Accepted: 11/02/2018] [Indexed: 02/07/2023]
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