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Kua GKB, Nguyen GKT, Li Z. Enzymatic Strategies for the Biosynthesis of N-Acyl Amino Acid Amides. Chembiochem 2024; 25:e202300672. [PMID: 38051126 DOI: 10.1002/cbic.202300672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
Amide bond-containing biomolecules are functionally significant and useful compounds with diverse applications. For example, N-acyl amino acids (NAAAs) are an important class of lipoamino acid amides with extensive use in food, cosmetic and pharmaceutical industries. Their conventional chemical synthesis involves the use of toxic chlorinating agents for carboxylic acid activation. Enzyme-catalyzed biotransformation for the green synthesis of these amides is therefore highly desirable. Here, we review a range of enzymes suitable for the synthesis of NAAA amides and their strategies adopted in carboxylic acid activation. Generally, ATP-dependent enzymes for NAAA biosynthesis are acyl-adenylating enzymes that couple the hydrolysis of phosphoanhydride bond in ATP with the formation of an acyl-adenylate intermediate. In contrast, ATP-independent enzymes involve hydrolases such as lipases or aminoacylases, which rely on the transient activation of the carboxylic acid. This occurs either through an acyl-enzyme intermediate or by favorable interactions with surrounding residues to anchor the acyl donor in a suitable orientation for the incoming amine nucleophile. Recently, the development of an alternative pathway involving ester-amide interconversion has unraveled another possible strategy for amide formation through esterification-aminolysis cascade reactions, potentially expanding the substrate scope for enzymes to catalyze the synthesis of a diverse range of NAAA amides.
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Affiliation(s)
- Glen Kai Bin Kua
- Wilmar International Limited, 28 Biopolis Road, Singapore, 138568
| | | | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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2
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Godana EA, Guo S, Yang Q, Zhang X, Zhao L, Wang K, Ackah M, Zhang H. A transcriptome profile of Wickerhamomyces anomalus incubated with chitosan revealed dynamic changes in gene expression and metabolic pathways. Int J Biol Macromol 2024; 258:128850. [PMID: 38114004 DOI: 10.1016/j.ijbiomac.2023.128850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
Previous studies have shown that Wickerhamomyces anomalus can control postharvest diseases of fruits and incubation of the yeast with chitosan can improve its efficiency. In this study, transcriptome study was conducted to determine molecular mechanisms involved in the yeast-chitosan interaction. The bioinformatics analysis of the RNA-seq data confirmed that incubating W. anomalus with 1 % chitosan for 24 h significantly altered the expression of differential genes involved in yeast metabolic and cellular activities. Genes involved in ethyl acetate production, reactive oxygen species regulation, cell wall reinforcement, stress resistance, and signalling were all significantly up-regulated. Pathways which have significant role in the yeast growth and reproduction, energy production, cellular homeostasis, signal transduction, catalytic, and antioxidant activities were significantly enriched. In general, incubation of the yeast with chitosan genes metabolic pathways which are important for the yeast survival, adaptation, and reproduction. Molecular studies are important in providing fundamental theoretical foundation for the practical application of antagonistic yeasts for future uses. As a result, this research will be an input for use of the antagonistic yeast as microbial or biochemical pesticides instead of synthetic chemicals which have both health and environmental effects.
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Affiliation(s)
- Esa Abiso Godana
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Shuaiying Guo
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Lina Zhao
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Michael Ackah
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
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Chae SY, Kim Y, Park CW. Oxidative Stress Induced by Lipotoxicity and Renal Hypoxia in Diabetic Kidney Disease and Possible Therapeutic Interventions: Targeting the Lipid Metabolism and Hypoxia. Antioxidants (Basel) 2023; 12:2083. [PMID: 38136203 PMCID: PMC10740440 DOI: 10.3390/antiox12122083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Oxidative stress, a hallmark pathophysiological feature in diabetic kidney disease (DKD), arises from the intricate interplay between pro-oxidants and anti-oxidants. While hyperglycemia has been well established as a key contributor, lipotoxicity emerges as a significant instigator of oxidative stress. Lipotoxicity encompasses the accumulation of lipid intermediates, culminating in cellular dysfunction and cell death. However, the mechanisms underlying lipotoxic kidney injury in DKD still require further investigation. The key role of cell metabolism in the maintenance of cell viability and integrity in the kidney is of paramount importance to maintain proper renal function. Recently, dysfunction in energy metabolism, resulting from an imbalance in oxygen levels in the diabetic condition, may be the primary pathophysiologic pathway driving DKD. Therefore, we aim to shed light on the pivotal role of oxidative stress related to lipotoxicity and renal hypoxia in the initiation and progression of DKD. Multifaceted mechanisms underlying lipotoxicity, including oxidative stress with mitochondrial dysfunction, endoplasmic reticulum stress activated by the unfolded protein response pathway, pro-inflammation, and impaired autophagy, are delineated here. Also, we explore potential therapeutic interventions for DKD, targeting lipotoxicity- and hypoxia-induced oxidative stress. These interventions focus on ameliorating the molecular pathways of lipid accumulation within the kidney and enhancing renal metabolism in the face of lipid overload or ameliorating subsequent oxidative stress. This review highlights the significance of lipotoxicity, renal hypoxia-induced oxidative stress, and its potential for therapeutic intervention in DKD.
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Affiliation(s)
- Seung Yun Chae
- Division of Nephrology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (S.Y.C.); (Y.K.)
| | - Yaeni Kim
- Division of Nephrology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (S.Y.C.); (Y.K.)
| | - Cheol Whee Park
- Division of Nephrology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (S.Y.C.); (Y.K.)
- Institute for Aging and Metabolic Disease, Seoul St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea
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4
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Cong H, Li C, Wang Y, Zhang Y, Ma D, Li L, Jiang J. The Mechanism of Transcription Factor Swi6 in Regulating Growth and Pathogenicity of Ceratocystis fimbriata: Insights from Non-Targeted Metabolomics. Microorganisms 2023; 11:2666. [PMID: 38004677 PMCID: PMC10673406 DOI: 10.3390/microorganisms11112666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Ceratocystis fimbriata (C. fimbriata) is a notorious pathogenic fungus that causes sweet potato black rot disease. The APSES transcription factor Swi6 in fungi is located downstream of the cell wall integrity (CWI)-mitogen-activated protein kinase (MAPK) signaling pathway and has been identified to be involved in cell wall integrity and virulence in several filamentous pathogenic fungi. However, the specific mechanisms by which Swi6 regulates the growth and pathogenicity of plant pathogenic fungi remain elusive. In this study, the SWI6 deletion mutants and complemented strains of C. fimbriata were generated. Deletion of Swi6 in C. fimbriata resulted in aberrant growth patterns. Pathogenicity assays on sweet potato storage roots revealed a significant decrease in virulence in the mutant. Non-targeted metabolomic analysis using LC-MS identified a total of 692 potential differentially accumulated metabolites (PDAMs) in the ∆Cfswi6 mutant compared to the wild type, and the results of KEGG enrichment analysis demonstrated significant enrichment of PDAMs within various metabolic pathways, including amino acid metabolism, lipid metabolism, nucleotide metabolism, GPI-anchored protein synthesis, and ABC transporter metabolism. These metabolic pathways were believed to play a crucial role in mediating the growth and pathogenicity of C. fimbriata through the regulation of CWI. Firstly, the deletion of the SWI6 gene led to abnormal amino acid and lipid metabolism, potentially exacerbating energy storage imbalance. Secondly, significant enrichment of metabolites related to GPI-anchored protein biosynthesis implied compromised cell wall integrity. Lastly, disruption of ABC transport protein metabolism may hinder intracellular transmembrane transport. Importantly, this study represents the first investigation into the potential regulatory mechanisms of SWI6 in plant filamentous pathogenic fungi from a metabolic perspective. The findings provide novel insights into the role of SWI6 in the growth and virulence of C. fimbriata, highlighting its potential as a target for controlling this pathogen.
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Affiliation(s)
- Hao Cong
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Changgen Li
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Yiming Wang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Yongjing Zhang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Daifu Ma
- Chinese Academy of Agricultural Sciences Sweet Potato Research Institute, Xuzhou 221131, China;
| | - Lianwei Li
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
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Kerkaert JD, Huberman LB. Regulation of nutrient utilization in filamentous fungi. Appl Microbiol Biotechnol 2023; 107:5873-5898. [PMID: 37540250 PMCID: PMC10983054 DOI: 10.1007/s00253-023-12680-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
Organisms must accurately sense and respond to nutrients to survive. In filamentous fungi, accurate nutrient sensing is important in the establishment of fungal colonies and in continued, rapid growth for the exploitation of environmental resources. To ensure efficient nutrient utilization, fungi have evolved a combination of activating and repressing genetic networks to tightly regulate metabolic pathways and distinguish between preferred nutrients, which require minimal energy and resources to utilize, and nonpreferred nutrients, which have more energy-intensive catabolic requirements. Genes necessary for the utilization of nonpreferred carbon sources are activated by transcription factors that respond to the presence of the specific nutrient and repressed by transcription factors that respond to the presence of preferred carbohydrates. Utilization of nonpreferred nitrogen sources generally requires two transcription factors. Pathway-specific transcription factors respond to the presence of a specific nonpreferred nitrogen source, while another transcription factor activates genes in the absence of preferred nitrogen sources. In this review, we discuss the roles of transcription factors and upstream regulatory genes that respond to preferred and nonpreferred carbon and nitrogen sources and their roles in regulating carbon and nitrogen catabolism. KEY POINTS: • Interplay of activating and repressing transcriptional networks regulates catabolism. • Nutrient-specific activating transcriptional pathways provide metabolic specificity. • Repressing regulatory systems differentiate nutrients in mixed nutrient environments.
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Affiliation(s)
- Joshua D Kerkaert
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Lori B Huberman
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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6
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Brands M, Dörmann P. Two AMP-Binding Domain Proteins from Rhizophagus irregularis Involved in Import of Exogenous Fatty Acids. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:464-476. [PMID: 35285673 DOI: 10.1094/mpmi-01-22-0026-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) colonize roots, where they provide nutrients in exchange for sugars and lipids. Because AMF lack genes for cytosolic fatty acid de novo synthase (FAS), they depend on host-derived fatty acids. AMF colonization is accompanied by expression of specific lipid genes and synthesis of sn-2 monoacylglycerols (MAGs). It is unknown how host-derived fatty acids are taken up by AMF. We describe the characterization of two AMP-binding domain protein genes from Rhizophagus irregularis, RiFAT1 and RiFAT2, with sequence similarity to Saccharomyces cerevisiae fatty acid transporter 1 (FAT1). Uptake of 13C-myristic acid (14:0) and, to a lesser extent, 13C-palmitic acid (16:0) was enhanced after expression of RiFAT1 or RiFAT2 in S. cerevisiae Δfat1 cells. The uptake of 2H-labeled fatty acids from 2H-myristoylglycerol or 2H-palmitoylglycerol was also increased after RiFAT1 and RiFAT2 expression in Δfat, but intact 2H-MAGs were not detected. RiFAT1 and RiFAT2 expression was induced in colonized roots compared with extraradical mycelium. 13C-label in the AMF-specific palmitvaccenic acid (16:1Δ11) and eicosatrienoic acid (20:3) were detected in colonized roots only when 13C2-acetate was supplemented but not 13C-fatty acids, demonstrating that de novo synthesized, host-derived fatty acids are rapidly taken up by R. irregularis from the roots. The results show that RiFAT1 and RiFAT2 are involved in the uptake of myristic acid (14:0) and palmitic acid (16:0), while fatty acids from MAGs are only taken up after hydrolysis. Therefore, the two proteins might be involved in fatty acid import into the fungal arbuscules in colonized roots.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mathias Brands
- University of Bonn, Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
- University of Cologne, Botanical Institute, Cologne Biocenter, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - Peter Dörmann
- University of Bonn, Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
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Yoon H, Shaw JL, Haigis MC, Greka A. Lipid metabolism in sickness and in health: Emerging regulators of lipotoxicity. Mol Cell 2021; 81:3708-3730. [PMID: 34547235 PMCID: PMC8620413 DOI: 10.1016/j.molcel.2021.08.027] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022]
Abstract
Lipids play crucial roles in signal transduction, contribute to the structural integrity of cellular membranes, and regulate energy metabolism. Questions remain as to which lipid species maintain metabolic homeostasis and which disrupt essential cellular functions, leading to metabolic disorders. Here, we discuss recent advances in understanding lipid metabolism with a focus on catabolism, synthesis, and signaling. Technical advances, including functional genomics, metabolomics, lipidomics, lipid-protein interaction maps, and advances in mass spectrometry, have uncovered new ways to prioritize molecular mechanisms mediating lipid function. By reviewing what is known about the distinct effects of specific lipid species in physiological pathways, we provide a framework for understanding newly identified targets regulating lipid homeostasis with implications for ameliorating metabolic diseases.
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Affiliation(s)
- Haejin Yoon
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Jillian L Shaw
- Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marcia C Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA.
| | - Anna Greka
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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8
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Tong X, Wang F, Zhang H, Bai J, Dong Q, Yue P, Jiang X, Li X, Wang L, Guo J. iTRAQ-based comparative proteome analyses of different growth stages revealing the regulatory role of reactive oxygen species in the fruiting body development of Ophiocordyceps sinensis. PeerJ 2021; 9:e10940. [PMID: 33717691 PMCID: PMC7936569 DOI: 10.7717/peerj.10940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/22/2021] [Indexed: 11/30/2022] Open
Abstract
In this study, using an isobaric tags for relative and absolute quantitation (iTRAQ ) approach coupled with LC-MS / MS and bioinformatics, the proteomes were analyzed for the crucial three stages covering the fruiting body development of Ophiocordyceps sinensis, including sclerotium (ST), primordium (PR) and mature fruiting body (MF), with a focus on fruiting body development-related proteins and the potential mechanisms of the development. A total of 1,875 proteins were identified. Principal Component Analysis (PCA) demonstrated that the protein patterns between PR and MF were more similar than ST. Differentially accumulated proteins (DAPs) analysis showed that there were 510, 173 and 514 DAPs in the comparisons of ST vs. PR, PR vs. MF and ST vs. MF, respectively. A total of 62 shared DAPs were identified and primarily enriched in proteins related to ‘carbon transport and mechanism’, ‘the response to oxidative stress’, ‘antioxidative activity’ and ‘translation’. KEGG and GO databases showed that the DAPs were enriched in terms of ‘primary metabolisms (amino acid/fatty acid/energy metabolism)’, ‘the response to oxidative stress’ and ‘peroxidase’. Furthermore, 34 DAPs involved in reactive oxygen species (ROS) metabolism were identified and clustered across the three stages using hierarchical clustering implemented in hCluster R package . It was suggested that their roles and the underlying mechanisms may be stage-specific. ROS may play a role in fungal pathogenicity in ST, the fruit-body initiation in PR, sexual reproduction and highland adaptation in MF. Crucial ROS-related proteins were identified, such as superoxide dismutase (SOD, T5A6F1), Nor-1 (T5AFX3), electron transport protein (T5AHD1), histidine phosphotransferase (HPt, T5A9Z5) and Glutathione peroxidase (T5A9V1). Besides, the accumulation of ROS at the three stages were assayed using 2,7-dichlorofuorescin diacetate (DCFH-DA) stanning. A much stronger ROS accumulation was detected at the stage MF, compared to the stages of PR and ST. Sections of ST and fruit-body part of MF were stained by DCFH-DA and observed under the fluorescencemicroscope, showing ROS was distributed within the conidiospore and ascus. Besides, SOD activity increased across the three stages, while CAT activity has a strong increasement in MF compared to the stages of ST and PR. It was suggested that ROS may act in gradient-dependent manner to regulate the fruiting body development. The coding region sequences of six DAPs were analyzed at mRNA level by quantitative real-time PCR (qRT-PCR). The results support the result of DAPs analysis and the proteome sequencing data. Our findings offer the perspective of proteome to understand the biology of fruiting body development and highland adaptation in O. sinensis, which would inform the big industry of this valuable fungus.
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Affiliation(s)
- Xinxin Tong
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Fang Wang
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Han Zhang
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jing Bai
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qiang Dong
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Pan Yue
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xinyi Jiang
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xinrui Li
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Li Wang
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jinlin Guo
- Key Laboratory of Standardization of Chinese Medicine, Ministry of Education; Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province-Key Laboratory Breeding Base founded by Sichuan Province, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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9
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Tomczyk MM, Dolinsky VW. The Cardiac Lipidome in Models of Cardiovascular Disease. Metabolites 2020; 10:E254. [PMID: 32560541 PMCID: PMC7344916 DOI: 10.3390/metabo10060254] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 12/19/2022] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide. There are numerous factors involved in the development of CVD. Among these, lipids have an important role in maintaining the myocardial cell structure as well as cardiac function. Fatty acids (FA) are utilized for energy, but also contribute to the pathogenesis of CVD and heart failure. Advances in mass spectrometry methods have enabled the comprehensive analysis of a plethora of lipid species from a single sample comprised of a heterogeneous population of lipid molecules. Determining cardiac lipid alterations in different models of CVD identifies novel biomarkers as well as reveals molecular mechanisms that underlie disease development and progression. This information could inform the development of novel therapeutics in the treatment of CVD. Herein, we provide a review of recent studies of cardiac lipid profiles in myocardial infarction, obesity, and diabetic and dilated cardiomyopathy models of CVD by methods of mass spectrometry analysis.
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Affiliation(s)
- Mateusz M. Tomczyk
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme of the Children’s Hospital Research Institute of Manitoba, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada;
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada
- Rady Faculty of Health Science, College of Medicine, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Vernon W. Dolinsky
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme of the Children’s Hospital Research Institute of Manitoba, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada;
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada
- Rady Faculty of Health Science, College of Medicine, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Steensels S, Ersoy BA. Fatty acid activation in thermogenic adipose tissue. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:79-90. [PMID: 29793055 DOI: 10.1016/j.bbalip.2018.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/10/2018] [Accepted: 05/17/2018] [Indexed: 02/07/2023]
Abstract
Channeling carbohydrates and fatty acids to thermogenic tissues, including brown and beige adipocytes, have garnered interest as an approach for the management of obesity-related metabolic disorders. Mitochondrial fatty acid oxidation (β-oxidation) is crucial for the maintenance of thermogenesis. Upon cellular fatty acid uptake or following lipolysis from triglycerides (TG), fatty acids are esterified to coenzyme A (CoA) to form active acyl-CoA molecules. This enzymatic reaction is essential for their utilization in β-oxidation and thermogenesis. The activation and deactivation of fatty acids are regulated by two sets of enzymes called acyl-CoA synthetases (ACS) and acyl-CoA thioesterases (ACOT), respectively. The expression levels of ACS and ACOT family members in thermogenic tissues will determine the substrate availability for β-oxidation, and consequently the thermogenic capacity. Although the role of the majority of ACS and ACOT family members in thermogenesis remains unclear, recent proceedings link the enzymatic activities of ACS and ACOT family members to metabolic disorders and thermogenesis. Elucidating the contributions of specific ACS and ACOT family members to trafficking of fatty acids towards thermogenesis may reveal novel targets for modulating thermogenic capacity and treating metabolic disorders.
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Affiliation(s)
- Sandra Steensels
- Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA
| | - Baran A Ersoy
- Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA.
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11
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Starr TL, Gonçalves AP, Meshgin N, Glass NL. The major cellulases CBH-1 and CBH-2 of Neurospora crassa rely on distinct ER cargo adaptors for efficient ER-exit. Mol Microbiol 2017; 107:229-248. [PMID: 29131484 DOI: 10.1111/mmi.13879] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2017] [Indexed: 12/17/2022]
Abstract
Filamentous fungi are native secretors of lignocellulolytic enzymes and are used as protein-producing factories in the industrial biotechnology sector. Despite the importance of these organisms in industry, relatively little is known about the filamentous fungal secretory pathway or how it might be manipulated for improved protein production. Here, we use Neurospora crassa as a model filamentous fungus to interrogate the requirements for trafficking of cellulase enzymes from the endoplasmic reticulum to the Golgi. We characterized the localization and interaction properties of the p24 and ERV-29 cargo adaptors, as well as their role in cellulase enzyme trafficking. We find that the two most abundantly secreted cellulases, CBH-1 and CBH-2, depend on distinct ER cargo adaptors for efficient exit from the ER. CBH-1 depends on the p24 proteins, whereas CBH-2 depends on the N. crassa homolog of yeast Erv29p. This study provides a first step in characterizing distinct trafficking pathways of lignocellulolytic enzymes in filamentous fungi.
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Affiliation(s)
- Trevor L Starr
- The Energy Biosciences Institute, The University of California, Berkeley, CA 94720, USA
| | - A Pedro Gonçalves
- The Energy Biosciences Institute, The University of California, Berkeley, CA 94720, USA.,Plant and Microbial Biology Department, The University of California, Berkeley, CA 94720, USA
| | - Neeka Meshgin
- The Energy Biosciences Institute, The University of California, Berkeley, CA 94720, USA
| | - N Louise Glass
- The Energy Biosciences Institute, The University of California, Berkeley, CA 94720, USA.,Plant and Microbial Biology Department, The University of California, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology Division, The Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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12
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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13
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Jia B, Song Y, Wu M, Lin B, Xiao K, Hu Z, Huang Y. Characterization of long-chain acyl-CoA synthetases which stimulate secretion of fatty acids in green algae Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:184. [PMID: 27588037 PMCID: PMC5007677 DOI: 10.1186/s13068-016-0598-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/19/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Microalgae biofuel has become the most promising renewable energy over the past few years. But limitations still exist because of its high cost. Although, efforts have been made in enhancement of lipid productivity, the major cost problem in harvesting and oil extraction is still intractable. Thus, the idea of fatty acids (FAs) secretion which can massively facilitate algae harvesting and oil extraction was investigated here. RESULTS The cDNAs of two long-chain acyl-CoA synthetases (LACSs) genes were cloned from Chlamydomonas reinhardtii and named as cracs1 and cracs2. They showed different substrate adaptation in the yeast complementation experiments. Cracs2 could utilize FAs C12:0, C14:0, C16:0, C18:0, C16:1 and C18:1, while crac1 could only utilize substrate C14:0, C16:1 and C18:1. Knockdown of cracs1 and cracs2 in C. reinhardtii resulted in accumulation of intracellular lipids. The total intracellular lipids contents of transgenic algae q-15 (knockdown of cracs1) and p-13 (knockdown of cracs2) were 45 and 55 %, respectively higher than that of cc849. Furthermore, FAs secretion was discovered in both transgenic algae. Secreted FAs can reach 8.19 and 9.66 mg/10(9) cells in q-15 and p-13, respectively. CONCLUSION These results demonstrated the possibility of FAs secretion by microalgae and may give a new strategy of low-cost oil extraction. According to our findings, we proposed that FAs secretion may also be achieved in other species besides Chlamydomonas reinhardtii by knocking-down cracs genes, which may promote the future industrial application of microalgae biofuels.
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Affiliation(s)
- Bin Jia
- Guangdong Engineering Research Centre for Marine Algal Biotechnology, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresouce and Eco-Enviromental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Microbial Engineering at the Institute of Biology, Industrial Enzyme Engineering Technology Research Center, Henan Academy of Sciences, Zhengzhou, 450008 People’s Republic of China
| | - Yanzi Song
- Guangdong Engineering Research Centre for Marine Algal Biotechnology, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresouce and Eco-Enviromental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Min Wu
- Guangdong Engineering Research Centre for Marine Algal Biotechnology, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresouce and Eco-Enviromental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Baicheng Lin
- Guangdong Engineering Research Centre for Marine Algal Biotechnology, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresouce and Eco-Enviromental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Kang Xiao
- Guangdong Engineering Research Centre for Marine Algal Biotechnology, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresouce and Eco-Enviromental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Engineering Research Centre for Marine Algal Biotechnology, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresouce and Eco-Enviromental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Ying Huang
- Guangdong Engineering Research Centre for Marine Algal Biotechnology, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresouce and Eco-Enviromental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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15
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Abstract
Siderophores are chelators synthesized by microbes to sequester iron. This article summarizes the knowledge on the fungal siderophore metabolism with a focus on Aspergillus fumigatus. In recent years, A. fumigatus became a role model for fungal biosynthesis, uptake and degradation of siderophores as well as regulation of siderophore-mediated iron handling and the elucidation of siderophore functions. Siderophore functions comprise uptake, intracellular transport and storage of iron. This proved to be crucial not only for adaptation to iron starvation conditions but also for germination, asexual and sexual propagation, antioxidative defense, mutual interaction, microbial competition as well as virulence in plant and animal hosts. Recent studies also indicate the high potential of siderophores and its biosynthetic pathway to improve diagnosis and therapy of fungal infections.
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Affiliation(s)
- Hubertus Haas
- Division of Molecular Biology/Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria.
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16
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Roche CM, Glass NL, Blanch HW, Clark DS. Engineering the filamentous fungusNeurospora crassafor lipid production from lignocellulosic biomass. Biotechnol Bioeng 2014; 111:1097-107. [DOI: 10.1002/bit.25211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/03/2014] [Accepted: 02/06/2014] [Indexed: 01/14/2023]
Affiliation(s)
- Christine M. Roche
- The Chemical and Biomolecular Engineering Department; The University of California; Berkeley California 94720
- The Energy Biosciences Institute; The University of California; Berkeley California 94720
| | - N. Louise Glass
- The Energy Biosciences Institute; The University of California; Berkeley California 94720
- The Plant and Microbial Biology Department; The University of California; Berkeley California
| | - Harvey W. Blanch
- The Chemical and Biomolecular Engineering Department; The University of California; Berkeley California 94720
- The Energy Biosciences Institute; The University of California; Berkeley California 94720
| | - Douglas S. Clark
- The Chemical and Biomolecular Engineering Department; The University of California; Berkeley California 94720
- The Energy Biosciences Institute; The University of California; Berkeley California 94720
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Abstract
Most fungal genomes are poorly annotated, and many fungal traits of industrial and biomedical relevance are not well suited to classical genetic screens. Assigning genes to phenotypes on a genomic scale thus remains an urgent need in the field. We developed an approach to infer gene function from expression profiles of wild fungal isolates, and we applied our strategy to the filamentous fungus Neurospora crassa. Using transcriptome measurements in 70 strains from two well-defined clades of this microbe, we first identified 2,247 cases in which the expression of an unannotated gene rose and fell across N. crassa strains in parallel with the expression of well-characterized genes. We then used image analysis of hyphal morphologies, quantitative growth assays, and expression profiling to test the functions of four genes predicted from our population analyses. The results revealed two factors that influenced regulation of metabolism of nonpreferred carbon and nitrogen sources, a gene that governed hyphal architecture, and a gene that mediated amino acid starvation resistance. These findings validate the power of our population-transcriptomic approach for inference of novel gene function, and we suggest that this strategy will be of broad utility for genome-scale annotation in many fungal systems. IMPORTANCE Some fungal species cause deadly infections in humans or crop plants, and other fungi are workhorses of industrial chemistry, including the production of biofuels. Advances in medical and industrial mycology require an understanding of the genes that control fungal traits. We developed a method to infer functions of uncharacterized genes by observing correlated expression of their mRNAs with those of known genes across wild fungal isolates. We applied this strategy to a filamentous fungus and predicted functions for thousands of unknown genes. In four cases, we experimentally validated the predictions from our method, discovering novel genes involved in the metabolism of nutrient sources relevant for biofuel production, as well as colony morphology and starvation resistance. Our strategy is straightforward, inexpensive, and applicable for predicting gene function in many fungal species.
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