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Wang Z, Hou X, Shang G, Deng G, Luo K, Peng M. Exploring Fatty Acid β-Oxidation Pathways in Bacteria: From General Mechanisms to DSF Signaling and Pathogenicity in Xanthomonas. Curr Microbiol 2024; 81:336. [PMID: 39223428 DOI: 10.1007/s00284-024-03866-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Fatty acids (FAs) participate in extensive physiological activities such as energy metabolism, transcriptional control, and cell signaling. In bacteria, FAs are degraded and utilized through various metabolic pathways, including β-oxidation. Over the past ten years, significant progress has been made in studying FA oxidation in bacteria, particularly in E. coli, where the processes and roles of FA β-oxidation have been comprehensively elucidated. Here, we provide an update on the new research achievements in FAs β-oxidation in bacteria. Using Xanthomonas as an example, we introduce the oxidation process and regulation mechanism of the DSF-family quorum sensing signal. Based on current findings, we propose the specific enzymes required for β-oxidation of several specific FAs. Finally, we discuss the future outlook on scientific issues that remain to be addressed. This paper supplies theoretical guidance for further study of the FA β-oxidation pathway with particular emphasis on its connection to the pathogenicity mechanisms of bacteria.
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Affiliation(s)
- Zhiyong Wang
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Xue Hou
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Guohui Shang
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Guangai Deng
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Kai Luo
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Mu Peng
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China.
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Zhila NO, Sapozhnikova KY, Kiselev EG, Shishatskaya EI, Volova TG. Biosynthesis of Polyhydroxyalkanoates in Cupriavidus necator B-10646 on Saturated Fatty Acids. Polymers (Basel) 2024; 16:1294. [PMID: 38732762 PMCID: PMC11085183 DOI: 10.3390/polym16091294] [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: 03/25/2024] [Revised: 04/20/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
It has been established that the wild-type Cupriavidus necator B-10646 strain uses saturated fatty acids (SFAs) for growth and polyhydroxyalkanoate (PHA) synthesis. It uses lauric (12:0), myristic (14:0), palmitic (16:0) and stearic (18:0) acids as carbon sources; moreover, the elongation of the C-chain negatively affects the biomass and PHA yields. When bacteria grow on C12 and C14 fatty acids, the total biomass and PHA yields are comparable up to 7.5 g/L and 75%, respectively, which twice exceed the values that occur on longer C16 and C18 acids. Regardless of the type of SFAs, bacteria synthesize poly(3-hydroxybutyrate), which have a reduced crystallinity (Cx from 40 to 57%) and a molecular weight typical for poly(3-hydroxybutyrate) (P(3HB)) (Mw from 289 to 465 kDa), and obtained polymer samples demonstrate melting and degradation temperatures with a gap of about 100 °C. The ability of bacteria to assimilate SFAs opens up the possibility of attracting the synthesis of PHAs on complex fat-containing substrates, including waste.
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Affiliation(s)
- Natalia O. Zhila
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Kristina Yu. Sapozhnikova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Evgeniy G. Kiselev
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Ekaterina I. Shishatskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Tatiana G. Volova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
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Mariam I, Krikigianni E, Rantzos C, Bettiga M, Christakopoulos P, Rova U, Matsakas L, Patel A. Transcriptomics aids in uncovering the metabolic shifts and molecular machinery of Schizochytrium limacinum during biotransformation of hydrophobic substrates to docosahexaenoic acid. Microb Cell Fact 2024; 23:97. [PMID: 38561811 PMCID: PMC10983653 DOI: 10.1186/s12934-024-02381-6] [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: 02/21/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Biotransformation of waste oil into value-added nutraceuticals provides a sustainable strategy. Thraustochytrids are heterotrophic marine protists and promising producers of omega (ω) fatty acids. Although the metabolic routes for the assimilation of hydrophilic carbon substrates such as glucose are known for these microbes, the mechanisms employed for the conversion of hydrophobic substrates are not well established. Here, thraustochytrid Schizochytrium limacinum SR21 was investigated for its ability to convert oils (commercial oils with varying fatty acid composition and waste cooking oil) into ω-3 fatty acid; docosahexaenoic acid (DHA). RESULTS Within 72 h SR21 consumed ~ 90% of the oils resulting in enhanced biomass (7.5 g L- 1) which was 2-fold higher as compared to glucose. Statistical analysis highlights C16 fatty acids as important precursors of DHA biosynthesis. Transcriptomic data indicated the upregulation of multiple lipases, predicted to possess signal peptides for secretory, membrane-anchored and cytoplasmic localization. Additionally, transcripts encoding for mitochondrial and peroxisomal β-oxidation along with acyl-carnitine transporters were abundant for oil substrates that allowed complete degradation of fatty acids to acetyl CoA. Further, low levels of oxidative biomarkers (H2O2, malondialdehyde) and antioxidants were determined for hydrophobic substrates, suggesting that SR21 efficiently mitigates the metabolic load and diverts the acetyl CoA towards energy generation and DHA accumulation. CONCLUSIONS The findings of this study contribute to uncovering the route of assimilation of oil substrates by SR21. The thraustochytrid employs an intricate crosstalk among the extracellular and intracellular molecular machinery favoring energy generation. The conversion of hydrophobic substrates to DHA can be further improved using synthetic biology tools, thereby providing a unique platform for the sustainable recycling of waste oil substrates.
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Affiliation(s)
- Iqra Mariam
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, Luleå, SE-971 87, Sweden
| | - Eleni Krikigianni
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, Luleå, SE-971 87, Sweden
| | - Chloe Rantzos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, Luleå, SE-971 87, Sweden
| | - Maurizio Bettiga
- Department of Life Sciences - LIFE, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
- Innovation Unit, Italbiotec Srl Società Benefit, Milan, Italy
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, Luleå, SE-971 87, Sweden
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, Luleå, SE-971 87, Sweden
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, Luleå, SE-971 87, Sweden
| | - Alok Patel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, Luleå, SE-971 87, Sweden.
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Xie YG, Xiao Y, Yu MY, Yang WC. Acyl-CoA synthetase 1 plays an important role on pollen development and male fertility in tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108523. [PMID: 38492487 DOI: 10.1016/j.plaphy.2024.108523] [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: 10/25/2023] [Revised: 01/11/2024] [Accepted: 03/09/2024] [Indexed: 03/18/2024]
Abstract
The development of pollen is critical to male reproduction in flowering plants. Acyl-CoA synthetase (ACOS) genes play conserved functions in regulating pollen development in various plants. Our previous work found that knockout of the SlACOS1 gene in tomato might decrease fruit setting. The current study further revealed that SlACOS1 was important to pollen development and male fertility. The SlACOS1 gene was preferentially expressed in the stamen of the flower with the highest expression at the tetrad stage of anther development. Mutation of the SlACOS1 gene by the CRISPR/Cas9-editing system reduced pollen number and viability as well as fruit setting. The tapetum layer exhibited premature degradation and the pollen showed abnormal development appearing irregular, shriveled, or anucleate in Slacos1 mutants at the tetrad stage. The fatty acid metabolism in anthers was significantly impacted by mutation of the SlACOS1 gene. Furthermore, targeted fatty acids profiling using GC-MS found that contents of most fatty acids except C18:1 and C18:2 were reduced. Yeast complementation assay demonstrated that the substrate preferences of SlACOS1 were C16:0 and C18:0 fatty acids. Male fertility of Slacos1 mutant could be slightly restored by applying exogenous palmitic acid, a type of C16:0 fatty acid. Taken together, SlACOS1 played important roles on pollen development and male fertility by regulating the fatty acid metabolism and the development of tapetum and tetrad. Our findings will facilitate unraveling the mechanism of pollen development and male fertility in tomato.
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Affiliation(s)
- Yin-Ge Xie
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
| | - Yao Xiao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China; Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Meng-Yi Yu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
| | - Wen-Cai Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education of the People's Republic of China, Beijing, 100193, China.
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Fan L, Jiang Z, Xiong Y, Xu Z, Yang X, Gu D, Ainiwaer M, Li L, Liu J, Chen F. Recent Advances in the HPPH-Based Third-Generation Photodynamic Agents in Biomedical Applications. Int J Mol Sci 2023; 24:17404. [PMID: 38139233 PMCID: PMC10743769 DOI: 10.3390/ijms242417404] [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: 11/16/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Photodynamic therapy has emerged as a recognized anti-tumor treatment involving three fundamental elements: photosensitizers, light, and reactive oxygen species. Enhancing the effectiveness of photosensitizers remains the primary avenue for improving the biological therapeutic outcomes of PDT. Through three generations of development, HPPH is a 2-(1-hexyloxyethyl)-2-devinyl derivative of pyropheophorbide-α, representing a second-generation photosensitizer already undergoing clinical trials for various tumors. The evolution toward third-generation photosensitizers based on HPPH involves structural modifications for multimodal applications and the combination of multifunctional compounds, leading to improved imaging localization and superior anti-tumor effects. While research into third-generation HPPH is beneficial for advancing PDT treatment, equal attention should also be directed toward the other two essential elements and personalized diagnosis and treatment methodologies.
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Affiliation(s)
- Lixiao Fan
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Zheng Jiang
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yu Xiong
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Zepeng Xu
- West China Clinical Medical College, Sichuan University, Chengdu 610064, China;
| | - Xin Yang
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Deying Gu
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Mailudan Ainiwaer
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Leyu Li
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Jun Liu
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Fei Chen
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610064, China; (L.F.); (Z.J.); (Y.X.); (X.Y.); (D.G.); (M.A.); (L.L.)
- Head and Neck Surgical Center, West China Hospital, Sichuan University, Chengdu 610064, China
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Lee GH, Kim DW, Jin YH, Kim SM, Lim ES, Cha MJ, Ko JK, Gong G, Lee SM, Um Y, Han SO, Ahn JH. Biotechnological Plastic Degradation and Valorization Using Systems Metabolic Engineering. Int J Mol Sci 2023; 24:15181. [PMID: 37894861 PMCID: PMC10607142 DOI: 10.3390/ijms242015181] [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: 09/22/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Various kinds of plastics have been developed over the past century, vastly improving the quality of life. However, the indiscriminate production and irresponsible management of plastics have led to the accumulation of plastic waste, emerging as a pressing environmental concern. To establish a clean and sustainable plastic economy, plastic recycling becomes imperative to mitigate resource depletion and replace non-eco-friendly processes, such as incineration. Although chemical and mechanical recycling technologies exist, the prevalence of composite plastics in product manufacturing complicates recycling efforts. In recent years, the biodegradation of plastics using enzymes and microorganisms has been reported, opening a new possibility for biotechnological plastic degradation and bio-upcycling. This review provides an overview of microbial strains capable of degrading various plastics, highlighting key enzymes and their role. In addition, recent advances in plastic waste valorization technology based on systems metabolic engineering are explored in detail. Finally, future perspectives on systems metabolic engineering strategies to develop a circular plastic bioeconomy are discussed.
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Affiliation(s)
- Ga Hyun Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Do-Wook Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Yun Hui Jin
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sang Min Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Eui Seok Lim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Min Ji Cha
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jung Ho Ahn
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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Sikkema WD, Cal AJ, Hathwaik UI, Orts WJ, Lee CC. Polyhydroxyalkanoate production in Pseudomonas putida from alkanoic acids of varying lengths. PLoS One 2023; 18:e0284377. [PMID: 37471433 PMCID: PMC10358918 DOI: 10.1371/journal.pone.0284377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/29/2023] [Indexed: 07/22/2023] Open
Abstract
Many studies have been conducted to produce microbial polyhydroxyalkanoates (PHA), a biopolymer, from Pseudomonas sp. fed with various alkanoic acids. Because this previous data was collected using methodologies that varied in critical aspects, such as culture media and size range of alkanoic acids, it has been difficult to compare the results for a thorough understanding of the relationship between feedstock and PHA production. Therefore, this study utilized consistent culture media with a wide range of alkanoic acids (C7-C14) to produce medium chain length PHAs. Three strains of Pseudomonas putida (NRRL B-14875, KT2440, and GN112) were used, and growth, cell dry weight, PHA titer, monomer distribution, and molecular weights were all examined. It was determined that although all the strains produced similar PHA titers using C7-C9 alkanoic acids, significant differences were observed with the use of longer chain feedstocks. Specifically, KT2440 and its derivative GN112 produced higher PHA titers compared to B-14875 when fed longer chain alkanoates. We also compared several analytical techniques for determining amounts of PHA and found they produced different results. In addition, the use of an internal standard had a higher risk of calculating inaccurate concentrations compared to an external standard. These observations highlight the importance of considering this aspect of analysis when evaluating different studies.
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Affiliation(s)
- W Dirk Sikkema
- Bioproducts Research Unit, USDA-ARS-WRRC, Albany, CA, United States of America
| | - Andrew J Cal
- Bioproducts Research Unit, USDA-ARS-WRRC, Albany, CA, United States of America
| | - Upul I Hathwaik
- Bioproducts Research Unit, USDA-ARS-WRRC, Albany, CA, United States of America
| | - William J Orts
- Bioproducts Research Unit, USDA-ARS-WRRC, Albany, CA, United States of America
| | - Charles C Lee
- Bioproducts Research Unit, USDA-ARS-WRRC, Albany, CA, United States of America
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8
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Sui Y, Guo X, Zhou R, Fu Z, Chai Y, Xia A, Zhao W. Photoenzymatic Decarboxylation to Produce Hydrocarbon Fuels: A Critical Review. Mol Biotechnol 2023:10.1007/s12033-023-00775-2. [PMID: 37349610 DOI: 10.1007/s12033-023-00775-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Photoenzymatic decarboxylation shows great promise as a pathway for the generation of hydrocarbon fuels. CvFAP, which is derived from Chlorella variabilis NC64A, is a photodecarboxylase capable of converting fatty acids into hydrocarbons. CvFAP is an example of coupling biocatalysis and photocatalysis to produce alkanes. The catalytic process is mild, and it does not yield toxic substances or excess by-products. However, the activity of CvFAP can be readily inhibited by several factors, and further enhancement is required to improve the enzyme yield and stability. In this article, we will examine the latest advancements in CvFAP research, with a particular focus on the enzyme's structural and catalytic mechanism, summarized some limitations in the application of CvFAP, and laboratory-level methods for enhancing enzyme activity and stability. This review can serve as a reference for future large-scale industrial production of hydrocarbon fuels.
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Affiliation(s)
- Yaqi Sui
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaobo Guo
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Rui Zhou
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhisong Fu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Yingxin Chai
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Ao Xia
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Wenhui Zhao
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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Trirocco R, Pasqua M, Tramonti A, Grossi M, Colonna B, Paiardini A, Prosseda G. Fatty Acids Abolish Shigella Virulence by Inhibiting Its Master Regulator, VirF. Microbiol Spectr 2023; 11:e0077823. [PMID: 37140433 PMCID: PMC10269687 DOI: 10.1128/spectrum.00778-23] [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: 02/20/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023] Open
Abstract
The pathogenicity of Shigella, the intracellular pathogen responsible for human bacillary dysentery, depends on a coordinated and tightly regulated expression of its virulence determinants. This is the result of a cascade organization of its positive regulators, with VirF, a transcriptional activator belonging to the AraC-XylS family, in a pivotal position. VirF itself is submitted to several well-known regulations at the transcriptional level. In this work, we present evidence for a novel posttranslational regulatory mechanism of VirF mediated by the inhibitory interaction with specific fatty acids. By homology modeling and molecular docking analyses, we identify a jelly roll motif in the structure of ViF capable of interacting with medium-chain saturated and long-chain unsaturated fatty acids. In vitro and in vivo assays show that capric, lauric, myristoleic, palmitoleic, and sapienic acids interact effectively with the VirF protein, abolishing its transcription-promoting activity. This silences the virulence system of Shigella, leading to a drastic reduction in its ability to invade epithelial cells and proliferate in their cytoplasm. IMPORTANCE In the absence of a valid vaccine, the main therapeutic approach currently used to treat shigellosis is based on the use of antibiotics. The emergence of antibiotic resistance jeopardizes the future effectiveness of this approach. The importance of the present work resides both in the identification of a new level of posttranslational regulation of the Shigella virulence system and in the characterization of a mechanism offering new opportunities for the design of antivirulence compounds, which may change the treatment paradigm of Shigella infections by limiting the emergence of antibiotic-resistant bacteria.
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Affiliation(s)
- Rita Trirocco
- Institute Pasteur Italia, Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Martina Pasqua
- Institute Pasteur Italia, Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Milena Grossi
- Institute Pasteur Italia, Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Bianca Colonna
- Institute Pasteur Italia, Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | | | - Gianni Prosseda
- Institute Pasteur Italia, Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
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10
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Lau MJ, Nie S, Yang Q, Harshman LG, Mao C, Williamson NA, Hoffmann AA. Lipidomic Profiling Reveals Concerted Temporal Patterns of Functionally Related Lipids in Aedes aegypti Females Following Blood Feeding. Metabolites 2023; 13:421. [PMID: 36984861 PMCID: PMC10051423 DOI: 10.3390/metabo13030421] [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: 02/02/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
We conducted a lipidomic analysis of the whole body of female Aedes aegypti mosquitoes at different time points over the course of feeding and reproduction. There were temporal biphasic increases of more than 80% of lipids identified at the time of feeding and from 16 h to 30 h post blood meal (PBM). During these two increases, the abundance of many lipids dropped while body weight remained stable, probably reflecting blood lipid digestion and the synthesis of vitellogenin in this period. A concerted temporal pattern was particularly strong at the second peak for membrane and signalling lipids such as phosphatidylethanolamine (PE), phosphatidylinositol (PI), cardiolipin (CL), hexosylceramide (HexCer) and lyso-phosphatidic acid (LPA). Lyso-glycerophospholipids showed three distinct change patterns that are functionally related: Lyso-PE and Lyso-phosphatidylcholine (LPC), which are membrane lipids, showed little change; LPA, a signalling lipid, showed a significant increase from 16 to 30 h PBM; Lyso-PI, a bioactive lipid, and both lyso-phosphatidylglycerol (LPG) and lyso-phosphatidylserine (LPS), which are bacterial membrane lipids, showed one significant increase from the time of feeding to 16 h post blood meal. The result of our study on the anautogenous insect Ae. aegypti point to specific lipids likely to be important in the reproductive process with a role in the formation and growth of ovarian follicles.
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Affiliation(s)
- Meng-Jia Lau
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Shuai Nie
- Mass Spectrometry and Proteomics Facility, Bio21 Institute, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Qiong Yang
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Lawrence G. Harshman
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Cungui Mao
- Department of Medicine and Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, NY 11794, USA
| | - Nicholas A. Williamson
- Mass Spectrometry and Proteomics Facility, Bio21 Institute, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, VIC 3052, Australia
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11
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Singh B, Kumar A, Saini AK, Saini RV, Thakur R, Mohammed SA, Tuli HS, Gupta VK, Areeshi MY, Faidah H, Jalal NA, Haque S. Strengthening microbial cell factories for efficient production of bioactive molecules. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36809927 DOI: 10.1080/02648725.2023.2177039] [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: 08/11/2022] [Accepted: 01/21/2023] [Indexed: 02/24/2023]
Abstract
High demand of bioactive molecules (food additives, antibiotics, plant growth enhancers, cosmetics, pigments and other commercial products) is the prime need for the betterment of human life where the applicability of the synthetic chemical product is on the saturation due to associated toxicity and ornamentations. It has been noticed that the discovery and productivity of such molecules in natural scenarios are limited due to low cellular yields as well as less optimized conventional methods. In this respect, microbial cell factories timely fulfilling the requirement of synthesizing bioactive molecules by improving production yield and screening more promising structural homologues of the native molecule. Where the robustness of the microbial host can be potentially achieved by taking advantage of cell engineering approaches such as tuning functional and adjustable factors, metabolic balancing, adapting cellular transcription machinery, applying high throughput OMICs tools, stability of genotype/phenotype, organelle optimizations, genome editing (CRISPER/Cas mediated system) and also by developing accurate model systems via machine-learning tools. In this article, we provide an overview from traditional to recent trends and the application of newly developed technologies, for strengthening the systemic approaches and providing future directions for enhancing the robustness of microbial cell factories to speed up the production of biomolecules for commercial purposes.
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Affiliation(s)
- Bharat Singh
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Ankit Kumar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gurugram, India
| | - Adesh Kumar Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Reena Vohra Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Rahul Thakur
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Shakeel A Mohammed
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Hardeep Singh Tuli
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Mohammed Y Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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12
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Medium-Chain-Length Fatty Acid Catabolism in Cupriavidus necator H16: Transcriptome Sequencing Reveals Differences from Long-Chain-Length Fatty Acid β-Oxidation and Involvement of Several Homologous Genes. Appl Environ Microbiol 2023; 89:e0142822. [PMID: 36541797 PMCID: PMC9888253 DOI: 10.1128/aem.01428-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The number of genes encoding β-oxidation enzymes in Cupriavidus necator H16 (synonym, Ralstonia eutropha H16) is high, but only the operons A0459-A0464 and A1526-A1531, each encoding four genes for β-oxidation enzymes, were expressed during growth with long-chain-length fatty acids (LCFAs). However, we observed that C. necator ΔA0459-A0464 ΔA1526-A1531 and C. necator H16 showed the same growth behavior during growth with decanoic acid and shorter FAs. The negative effect of the deletion of these two operons increased with an increasing chain length of the utilized FAs. Transcriptome sequencing (RNA-Seq) revealed the expression profiles of genes involved in the catabolism of medium-chain-length fatty acids (MCFAs) in C. necator H16. Operon A0459-A0464 was expressed only during growth with nonanoic acid, whereas operon A1526-A1531 was highly expressed during growth with octanoic and nonanoic acid. The gene clusters B1187-B1192 and B0751-B0759 showed a log2 fold change in expression of up to 4.29 and 4.02, respectively, during growth with octanoic acid and up to 8.82 and 5.50, respectively, with nonanoic acid compared to sodium gluconate-grown cells. Several acyl-CoA ligases catalyze the activation of MCFAs with coenzyme A (CoA), but fadD3 (A3288), involved in activation of LCFAs, was not detected. The expression profiles of C. necator strain ΔA0459-A0464 ΔA1526-A1531 showed that the growth with nonanoic acid resulted in the expression of further β-oxidation enzyme-encoding genes. Additional insights into the transport of FAs in C. necator H16 revealed the complexity and putative involvement of the DegV-like protein encoded by A0463 in the transport of odd-chain-length FAs and of siderophore biosynthesis in the transport mechanism. IMPORTANCE Although Cupriavidus necator H16 has been used in several studies to produce polyhydroxyalkanoates from various lipids, the fatty acid metabolism is poorly understood. The β-oxidation of long-chain-length FAs has been investigated, but the tremendous number of homologous genes encoding β-oxidation enzymes hides the potential for variances in the expressed genes for catabolism of shorter FAs. The catabolism of medium-chain-length FAs and connected pathways has not been investigated yet. As more sustainable substrates such as lipids and the production of fatty acids and fatty acid derivates become more critical with the dependency on fossil-based substances, understanding the complex metabolism in this highly diverse workhorse for biotechnology, C. necator, is inevitable. For further metabolic engineering and construction of production strains, we investigated the metabolism during growth on medium-chain-length FAs by RNA-Seq.
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13
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Giacometti SI, MacRae MR, Dancel-Manning K, Bhabha G, Ekiert DC. Lipid Transport Across Bacterial Membranes. Annu Rev Cell Dev Biol 2022; 38:125-153. [PMID: 35850151 DOI: 10.1146/annurev-cellbio-120420-022914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport.
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Affiliation(s)
- Sabrina I Giacometti
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Kristen Dancel-Manning
- Office of Science and Research, New York University School of Medicine, New York, NY, USA;
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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14
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Mater V, Eisner S, Seidel C, Schneider D. The peripherally membrane-attached protein MbFACL6 of Mycobacterium tuberculosis activates a broad spectrum of substrates. J Mol Biol 2022; 434:167842. [PMID: 36179886 DOI: 10.1016/j.jmb.2022.167842] [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: 06/10/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022]
Abstract
The infectious disease tuberculosis is one of the fifteen most common causes of death worldwide (according to the WHO). About every fourth person is infected with the main causative agent Mycobacterium tuberculosis (Mb). A characteristic of the pathogen is its entrance into a dormant state in which a phenotypic antibiotic resistance is achieved. To target resistant strains, novel dormancy-specific targets are very promising. Such a possible target is the Mb "fatty acid-CoA ligase 6" (MbFACL6), which activates fatty acids and thereby modulates the accumulation of triacylglycerol-containing lipid droplets that are used by Mb as an energy source during dormancy. We investigated the membrane association of MbFACL6 in E. coli and its specific activity towards different substrates after establishing a novel MbFACL6 activity assay. Despite a high homology to the mammalian family of fatty acid transport proteins, which are typically transmembrane proteins, our results indicate that MbFACL6 is a peripheral membrane-attached protein. Furthermore, MbFACL6 tolerates a broad spectrum of substrates including saturated and unsaturated fatty acids (C12-C20), some cholic acid derivatives, and even synthetic fatty acids, such as 9(E)-nitrooleicacid. Therefore, the substrate selectivity of MbFACL6 appears to be much broader than previously assumed.
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Affiliation(s)
- Veronika Mater
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany.
| | - Sabine Eisner
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany.
| | - Cornelia Seidel
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany.
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany.
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15
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Degradation of Exogenous Fatty Acids in Escherichia coli. Biomolecules 2022; 12:biom12081019. [PMID: 35892328 PMCID: PMC9329746 DOI: 10.3390/biom12081019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Many bacteria possess all the machineries required to grow on fatty acids (FA) as a unique source of carbon and energy. FA degradation proceeds through the β-oxidation cycle that produces acetyl-CoA and reduced NADH and FADH cofactors. In addition to all the enzymes required for β-oxidation, FA degradation also depends on sophisticated systems for its genetic regulation and for FA transport. The fact that these machineries are conserved in bacteria suggests a crucial role in environmental conditions, especially for enterobacteria. Bacteria also possess specific enzymes required for the degradation of FAs from their environment, again showing the importance of this metabolism for bacterial adaptation. In this review, we mainly describe FA degradation in the Escherichia coli model, and along the way, we highlight and discuss important aspects of this metabolism that are still unclear. We do not detail exhaustively the diversity of the machineries found in other bacteria, but we mention them if they bring additional information or enlightenment on specific aspects.
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16
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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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17
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Bashiri R, Allen B, Shamurad B, Pabst M, Curtis TP, Ofiţeru ID. Looking for lipases and lipolytic organisms in low-temperature anaerobic reactors treating domestic wastewater. WATER RESEARCH 2022; 212:118115. [PMID: 35092910 DOI: 10.1016/j.watres.2022.118115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Poor lipid degradation limits low-temperature anaerobic treatment of domestic wastewater even when psychrophiles are used. We combined metagenomics and metaproteomics to find lipolytic bacteria and their potential, and actual, cold-adapted extracellular lipases in anaerobic membrane bioreactors treating domestic wastewater at 4 and 15 °C. Of the 40 recovered putative lipolytic metagenome-assembled genomes (MAGs), only three (Chlorobium, Desulfobacter, and Mycolicibacterium) were common and abundant (relative abundance ≥ 1%) in all reactors. Notably, some MAGs that represented aerobic autotrophs contained lipases. Therefore, we hypothesised that the lipases we found are not always associated with exogenous lipid degradation and can have other roles such as polyhydroxyalkanoates (PHA) accumulation/degradation and interference with the outer membranes of other bacteria. Metaproteomics did not provide sufficient proteome coverage for relatively lower abundant proteins such as lipases though the expression of fadL genes, long-chain fatty acid transporters, was confirmed for four genera (Dechloromonas, Azoarcus, Aeromonas and Sulfurimonas), none of which were recovered as putative lipolytic MAGs. Metaproteomics also confirmed the presence of 15 relatively abundant (≥ 1%) genera in all reactors, of which at least 6 can potentially accumulate lipid/polyhydroxyalkanoates. For most putative lipolytic MAGs, there was no statistically significant correlation between the read abundance and reactor conditions such as temperature, phase (biofilm and bulk liquid), and feed type (treated by ultraviolet light or not). Results obtained by metagenomics and metaproteomics did not confirm each other and extracellular lipases and lipolytic bacteria were not easily identifiable in the anaerobic membrane reactors used in this study. Further work is required to identify the true lipid degraders in these systems.
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Affiliation(s)
- Reihaneh Bashiri
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
| | - Ben Allen
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
| | - Burhan Shamurad
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
| | - Irina D Ofiţeru
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom.
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18
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Wang S, Ren H, Zhong H, Zhao X, Li C, Ma J, Gu X, Xue Y, Huang S, Yang J, Chen L, Chen G, Qu S, Liang J, Qin L, Huang Q, Peng Y, Li Q, Wang X, Zou Y, Shi Z, Li X, Li T, Yang H, Lai S, Xu G, Li J, Zhang Y, Gu Y, Wang W. Combined berberine and probiotic treatment as an effective regimen for improving postprandial hyperlipidemia in type 2 diabetes patients: a double blinded placebo controlled randomized study. Gut Microbes 2022; 14:2003176. [PMID: 34923903 PMCID: PMC8726654 DOI: 10.1080/19490976.2021.2003176] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Non-fasting lipidemia (nFL), mainly contributed by postprandial lipidemia (PL), has recently been recognized as an important cardiovascular disease (CVD) risk as fasting lipidemia (FL). PL serves as a common feature of dyslipidemia in Type 2 Diabetes (T2D), albeit effective therapies targeting on PL were limited. In this study, we aimed to evaluate whether the therapy combining probiotics (Prob) and berberine (BBR), a proven antidiabetic and hypolipidemic regimen via altering gut microbiome, could effectively reduce PL in T2D and to explore the underlying mechanism. Blood PL (120 min after taking 100 g standard carbohydrate meal) was examined in 365 participants with T2D from the Probiotics and BBR on the Efficacy and Change of Gut Microbiota in Patients with Newly Diagnosed Type 2 Diabetes (PREMOTE study), a random, placebo-controlled, and multicenter clinical trial. Prob+BBR was superior to BBR or Prob alone in improving postprandial total cholesterol (pTC) and low-density lipoprotein cholesterol (pLDLc) levels with decrement of multiple species of postprandial lipidomic metabolites after 3 months follow-up. This effect was linked to the changes of fecal Bifidobacterium breve level responding to BBR alone or Prob+BBR treatment. Four fadD genes encoding long-chain acyl-CoA synthetase were identified in the genome of this B. breve strain, and transcriptionally activated by BBR. In vitro BBR treatment further decreased the concentration of FFA in the culture medium of B. breve compared to vehicle. Thus, the activation of fadD by BBR could enhance FFA import and mobilization in B. breve and diliminish the intraluminal lipids for absorption to mediate the effect of Prob+BBR on PL. Our study confirmed that BBR and Prob (B. breve) could exert a synergistic hypolipidemic effect on PL, acting as a gut lipid sink to achieve better lipidemia and CVD risk control in T2D.
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Affiliation(s)
- Shujie Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the Pr China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huahui Ren
- BGI-Shenzhen, Shenzhen, China,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Xinjie Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Changkun Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the Pr China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Ma
- Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuejiang Gu
- Department of Endocrinology, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang Province, China
| | - Yaoming Xue
- Nanfang Hospital, Southern Medical University, Guangdong Province, China
| | - Shan Huang
- Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialin Yang
- Department of Endocrinology, Central Hospital of Minhang District, Shanghai, China
| | - Li Chen
- Department of Endocrinology, Qilu Hospital of Shandong University, Shandong Province, China
| | - Gang Chen
- Department of Endocrinology, Fujian Provincial Hospital, Fujian Province, China
| | - Shen Qu
- Department of Endocrinology, Shanghai Tenth People’s Hospital of Tong Ji University, Shanghai, China
| | - Jun Liang
- Department of Endocrinology, Xuzhou Central Hospital, Jiangsu Province, China
| | - Li Qin
- Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qin Huang
- Chang Hai Hospital, Second Military Medical University, Shanghai, China
| | - Yongde Peng
- Shanghai First People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Li
- Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Xiaolin Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | | | | | - Xuelin Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the Pr China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingting Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the Pr China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Shenghan Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Guowang Xu
- Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, China,CONTACT Junhua Li BGI-Shenzhen, Shenzhen, China
| | - Yifei Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the Pr China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Yifei Zhang Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanyun Gu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the Pr China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Yanyun Gu Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the Pr China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Weiqing Wang, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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19
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Li XH, Peng YJ, Ding JL, Feng MG, Ying SH. A homologue of yeast acyl-CoA synthetase Faa1 contributes to cytomembrane functionality involved in development and virulence in the insect pathogenic fungus Beauveria bassiana. Microb Pathog 2022; 164:105419. [DOI: 10.1016/j.micpath.2022.105419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
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20
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Ma Y, Nenkov M, Chen Y, Press AT, Kaemmerer E, Gassler N. Fatty acid metabolism and acyl-CoA synthetases in the liver-gut axis. World J Hepatol 2021; 13:1512-1533. [PMID: 34904027 PMCID: PMC8637682 DOI: 10.4254/wjh.v13.i11.1512] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/28/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023] Open
Abstract
Fatty acids are energy substrates and cell components which participate in regulating signal transduction, transcription factor activity and secretion of bioactive lipid mediators. The acyl-CoA synthetases (ACSs) family containing 26 family members exhibits tissue-specific distribution, distinct fatty acid substrate preferences and diverse biological functions. Increasing evidence indicates that dysregulation of fatty acid metabolism in the liver-gut axis, designated as the bidirectional relationship between the gut, microbiome and liver, is closely associated with a range of human diseases including metabolic disorders, inflammatory disease and carcinoma in the gastrointestinal tract and liver. In this review, we depict the role of ACSs in fatty acid metabolism, possible molecular mechanisms through which they exert functions, and their involvement in hepatocellular and colorectal carcinoma, with particular attention paid to long-chain fatty acids and small-chain fatty acids. Additionally, the liver-gut communication and the liver and gut intersection with the microbiome as well as diseases related to microbiota imbalance in the liver-gut axis are addressed. Moreover, the development of potentially therapeutic small molecules, proteins and compounds targeting ACSs in cancer treatment is summarized.
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Affiliation(s)
- Yunxia Ma
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena 07747, Germany
| | - Miljana Nenkov
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena 07747, Germany
| | - Yuan Chen
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena 07747, Germany
| | - Adrian T Press
- Department of Anesthesiology and Intensive Care Medicine and Center for Sepsis Control and Care, Jena University Hospital, Friedrich Schiller University Jena, Jena 07747, Germany
| | - Elke Kaemmerer
- Department of Pediatrics, Jena University Hospital, Friedrich Schiller University Jena, Jena 07747, Germany
| | - Nikolaus Gassler
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena 07747, Germany.
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21
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Matson MM, Cepeda MM, Zhang A, Case AE, Kavvas ES, Wang X, Carroll AL, Tagkopoulos I, Atsumi S. Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli. Metab Eng 2021; 69:50-58. [PMID: 34763090 DOI: 10.1016/j.ymben.2021.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/14/2021] [Accepted: 11/04/2021] [Indexed: 02/08/2023]
Abstract
Previously, Escherichia coli was engineered to produce isobutyl acetate (IBA). Titers greater than the toxicity threshold (3 g/L) were achieved by using layer-assisted production. To avoid this costly and complex method, adaptive laboratory evolution (ALE) was applied to E. coli for improved IBA tolerance. Over 37 rounds of selective pressure, 22 IBA-tolerant mutants were isolated. Remarkably, these mutants not only tolerate high IBA concentrations, they also produce higher IBA titers. Using whole-genome sequencing followed by CRISPR/Cas9 mediated genome editing, the mutations (SNPs in metH, rho and deletion of arcA) that confer improved tolerance and higher titers were elucidated. The improved IBA titers in the evolved mutants were a result of an increased supply of acetyl-CoA and altered transcriptional machinery. Without the use of phase separation, a strain capable of 3.2-fold greater IBA production than the parent strain was constructed by combing select beneficial mutations. These results highlight the impact improved tolerance has on the production capability of a biosynthetic system.
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Affiliation(s)
- Morgan M Matson
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Mateo M Cepeda
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Angela Zhang
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Anna E Case
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Erol S Kavvas
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Xiaokang Wang
- Genome Center, University of California, Davis, CA, 95616, USA; Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Austin L Carroll
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Ilias Tagkopoulos
- Genome Center, University of California, Davis, CA, 95616, USA; Department of Computer Science, University of California, Davis, CA, 95616, USA
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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22
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Abstract
Aryl coenzyme A (CoA) ligases belong to class I of the adenylate-forming enzyme superfamily (ANL superfamily). They catalyze the formation of thioester bonds between aromatic compounds and CoA and occur in nearly all forms of life. These ligases are involved in various metabolic pathways degrading benzene, toluene, ethylbenzene, and xylene (BTEX) or polycyclic aromatic hydrocarbons (PAHs). They are often necessary to produce the central intermediate benzoyl-CoA that occurs in various anaerobic pathways. The substrate specificity is very diverse between enzymes within the same class, while the dependency on Mg2+, ATP, and CoA as well as oxygen insensitivity are characteristics shared by the whole enzyme class. Some organisms employ the same aryl-CoA ligase when growing aerobically and anaerobically, while others induce different enzymes depending on the environmental conditions. Aryl-CoA ligases can be divided into two major groups, benzoate:CoA ligase-like enzymes and phenylacetate:CoA ligase-like enzymes. They are widely distributed between the phylogenetic clades of the ANL superfamily and show closer relationships within the subfamilies than to other aryl-CoA ligases. This, together with residual CoA ligase activity in various other enzymes of the ANL superfamily, leads to the conclusion that CoA ligases might be the ancestral proteins from which all other ANL superfamily enzymes developed.
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23
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Lee J, Kim Y, Khadke SK, Lee J. Antibiofilm and antifungal activities of medium-chain fatty acids against Candida albicans via mimicking of the quorum-sensing molecule farnesol. Microb Biotechnol 2021; 14:1353-1366. [PMID: 33252828 PMCID: PMC8313291 DOI: 10.1111/1751-7915.13710] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/20/2022] Open
Abstract
Candida biofilms are tolerant to conventional antifungal therapeutics and the host immune system. The transition of yeast cells to hyphae is considered a key step in C. albicans biofilm development, and this transition is inhibited by the quorum-sensing molecule farnesol. We hypothesized that fatty acids mimicking farnesol might influence hyphal and biofilm formation by C. albicans. Among 31 saturated and unsaturated fatty acids, six medium-chain saturated fatty acids, that is, heptanoic acid, octanoic acid, nonanoic acid, decanoic acid, undecanoic acid and lauric acid, effectively inhibited C. albicans biofilm formation by more than 75% at 2 µg ml-1 with MICs in the range 100-200 µg ml-1 . These six fatty acids at 2 µg ml-1 and farnesol at 100 µg ml-1 inhibited hyphal growth and cell aggregation. The addition of fatty acids to C. albicans cultures decreased the productions of farnesol and sterols. Furthermore, down-regulation of several hyphal and biofilm-related genes caused by heptanoic or nonanoic acid closely resembled the changes caused by farnesol. In addition, nonanoic acid, the most effective compound diminished C. albicans virulence in a Caenorhabditis elegans model. Our results suggest that medium-chain fatty acids inhibit more effectively hyphal growth and biofilm formation than farnesol.
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Affiliation(s)
- Jin‐Hyung Lee
- School of Chemical EngineeringYeungnam UniversityGyeongsanKorea
| | - Yong‐Guy Kim
- School of Chemical EngineeringYeungnam UniversityGyeongsanKorea
| | | | - Jintae Lee
- School of Chemical EngineeringYeungnam UniversityGyeongsanKorea
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24
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Knoll KE, Lindeque Z, Adeniji AA, Oosthuizen CB, Lall N, Loots DT. Elucidating the Antimycobacterial Mechanism of Action of Ciprofloxacin Using Metabolomics. Microorganisms 2021; 9:microorganisms9061158. [PMID: 34071153 PMCID: PMC8228629 DOI: 10.3390/microorganisms9061158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 12/21/2022] Open
Abstract
In the interest of developing more effective and safer anti-tuberculosis drugs, we used a GCxGC-TOF-MS metabolomics research approach to investigate and compare the metabolic profiles of Mtb in the presence and absence of ciprofloxacin. The metabolites that best describe the differences between the compared groups were identified as markers characterizing the changes induced by ciprofloxacin. Malic acid was ranked as the most significantly altered metabolite marker induced by ciprofloxacin, indicative of an inhibition of the tricarboxylic acid (TCA) and glyoxylate cycle of Mtb. The altered fatty acid, myo-inositol, and triacylglycerol metabolism seen in this group supports previous observations of ciprofloxacin action on the Mtb cell wall. Furthermore, the altered pentose phosphate intermediates, glycerol metabolism markers, glucose accumulation, as well as the reduction in the glucogenic amino acids specifically, indicate a flux toward DNA (as well as cell wall) repair, also supporting previous findings of DNA damage caused by ciprofloxacin. This study further provides insights useful for designing network whole-system strategies for the identification of possible modes of action of various drugs and possibly adaptations by Mtb resulting in resistance.
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Affiliation(s)
- Kirsten E. Knoll
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Zander Lindeque
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Adetomiwa A. Adeniji
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Carel B. Oosthuizen
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
| | - Namrita Lall
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Du Toit Loots
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
- Correspondence: ; Tel.: +27-(0)18-299-1818
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25
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Salvador López JM, Van Bogaert INA. Microbial fatty acid transport proteins and their biotechnological potential. Biotechnol Bioeng 2021; 118:2184-2201. [PMID: 33638355 DOI: 10.1002/bit.27735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 12/11/2022]
Abstract
Fatty acid metabolism has been widely studied in various organisms. However, fatty acid transport has received less attention, even though it plays vital physiological roles, such as export of toxic free fatty acids or uptake of exogenous fatty acids. Hence, there are important knowledge gaps in how fatty acids cross biological membranes, and many mechanisms and proteins involved in these processes still need to be determined. The lack of information is more predominant in microorganisms, even though the identification of fatty acids transporters in these cells could lead to establishing new drug targets or improvements in microbial cell factories. This review provides a thorough analysis of the current information on fatty acid transporters in microorganisms, including bacteria, yeasts and microalgae species. Most available information relates to the model organisms Escherichia coli and Saccharomyces cerevisiae, but transport systems of other species are also discussed. Intracellular trafficking of fatty acids and their transport through organelle membranes in eukaryotic organisms is described as well. Finally, applied studies and engineering efforts using fatty acids transporters are presented to show the applied potential of these transporters and to stress the need for further identification of new transporters and their engineering.
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Affiliation(s)
- José M Salvador López
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Inge N A Van Bogaert
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
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26
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Scheel RA, Ho T, Kageyama Y, Masisak J, McKenney S, Lundgren BR, Nomura CT. Optimizing a Fed-Batch High-Density Fermentation Process for Medium Chain-Length Poly(3-Hydroxyalkanoates) in Escherichia coli. Front Bioeng Biotechnol 2021; 9:618259. [PMID: 33718339 PMCID: PMC7953831 DOI: 10.3389/fbioe.2021.618259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/08/2021] [Indexed: 11/15/2022] Open
Abstract
Production of medium chain-length poly(3-hydroxyalkanoates) [PHA] polymers with tightly defined compositions is an important area of research to expand the application and improve the properties of these promising biobased and biodegradable materials. PHA polymers with homopolymeric or defined compositions exhibit attractive material properties such as increased flexibility and elasticity relative to poly(3-hydroxybutyrate) [PHB]; however, these polymers are difficult to biosynthesize in native PHA-producing organisms, and there is a paucity of research toward developing high-density cultivation methods while retaining compositional control. In this study, we developed and optimized a fed-batch fermentation process in a stirred tank reactor, beginning with the biosynthesis of poly(3-hydroxydecanoate) [PHD] from decanoic acid by β-oxidation deficient recombinant Escherichia coli LSBJ using glucose as a co-substrate solely for growth. Bacteria were cultured in two stages, a biomass accumulation stage (37°C, pH 7.0) with glucose as the primary carbon source and a PHA biosynthesis stage (30°C, pH 8.0) with co-feeding of glucose and a fatty acid. Through iterative optimizations of semi-defined media composition and glucose feed rate, 6.0 g of decanoic acid was converted to PHD with an 87.5% molar yield (4.54 g L-1). Stepwise increases in the amount of decanoic acid fed during the fermentation correlated with an increase in PHD, resulting in a final decanoic acid feed of 25 g converted to PHD at a yield of 89.4% (20.1 g L-1, 0.42 g L-1 h-1), at which point foaming became uncontrollable. Hexanoic acid, octanoic acid, 10-undecenoic acid, and 10-bromodecanoic acid were all individually supplemented at 20 g each and successfully polymerized with yields ranging from 66.8 to 99.0% (9.24 to 18.2 g L-1). Using this bioreactor strategy, co-fatty acid feeds of octanoic acid/decanoic acid and octanoic acid/10-azidodecanoic acid (8:2 mol ratio each) resulted in the production of their respective copolymers at nearly the same ratio and at high yield, demonstrating that these methods can be used to control PHA copolymer composition.
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Affiliation(s)
- Ryan A. Scheel
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Truong Ho
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Yuki Kageyama
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
- Division of Applied Chemistry, Department of Engineering, Hokkaido University, Sapporo, Japan
| | - Jessica Masisak
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Seamus McKenney
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Benjamin R. Lundgren
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Christopher T. Nomura
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, ID, United States
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27
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The role of transport proteins in the production of microbial glycolipid biosurfactants. Appl Microbiol Biotechnol 2021; 105:1779-1793. [PMID: 33576882 DOI: 10.1007/s00253-021-11156-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 01/20/2023]
Abstract
Several microorganisms are currently being used as production platform for glycolipid biosurfactants, providing a greener alternative to chemical biosurfactants. One of the reasons why these processes are commercially competitive is the fact that microbial producers can efficiently export their product to the extracellular environment, reaching high product titers. Glycolipid biosynthetic genes are often found in a dedicated cluster, amidst which genes encoding a dedicated transporter committed to shuttle the glycolipid to the extracellular environment are often found, as is the case for many other secondary metabolites. Knowing this, one can rely on gene clustering features to screen for novel putative transporters, as described and performed in this review. The above strategy proves to be very powerful to identify glycolipid transporters in fungi but is less valid for bacterial systems. Indeed, the genetics of these export systems are currently largely unknown, but some hints are given. Apart from the direct export of the glycolipid, several other transport systems have an indirect effect on glycolipid production. Specific importers dictate which hydrophilic and hydrophobic substrates can be used for production and influence the final yields. In eukaryotes, cellular compartmentalization allows the assembly of glycolipid building blocks in a highly specialized and efficient way. Yet, this requires controlled transport across intracellular membranes. Next to the direct export of glycolipids, the current state of the art regarding this indirect involvement of transporter systems in microbial glycolipid synthesis is summarized in this review. KEY POINTS: • Transporters are directly and indirectly involved in microbial glycolipid synthesis. • Yeast glycolipid transporters are found in their biosynthetic gene cluster. • Hydrophilic and hydrophobic substrate uptake influence microbial glycolipid synthesis.
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28
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A Futile Metabolic Cycle of Fatty Acyl-CoA Hydrolysis and Resynthesis in Corynebacterium glutamicum and Its Disruption Leading to Fatty Acid Production. Appl Environ Microbiol 2021; 87:AEM.02469-20. [PMID: 33310719 PMCID: PMC7851686 DOI: 10.1128/aem.02469-20] [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] [Indexed: 11/26/2022] Open
Abstract
Fatty acyl-CoA thioesterase (Tes) and acyl-CoA synthetase (FadD) catalyze opposing reactions between acyl-CoAs and free fatty acids. Within the genome of Corynebacterium glutamicum, several candidate genes for each enzyme are present, although their functions remain unknown. Modified expressions of the candidate genes in the fatty acid producer WTΔfasR led to identification of one tes gene (tesA) and two fadD genes (fadD5 and fadD15), which functioned positively and negatively in fatty acid production, respectively. Genetic analysis showed that fadD5 and fadD15 are responsible for utilization of exogenous fatty acids and that tesA plays a role in supplying fatty acids for synthesis of the outer layer components mycolic acids. Enzyme assays and expression analysis revealed that tesA, fadD5, and fadD15 were co-expressed to create a cyclic route between acyl-CoAs and fatty acids. When fadD5 or fadD15 was disrupted in wild-type C. glutamicum, both disruptants excreted fatty acids during growth. Double disruptions of them resulted in a synergistic increase in production. Additional disruption of tesA revealed a canceling effect on production. These results indicate that the FadDs normally shunt the surplus of TesA-generated fatty acids back to acyl-CoAs for lipid biosynthesis and that interception of this shunt provokes cells to overproduce fatty acids. When this strategy was applied to a fatty acid high-producer, the resulting fadDs-disrupted and tesA-amplified strain exhibited a 72% yield increase relative to its parent and produced fatty acids, which consisted mainly of oleic acid, palmitic acid, and stearic acid, on the gram scale per liter from 1% glucose.IMPORTANCE The industrial amino acid producer Corynebacterium glutamicum has currently evolved into a potential workhorse for fatty acid production. In this organism, we obtained evidence showing the presence of a unique mechanism of lipid homeostasis, namely, a formation of a futile cycle of acyl-CoA hydrolysis and resynthesis mediated by acyl-CoA thioesterase (Tes) and acyl-CoA synthetase (FadD), respectively. The biological role of the coupling of Tes and FadD would be to supply free fatty acids for synthesis of the outer layer components mycolic acids and to recycle their surplusage to acyl-CoAs for membrane lipid synthesis. We further demonstrated that engineering of the cycle in a fatty acid high-producer led to dramatically improved production, which provides a useful engineering strategy for fatty acid production in this industrially important microorganism.
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29
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Kuprat T, Johnsen U, Ortjohann M, Schönheit P. Acetate Metabolism in Archaea: Characterization of an Acetate Transporter and of Enzymes Involved in Acetate Activation and Gluconeogenesis in Haloferax volcanii. Front Microbiol 2020; 11:604926. [PMID: 33343547 PMCID: PMC7746861 DOI: 10.3389/fmicb.2020.604926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/13/2020] [Indexed: 02/01/2023] Open
Abstract
The haloarchaeon Haloferax volcanii grows on acetate as sole carbon and energy source. The genes and proteins involved in uptake and activation of acetate and in gluconeogenesis were identified and analyzed by characterization of enzymes and by growth experiments with the respective deletion mutants. (i) An acetate transporter of the sodium: solute-symporter family (SSF) was characterized by kinetic analyses of acetate uptake into H. volcanii cells. The functional involvement of the transporter was proven with a Δssf mutant. (ii) Four paralogous AMP-forming acetyl-CoA synthetases that belong to different phylogenetic clades were shown to be functionally involved in acetate activation. (iii) The essential involvement of the glyoxylate cycle as an anaplerotic sequence was concluded from growth experiments with an isocitrate lyase knock-out mutant excluding the operation of the methylaspartate cycle reported for Haloarcula species. (iv) Enzymes involved in phosphoenolpyruvate synthesis from acetate, namely two malic enzymes and a phosphoenolpyruvate synthetase, were identified and characterized. Phylogenetic analyses of haloarchaeal malic enzymes indicate a separate evolutionary line distinct from other archaeal homologs. The exclusive function of phosphoenolpyruvate synthetase in gluconeogenesis was proven by the respective knock-out mutant. Together, this is a comprehensive study of acetate metabolism in archaea.
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Affiliation(s)
- Tom Kuprat
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Ulrike Johnsen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Marius Ortjohann
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
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30
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Al-Thihli K, Afting C, Al-Hashmi N, Mohammed M, Sliwinski S, Al Shibli N, Al-Said K, Al-Kasbi G, Al-Kharusi K, Merle U, Füllekrug J, Al-Maawali A. Deficiency of acyl-CoA synthetase 5 is associated with a severe and treatable failure to thrive of neonatal onset. Clin Genet 2020; 99:376-383. [PMID: 33191500 DOI: 10.1111/cge.13883] [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: 09/07/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 12/01/2022]
Abstract
Failure to thrive (FTT) causes significant morbidity, often without clear etiologies. Six individuals of a large consanguineous family presented in the neonatal period with recurrent vomiting and diarrhea, leading to severe FTT. Standard diagnostic work up did not ascertain an etiology. Autozygosity mapping and whole exome sequencing identified homozygosity for a novel genetic variant of the long chain fatty acyl-CoA synthetase 5 (ACSL5) shared among the affected individuals (NM_203379.1:c.1358C>A:p.(Thr453Lys)). Autosomal recessive genotype-phenotype segregation was confirmed by Sanger sequencing. Functional in vitro analysis of the ACSL5 variant by immunofluorescence, western blotting and enzyme assay suggested that Thr453Lys is a loss-of-function mutation without any remaining activity. ACSL5 belongs to an essential enzyme family required for lipid metabolism and is known to contribute the major activity in the mouse intestine. Based on the function of ACSL5 in intestinal long chain fatty acid metabolism and the gastroenterological symptoms, affected individuals were treated with total parenteral nutrition or medium-chain triglyceride-based formula restricted in long-chain triglycerides. The patients responded well and follow up suggests that treatment is only required during early life.
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Affiliation(s)
- Khalid Al-Thihli
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Cassian Afting
- Department of Internal Medicine IV, Heidelberg University Hospital, Heidelberg, Germany
| | - Nadia Al-Hashmi
- Department of Pediatrics and National Genetic Center, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Mohammed Mohammed
- Department of Pediatrics and National Genetic Center, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Svenja Sliwinski
- Department of Internal Medicine IV, Heidelberg University Hospital, Heidelberg, Germany
| | - Naema Al Shibli
- Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Khoula Al-Said
- Department of Pediatrics and National Genetic Center, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Ghalia Al-Kasbi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Khalsa Al-Kharusi
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Uta Merle
- Department of Internal Medicine IV, Heidelberg University Hospital, Heidelberg, Germany
| | - Joachim Füllekrug
- Department of Internal Medicine IV, Heidelberg University Hospital, Heidelberg, Germany
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
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Gao L, Wang Z, van der Veen S. Gonococcal Adaptation to Palmitic Acid Through farAB Expression and FadD Activity Mutations Increases In Vivo Fitness in a Murine Genital Tract Infection Model. J Infect Dis 2020; 224:141-150. [PMID: 33170275 DOI: 10.1093/infdis/jiaa701] [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: 09/02/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022] Open
Abstract
Neisseria gonorrhoeae is a bacterial pathogen that colonizes mucosal epithelia that are rich in antimicrobial molecules such as long-chain fatty acids. Here we studied the mechanisms involved in palmitic acid resistance and their impact on in vivo biological fitness in a murine genital tract infection model. A stable palmitic acid-resistant derivative was obtained by serial passage with incremental palmitic acid concentrations. This derivative outcompeted its parent strain for colonization and survival in the murine infection model. Subsequent whole-genome sequencing resulted in the identification of the 3 resistance-related SNPs ihfAC5T, fadDC772T, and farAG-52T (promoter) that were verified for resistance against palmitic acid. Subsequent characterization of the associated resistance determinants showed that ihfAC5T and farAG-52T induced gene expression of the FarAB efflux pump, whereas fadDC772T increased the maximum enzyme activity of the FadD long-chain fatty acid-coenzyme A ligase. Our results highlight the mechanisms involved in gonococcal adaptation to the murine host environment.
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Affiliation(s)
- Lingyu Gao
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhemin Wang
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Stijn van der Veen
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Dermatology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Effects of High-Fat Diet Induced Obesity and Fructooligosaccharide Supplementation on Cardiac Protein Expression. Nutrients 2020; 12:nu12113404. [PMID: 33167590 PMCID: PMC7694524 DOI: 10.3390/nu12113404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 01/12/2023] Open
Abstract
The mechanism by which high fat-diet induced obesity affects cardiac protein expression is unclear, and the extent to which this is modulated by prebiotic treatment is not known. These outcomes were assessed in rats initially fed a high-fat diet, then the top 40% weight gain group were randomly allocated to control (CON), high-fat (HF) and HF supplemented with fructooligosaccharide (32 g; HF-FOS) treatments for 12 weeks (n = 10/group). At sacrifice, left ventricles were either frozen or preserved in formalin. Serum was stored for glucose and insulin measurements. Protein spectra was obtained using an Orbitrap analyzer, processed with Sequest and fold changes assessed with Scaffold Q +. Treatment effects for body weights, glucose and insulin were assessed using one-way ANOVA, and the differential protein expression was assessed by a Mann-Whitney U test. The Database for Annotation, Visualization and Integrated Discovery and the Kyoto Encyclopedia of Genes and Genomes identified pathways containing overrepresented proteins. Hematoxylin and eosin sections were graded for hypertrophy and also quantified; differences were identified using Chi-square analyses and Mann-Whitney U tests. HF diet fed rats were significantly (p < 0.05) heavier than CON, and 23 proteins involved in mitochondrial function and lipid metabolism were differentially expressed between HF and CON. Between HF-FOS and HF, 117 proteins involved in contractility, lipid and carbohydrate metabolism were differentially expressed. HF cardiomyocytes were significantly (p < 0.05) more hypertrophic than CON. We conclude that high-fat feeding and FOS are associated with subcellular deviations in cardiac metabolism and contractility, which may influence myocardial function and alter the risk of cardiovascular disease.
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Herndon JL, Peters RE, Hofer RN, Simmons TB, Symes SJ, Giles DK. Exogenous polyunsaturated fatty acids (PUFAs) promote changes in growth, phospholipid composition, membrane permeability and virulence phenotypes in Escherichia coli. BMC Microbiol 2020; 20:305. [PMID: 33046008 PMCID: PMC7552566 DOI: 10.1186/s12866-020-01988-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The utilization of exogenous fatty acids by Gram-negative bacteria has been linked to many cellular processes, including fatty acid oxidation for metabolic gain, assimilation into membrane phospholipids, and control of phenotypes associated with virulence. The expanded fatty acid handling capabilities have been demonstrated in several bacteria of medical importance; however, a survey of the polyunsaturated fatty acid responses in the model organism Escherichia coli has not been performed. The current study examined the impacts of exogenous fatty acids on E. coli. RESULTS All PUFAs elicited higher overall growth, with several fatty acids supporting growth as sole carbon sources. Most PUFAs were incorporated into membrane phospholipids as determined by Ultra performance liquid chromatography-mass spectrometry, whereas membrane permeability was variably affected as measured by two separate dye uptake assays. Biofilm formation, swimming motility and antimicrobial peptide resistance were altered in the presence of PUFAs, with arachidonic and docosahexaenoic acids eliciting strong alteration to these phenotypes. CONCLUSIONS The findings herein add E. coli to the growing list of Gram-negative bacteria with broader capabilities for utilizing and responding to exogenous fatty acids. Understanding bacterial responses to PUFAs may lead to microbial behavioral control regimens for disease prevention.
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Affiliation(s)
- Joshua L. Herndon
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - Rachel E. Peters
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - Rachel N. Hofer
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - Timothy B. Simmons
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - Steven J. Symes
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - David K. Giles
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN USA
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Mu DS, Wang S, Liang QY, Du ZZ, Tian R, Ouyang Y, Wang XP, Zhou A, Gong Y, Chen GJ, Van Nostrand J, Yang Y, Zhou J, Du ZJ. Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. MICROBIOME 2020; 8:126. [PMID: 32867860 PMCID: PMC7460792 DOI: 10.1186/s40168-020-00902-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/27/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown. RESULTS Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. CONCLUSIONS Bradymonabacteria have unique living strategies that are transitional between the "obligate" and the so-called facultative predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments. Video abstract.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Shuo Wang
- Marine College, Shandong University, Weihai, 264209, China
| | - Qi-Yun Liang
- Marine College, Shandong University, Weihai, 264209, China
| | - Zhao-Zhong Du
- Marine College, Shandong University, Weihai, 264209, China
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Xin-Peng Wang
- Marine College, Shandong University, Weihai, 264209, China
| | - Aifen Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Joy Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China.
- Marine College, Shandong University, Weihai, 264209, China.
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Two Functional Fatty Acyl Coenzyme A Ligases Affect Free Fatty Acid Metabolism To Block Biosynthesis of an Antifungal Antibiotic in Lysobacter enzymogenes. Appl Environ Microbiol 2020; 86:AEM.00309-20. [PMID: 32144106 PMCID: PMC7205486 DOI: 10.1128/aem.00309-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/04/2020] [Indexed: 11/20/2022] Open
Abstract
In Lysobacter enzymogenes OH11, RpfB1 and RpfB2 were predicted to encode acyl coenzyme A (CoA) ligases. RpfB1 is located in the Rpf gene cluster. Interestingly, we found an RpfB1 homolog (RpfB2) outside this canonical gene cluster, and nothing is known about its functionality or mechanism. Here, we report that rpfB1 and rpfB2 can functionally replace EcFadD in the Escherichia coli fadD mutant JW1794. RpfB activates long-chain fatty acids (n-C16:0 and n-C18:0) for the corresponding fatty acyl-CoA ligase (FCL) activity in vitro, and Glu-361 plays critical roles in the catalytic mechanism of RpfB1 and RpfB2. Deletion of rpfB1 and rpfB2 resulted in significantly increased heat-stable antifungal factor (HSAF) production, and overexpression of rpfB1 or rpfB2 completely suppressed HSAF production. Deletion of rpfB1 and rpfB2 resulted in increased L. enzymogenes diffusible signaling factor 3 (LeDSF3) synthesis in L. enzymogenes Overall, our results showed that changes in intracellular free fatty acid levels significantly altered HSAF production. Our report shows that intracellular free fatty acids are required for HSAF production and that RpfB affects HSAF production via FCL activity. The global transcriptional regulator Clp directly regulated the expression of rpfB1 and rpfB2 In conclusion, these findings reveal new roles of RpfB in antibiotic biosynthesis in L. enzymogenes IMPORTANCE Understanding the biosynthetic and regulatory mechanisms of heat-stable antifungal factor (HSAF) could improve the yield in Lysobacter enzymogenes Here, we report that RpfB1 and RpfB2 encode acyl coenzyme A (CoA) ligases. Our research shows that RpfB1 and RpfB2 affect free fatty acid metabolism via fatty acyl-CoA ligase (FCL) activity to reduce the substrate for HSAF synthesis and, thereby, block HSAF production in L. enzymogenes Furthermore, these findings reveal new roles for the fatty acyl-CoA ligases RpfB1 and RpfB2 in antibiotic biosynthesis in L. enzymogenes Importantly, the novelty of this work is the finding that RpfB2 lies outside the Rpf gene cluster and plays a key role in HSAF production, which has not been reported in other diffusible signaling factor (DSF)/Rpf-producing bacteria.
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Zhang X, Yang F, Chen L, Feng H, Yin S, Chen M. Insights into ecological roles and potential evolution of Mlr-dependent microcystin-degrading bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136401. [PMID: 31926423 DOI: 10.1016/j.scitotenv.2019.136401] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/12/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Over decades many studies have focused on the biodegradation of microcystins (MCs), and some Mlr-dependent MC-degrading bacteria were recorded, but the ecological functions, metabolic traits, and potential evolution of these organisms remain poorly understood. In this study, 16S rRNA-based phylogeny unraveled a wide range of genetic diversity across bacterial lineage, accompanied by re-evaluation of taxonomic placement of some MC-degrading species. Genome-wide comparison showed that considerable genes unique in individual organisms were identified, suggesting genetic differentiation among these Mlr-dependent MC-degrading bacteria. Notably, analyses of metabolic profiles first revealed the presence of functional genes involved in phenylacetate biodegradation in the specialized genomic regions, and mlr gene cluster was located around the neighborhood. The identification of transposable elements further indicated that these genomic regions might undergo horizontal gene transfer events to recruit novel functionalities, suggesting an adaptive force driving genome evolution of these organisms. In short, phylogenetic and genetic content analyses of Mlr-dependent MC-degraders shed light on their metabolic potential, ecological roles, and bacterial evolution, and expand the understanding of ecological status of MCs biodegradation.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China; Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Central South University, Changsha, China
| | - Lv Chen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Hai Feng
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Shiqian Yin
- School of Environmental Science and Engineering, Qilu University of Technology, Jinan, China
| | - Mengshi Chen
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
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37
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Kalinger RS, Pulsifer IP, Hepworth SR, Rowland O. Fatty Acyl Synthetases and Thioesterases in Plant Lipid Metabolism: Diverse Functions and Biotechnological Applications. Lipids 2020; 55:435-455. [PMID: 32074392 DOI: 10.1002/lipd.12226] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Plants use fatty acids to synthesize acyl lipids for many different cellular, physiological, and defensive roles. These roles include the synthesis of essential membrane, storage, or surface lipids, as well as the production of various fatty acid-derived metabolites used for signaling or defense. Fatty acids are activated for metabolic processing via a thioester linkage to either coenzyme A or acyl carrier protein. Acyl synthetases metabolically activate fatty acids to their thioester forms, and acyl thioesterases deactivate fatty acyl thioesters to free fatty acids by hydrolysis. These two enzyme classes therefore play critical roles in lipid metabolism. This review highlights the surprisingly complex and varying roles of fatty acyl synthetases in plant lipid metabolism, including roles in the intracellular trafficking of fatty acids. This review also surveys the many specialized fatty acyl thioesterases characterized to date in plants, which produce a great diversity of fatty acid products in a tissue-specific manner. While some acyl thioesterases produce fatty acids that clearly play roles in plant-insect or plant-microbial interactions, most plant acyl thioesterases have yet to be fully characterized both in terms of their substrate specificities and their functions. The biotechnological applications of plant acyl thioesterases and synthetases are also discussed, as there is significant interest in these enzymes as catalysts for the sustainable production of fatty acids and their derivatives for industrial uses.
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Affiliation(s)
- Rebecca S Kalinger
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ian P Pulsifer
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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Radka CD, Frank MW, Rock CO, Yao J. Fatty acid activation and utilization by Alistipes finegoldii, a representative Bacteroidetes resident of the human gut microbiome. Mol Microbiol 2020; 113:807-825. [PMID: 31876062 DOI: 10.1111/mmi.14445] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022]
Abstract
Members of the Bacteroidetes phylum, represented by Alistipes finegoldii, are prominent anerobic, Gram-negative inhabitants of the gut microbiome. The lipid biosynthetic pathways were analyzed using bioinformatic analyses, lipidomics, metabolic labeling and biochemistry to characterize exogenous fatty acid metabolism. A. finegoldii only produced the saturated fatty acids. The most abundant lipids were phosphatidylethanolamine (PE) and sulfonolipid (SL). Neither phosphatidylglycerol nor cardiolipin are present. PE synthesis is initiated by the PlsX/PlsY/PlsC pathway, whereas the SL pathway is related to sphingolipid biosynthesis. A. finegoldii incorporated medium-chain fatty acids (≤14 carbons) into PE and SL after their elongation, whereas long-chain fatty acids (≥16 carbons) were not elongated. Fatty acids >16 carbons were primarily incorporated into the 2-position of phosphatidylethanolamine at the PlsC step, the only biosynthetic enzyme that utilizes long-chain acyl-ACP. The ability to assimilate a broad-spectrum of fatty acid chain lengths present in the gut environment is due to the expression of two acyl-acyl carrier protein (ACP) synthetases. Acyl-ACP synthetase 1 had a substrate preference for medium-chain fatty acids and synthetase 2 had a substrate preference for long-chain fatty acids. This unique combination of synthetases allows A. finegoldii to utilize both the medium- and long-chain fatty acid nutrients available in the gut environment to assemble its membrane lipids.
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Affiliation(s)
- Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Matthew W Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
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Tian Y, Lv X, Xie G, Wang L, Dai T, Qin X, Chen F, Xu Y. FAX2 Mediates Fatty Acid Export from Plastids in Developing Arabidopsis Seeds. PLANT & CELL PHYSIOLOGY 2019; 60:2231-2242. [PMID: 31198959 DOI: 10.1093/pcp/pcz117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/01/2019] [Indexed: 05/25/2023]
Abstract
Vegetable oils are mainly stored in the form of triacylglycerol (TAG) in oilseeds. Fatty acids (FAs), one of the building blocks for TAG assembly, are synthesized in plastids and then exported to the endoplasmic reticulum for storage oil synthesis. A recent study demonstrated that the export of FAs from plastids was mediated by a FAX (FA export) family protein. However, the significance of FAs export from plastid during seed oil accumulation has not been investigated. In this study, we found that FAX2 was highly expressed in developing Arabidopsis seeds and the expression level was consistent with FAs synthesis activity. FAX2 mutant seeds showed an approximately 18% reduction of lipid levels compared with wild-type seeds. By contrast, overexpression of FAX2 enhanced seed lipid accumulation by up to 30%. The FAs export activity of FAX2 was confirmed by yeast mutant cell complementation analysis. Our results showed that FAX2 could interact with other proteins to facilitate FAs transport. Taken together, these results indicate that FAX2-mediated FA export from plastids is important for seed oil accumulation, and that FAX2 can be used as a target gene for increasing lipid production in oilseeds.
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Affiliation(s)
- Yinshuai Tian
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou District, Chengdu, China
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chengdu, China
| | - Xueyan Lv
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou District, Chengdu, China
| | - Guilan Xie
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou District, Chengdu, China
| | - Linghui Wang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou District, Chengdu, China
| | - Tingwei Dai
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou District, Chengdu, China
| | - Xiaobo Qin
- Sichuan Natural Resource Institute, Chengdu, China
| | - Fang Chen
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou District, Chengdu, China
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chengdu, China
| | - Ying Xu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou District, Chengdu, China
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Semenec L, Vergara IA, Laloo AE, Mathews ER, Bond PL, Franks AE. Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions. MICROBIAL ECOLOGY 2019; 78:618-630. [PMID: 30759269 DOI: 10.1007/s00248-019-01316-8] [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: 03/08/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
Geobacter sulfurreducens pili enable extracellular electron transfer and play a role in secretion of c-type cytochromes such as OmcZ. PilA-deficient mutants of G. sulfurreducens have previously been shown to accumulate cytochromes within their membranes. This cytochrome retaining phenotype allowed for enhanced growth of PilA-deficient mutants in electron donor and carbon-limited conditions where formate and fumarate are provided as the sole electron donor and acceptor with no supplementary carbon source. Conversely, wild-type G. sulfurreducens, which has normal secretion of cytochromes, has comparative limited growth in these conditions. This growth is further impeded for OmcZ-deficient and OmcS-deficient mutants. A PilB-deficient mutant which prevents pilin production but allows for secretion of OmcZ had moderate growth in these conditions, indicating a role for cytochrome localization to enabling survival in the electron donor and carbon-limited conditions. To determine which pathways enhanced growth using formate, Sequential Window Acquisition of all Theoretical Mass Spectra mass spectrometry (SWATH-MS) proteomics of formate adapted PilA-deficient mutants and acetate grown wild type was performed. PilA-deficient mutants had an overall decrease in tricarboxylic acid (TCA) cycle enzymes and significant upregulation of electron transport chain associated proteins including many c-type cytochromes and [NiFe]-hydrogenases. Whole genome sequencing of the mutants shows strong convergent evolution and emergence of genetic subpopulations during adaptation to growth on formate. The results described here suggest a role for membrane constrained c-type cytochromes to the enhancement of survival and growth in electron donor and carbon-limited conditions.
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Affiliation(s)
- Lucie Semenec
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Ismael A Vergara
- Bioinformatics and Cancer Genomics, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Andrew E Laloo
- Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Elizabeth R Mathews
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia.
- Centre for Future Landscapes, La Trobe University, Melbourne, Australia.
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Yakah W, Singh P, Perides G, Brown J, Freedman SD, Martin CR. Developmental Accretion of Docosahexaenoic Acid Is Independent of Fatty Acid Transporter Expression in Brain and Lung Tissues of C57BL/6 and Fat1 Mice. J Nutr 2019; 149:1724-1731. [PMID: 31179494 PMCID: PMC6768804 DOI: 10.1093/jn/nxz074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/21/2018] [Accepted: 03/26/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Developmental expression of fatty acid transporters and their role in polyunsaturated fatty acid concentrations in the postnatal period have not been evaluated. OBJECTIVE We hypothesized that transporter expression is developmentally regulated, tissue-specific, and that expression can modulate fatty acid accretion independently of diet. METHODS Brain and lung transporter expression were quantified in C57BL/6 wild-type (WT) and Fat1 mice. Pups were dam-fed until day 21. Dams were fed AIN-76A 10% corn oil to represent a typical North American/European diet. After weaning, mice were fed the same diet as dams. Gene expression of Fatp1, Fatp4, Fabp5, and Fat/cd36 was quantified by quantitative reverse transcriptase-polymerase chain reaction. Fatty acid concentrations were measured by GC-MS. RESULTS Brain docosahexaenoic acid (DHA) concentrations increased from day 3 to day 28 in both genotypes, with higher concentrations at days 3 and 14 in Fat1 than in WT mice [median (IQR)]: 10.7 (10.6-11.2) mol% compared with 6.6 (6.4-7.2) mol% and 12.5 (12.4-12.9) mol% compared with 8.9 (8.7-9.1) mol%, respectively; P < 0.05). During DHA accrual, transporter expression decreased. Fold changes in brain Fatp4, Fabp5, and Fat/cd36 were inversely correlated with fold changes in brain DHA concentrations in Fat1 relative to WT mice (ρ = -0.85, -0.75, and -0.78, respectively; P ≤ 0.001). Lung DHA concentrations were unchanged across the 3 time points for both genotypes. Despite unchanging DHA concentrations, there was increased expression of Fatp1 at days 14 and 28 (5-fold), Fatp4 at day 14 (2.3-fold), and Fabp5 at day 14 (3.8-fold) relative to day 3 in Fat1 mice. In WT mice, Fatp1 increased almost 5-fold at day 28 relative to day 3. There was no correlation between lung transporters and DHA concentrations in Fat1 relative to WT mice. CONCLUSIONS Development of fatty acid transporter expression in C57BL/6 WT and Fat1 mice is genotype and tissue specific. Further, postnatal accretion of brain DHA appears independent of transporter status, with tissue concentrations representing dietary contributions.
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Affiliation(s)
- William Yakah
- Department of Neuroscience, Michigan State University, East Lansing, MI
| | | | | | | | - Steven D Freedman
- Division of Gastroenterology, Boston, MA,Division of Translational Research, Boston, MA
| | - Camilia R Martin
- Division of Translational Research, Boston, MA,Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA,Address correspondence to CRM (e-mail: )
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Tejima K, Chen X, Iwatani S, Kajiwara S. Long-Chain Acyl-CoA Synthetase is Associated with the Growth of Malassezia spp. J Fungi (Basel) 2019; 5:E88. [PMID: 31546626 PMCID: PMC6958399 DOI: 10.3390/jof5040088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022] Open
Abstract
The lipophilic fungal pathogen Malassezia spp. must acquire long-chain fatty acids (LCFAs) from outside the cell. To clarify the mechanism of LCFA acquisition, we investigated fatty acid uptake by this fungus and identified the long-chain acyl-CoA synthetase (ACS) gene FAA1 in three Malassezia spp.: M. globosa, M. pachydermatis, and M. sympodialis. These FAA1 genes could compensate for the double mutation of FAA1 and FAA4 in Saccharomyces cerevisiae, suggesting that Malassezia Faa1 protein recognizes exogenous LCFAs. MgFaa1p and MpFaa1p utilized a medium-chain fatty acid, lauric acid (C12:0). Interestingly, the ACS inhibitor, triacsin C, affected the activity of the Malassezia Faa1 proteins but not that of S. cerevisiae. Triacsin C also reduced the growth of M. globosa, M. pachydermatis, and M. sympodialis. These results suggest that triacsin C and its derivatives are potential compounds for the development of new anti-Malassezia drugs.
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Affiliation(s)
- Kengo Tejima
- School of Life Science and Technology, Tokyo Institute of Technology, J3-7, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Xinyue Chen
- School of Life Science and Technology, Tokyo Institute of Technology, J3-7, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Shun Iwatani
- School of Life Science and Technology, Tokyo Institute of Technology, J3-7, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Susumu Kajiwara
- School of Life Science and Technology, Tokyo Institute of Technology, J3-7, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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43
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Lin MH, Hsu FF, Crumrine D, Meyer J, Elias PM, Miner JH. Fatty acid transport protein 4 is required for incorporation of saturated ultralong-chain fatty acids into epidermal ceramides and monoacylglycerols. Sci Rep 2019; 9:13254. [PMID: 31519952 PMCID: PMC6744566 DOI: 10.1038/s41598-019-49684-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/29/2019] [Indexed: 01/15/2023] Open
Abstract
Fatty acid transport protein 4 (FATP4) is an acyl-CoA synthetase that is required for normal permeability barrier in mammalian skin. FATP4 (SLC27A4) mutations cause ichthyosis prematurity syndrome, a nonlethal disorder. In contrast, Fatp4-/- mice die neonatally from a defective barrier. Here we used electron microscopy and lipidomics to characterize defects in Fatp4-/- mice. Mutants showed lamellar body, corneocyte lipid envelope, and cornified envelope abnormalities. Lipidomics identified two lipids previously speculated to be present in mouse epidermis, sphingosine β-hydroxyceramide and monoacylglycerol; mutants displayed decreased proportions of these and the two ceramide classes that carry ultralong-chain, amide-linked fatty acids (FAs) thought to be critical for barrier function, unbound ω-O-acylceramide and bound ω-hydroxyceramide, the latter constituting the major component of the corneocyte lipid envelope. Other abnormalities included elevated amounts of sphingosine α-hydroxyceramide, phytosphingosine non-hydroxyceramide, and 1-O-acylceramide. Acyl chain length alterations in ceramides also suggested roles for FATP4 in esterifying saturated non-hydroxy and β-hydroxy FAs with at least 25 carbons and saturated or unsaturated ω-hydroxy FAs with at least 30 carbons to CoA. Our lipidomic analysis is the most thorough such study of the Fatp4-/- mouse skin barrier to date, providing information about how FATP4 can contribute to barrier function by regulating fatty acyl moieties in various barrier lipids.
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Affiliation(s)
- Meei-Hua Lin
- Division of Nephrology, Washington University School of Medicine, 4523 Clayton Ave., St. Louis, MO, 63110, United States
| | - Fong-Fu Hsu
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, 4523 Clayton Ave., St. Louis, MO, 63110, United States
| | - Debra Crumrine
- Dermatology Service, VA Medical Center and Department of Dermatology, University of California-San Francisco, 4150 Clement St., San Francisco, CA, 94121, United States
| | - Jason Meyer
- Dermatology Service, VA Medical Center and Department of Dermatology, University of California-San Francisco, 4150 Clement St., San Francisco, CA, 94121, United States
| | - Peter M Elias
- Dermatology Service, VA Medical Center and Department of Dermatology, University of California-San Francisco, 4150 Clement St., San Francisco, CA, 94121, United States
| | - Jeffrey H Miner
- Division of Nephrology, Washington University School of Medicine, 4523 Clayton Ave., St. Louis, MO, 63110, United States.
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, 4523 Clayton Ave., St. Louis, MO, 63110, United States.
- Department of Cell Biology and Physiology, Washington University School of Medicine, 4523 Clayton Ave., St. Louis, MO, 63110, United States.
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44
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Claus S, Jezierska S, Van Bogaert INA. Protein‐facilitated transport of hydrophobic molecules across the yeast plasma membrane. FEBS Lett 2019; 593:1508-1527. [DOI: 10.1002/1873-3468.13469] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Silke Claus
- Biochemical and Microbial Technology Universiteit Gent Belgium
| | | | - Inge N. A. Van Bogaert
- Lab. of Industrial Microbiology and Biocatalysis Faculty of Bioscience Engineering Ghent University Belgium
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45
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Allemann MN, Shulse CN, Allen EE. Linkage of Marine Bacterial Polyunsaturated Fatty Acid and Long-Chain Hydrocarbon Biosynthesis. Front Microbiol 2019; 10:702. [PMID: 31024488 PMCID: PMC6463001 DOI: 10.3389/fmicb.2019.00702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/20/2019] [Indexed: 11/13/2022] Open
Abstract
Various marine gamma-proteobacteria produce omega-3 polyunsaturated fatty acids, such as eicosapentaenoic acid (20:5, EPA) and docosahexaenoic acid (22:6, DHA), which are incorporated into membrane phospholipids. Five genes, designated pfaABCDE, encode the polyketide/fatty acid synthase necessary for production of these long-chain fatty acids. In addition to de novo biosynthesis of EPA and DHA, the "Pfa synthase" is also involved with production of a long-chain polyunsaturated hydrocarbon product (31:9, PUHC) in conjunction with the oleABCD hydrocarbon biosynthesis pathway. In this work, we demonstrate that OleA mediates the linkage between these two pathways in vivo. Co-expression of pfaA-E along with oleA from Shewanella pealeana in Escherichia coli yielded the expected product, a 31:8 ketone along with a dramatic ∼10-fold reduction in EPA content. The decrease in EPA content was independent of 31:8 ketone production as co-expression of an OleA active site mutant also led to identical decreases in EPA content. We also demonstrate that a gene linked with either pfa and/or ole operons in diverse bacterial lineages, herein designated pfaT, plays a role in maintaining optimal production of Pfa synthase derived products in Photobacterium and Shewanella species.
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Affiliation(s)
- Marco N Allemann
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Christine N Shulse
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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46
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Exterkate M, Driessen AJM. Synthetic Minimal Cell: Self-Reproduction of the Boundary Layer. ACS OMEGA 2019; 4:5293-5303. [PMID: 30949617 PMCID: PMC6443216 DOI: 10.1021/acsomega.8b02955] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/01/2019] [Indexed: 05/09/2023]
Abstract
A critical aspect in the bottom-up construction of a synthetic minimal cell is to develop an entity that is capable of self-reproduction. A key role in this process is the expansion and division of the boundary layer that surrounds the compartment, a process in which content loss has to be avoided and the barrier function maintained. Here, we describe the latest developments regarding self-reproduction of a boundary layer with a focus on the growth and division of phospholipid-based membranes in the context of a synthetic minimal cell.
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Affiliation(s)
- Marten Exterkate
- Department of Molecular Microbiology,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
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47
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Fanning S, Haque A, Imberdis T, Baru V, Barrasa MI, Nuber S, Termine D, Ramalingam N, Ho GPH, Noble T, Sandoe J, Lou Y, Landgraf D, Freyzon Y, Newby G, Soldner F, Terry-Kantor E, Kim TE, Hofbauer HF, Becuwe M, Jaenisch R, Pincus D, Clish CB, Walther TC, Farese RV, Srinivasan S, Welte MA, Kohlwein SD, Dettmer U, Lindquist S, Selkoe D. Lipidomic Analysis of α-Synuclein Neurotoxicity Identifies Stearoyl CoA Desaturase as a Target for Parkinson Treatment. Mol Cell 2019; 73:1001-1014.e8. [PMID: 30527540 PMCID: PMC6408259 DOI: 10.1016/j.molcel.2018.11.028] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 09/05/2018] [Accepted: 11/19/2018] [Indexed: 01/08/2023]
Abstract
In Parkinson's disease (PD), α-synuclein (αS) pathologically impacts the brain, a highly lipid-rich organ. We investigated how alterations in αS or lipid/fatty acid homeostasis affect each other. Lipidomic profiling of human αS-expressing yeast revealed increases in oleic acid (OA, 18:1), diglycerides, and triglycerides. These findings were recapitulated in rodent and human neuronal models of αS dyshomeostasis (overexpression; patient-derived triplication or E46K mutation; E46K mice). Preventing lipid droplet formation or augmenting OA increased αS yeast toxicity; suppressing the OA-generating enzyme stearoyl-CoA-desaturase (SCD) was protective. Genetic or pharmacological SCD inhibition ameliorated toxicity in αS-overexpressing rat neurons. In a C. elegans model, SCD knockout prevented αS-induced dopaminergic degeneration. Conversely, we observed detrimental effects of OA on αS homeostasis: in human neural cells, excess OA caused αS inclusion formation, which was reversed by SCD inhibition. Thus, monounsaturated fatty acid metabolism is pivotal for αS-induced neurotoxicity, and inhibiting SCD represents a novel PD therapeutic approach.
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Affiliation(s)
- Saranna Fanning
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Aftabul Haque
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Thibaut Imberdis
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Valeriya Baru
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Silke Nuber
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Termine
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Nagendran Ramalingam
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Gary P H Ho
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tallie Noble
- Mira Costa College, 1 Barnard Drive, Oceanside, CA 92056, USA
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yali Lou
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dirk Landgraf
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yelena Freyzon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Gregory Newby
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Frank Soldner
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Elizabeth Terry-Kantor
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tae-Eun Kim
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Harald F Hofbauer
- Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, 8010 Graz, Austria
| | - Michel Becuwe
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias C Walther
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; HHMI, Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
| | - Robert V Farese
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Supriya Srinivasan
- Department of Chemical Physiology and The Dorris Neuroscience Center, 1 Barnard Drive, Oceanside, CA 92056, USA; The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael A Welte
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Sepp D Kohlwein
- Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, 8010 Graz, Austria
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; HHMI, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Dennis Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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Phetcharat T, Dawkrajai P, Chitov T, Mhuantong W, Champreda V, Bovonsombut S. Biosurfactant-Producing Capability and Prediction of Functional Genes Potentially Beneficial to Microbial Enhanced Oil Recovery in Indigenous Bacterial Communities of an Onshore Oil Reservoir. Curr Microbiol 2019; 76:382-391. [PMID: 30734843 DOI: 10.1007/s00284-019-01641-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 01/28/2019] [Indexed: 11/25/2022]
Abstract
Microbial enhanced oil recovery (MEOR) is a bio-based technology with economic and environmental benefits. The success of MEOR depends greatly on the types and characteristics of indigenous microbes. The aim of this study was to evaluate the feasibility of applying MEOR at Mae Soon Reservoir, an onshore oil reservoir experiencing a decline in its production rate. We investigated the capability of the reservoir's bacteria to produce biosurfactants, and evaluated the potentials of uncultured indigenous bacteria to support MEOR by means of prediction of MEOR-related functional genes, based on a set of metagenomic 16s rRNA gene data. The biosurfactant-producing bacteria isolated from the oil-bearing sandstones from the reservoir belonged to one species: Bacillus licheniformis, with one having the ability to decrease surface tension from 72 to 32 mN/m. Gene sequences responsible for biosurfactant (licA3), lipase (lipP1) and catechol 2,3-dioxygenase (C23O) were detected in these isolates. The latter two, and other genes encoding MEOR-related functional proteins such as enoyl-CoA hydratase and alkane 1-monooxygenase, were predicted in the bacterial communities residing the reservoir's sandstones. Exposure of these sandstones to nutrients, consisting of KNO3 and NaH2PO4, resulted in an increase in the proportions of some predicted functional genes. These results indicated the potentials of MEOR application at Mae Soon site. Using the approaches demonstrated in this study would also assist evaluation of the feasibility of applying MEOR in oil reservoirs, which may be enhanced by an appropriate nutrient treatment.
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Affiliation(s)
- Thanachai Phetcharat
- Interdisciplinary Program in Biotechnology, Graduate School, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pinan Dawkrajai
- Defence Energy Department, Northern Petroleum Development Center, Fang, Chiang Mai, 50110, Thailand
| | - Thararat Chitov
- Division of Microbiology, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Environmental Science Research Center (ESRC), Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, The National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, The National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Sakunnee Bovonsombut
- Division of Microbiology, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Environmental Science Research Center (ESRC), Chiang Mai University, Chiang Mai, 50200, Thailand. .,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.
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49
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Neethu CS, Saravanakumar C, Purvaja R, Robin RS, Ramesh R. Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices. Sci Rep 2019; 9:1354. [PMID: 30718727 PMCID: PMC6361881 DOI: 10.1038/s41598-018-37903-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
Microbial degradation has long been recognized as the key rescue mechanism in shaping the oil polluted marine environments and the role of indigenous populations or their functional genomics have never been explored from Indian marine environments, post an oil spill event. In the current study, high throughput metagenomic analysis, PLFA profiling and mass spectrophotometric analysis was performed in combination with metabolomics to capture signature variations among the microbial communities in sediment, water and laboratory enrichments. Contrary to the previous reports, the bloom of Pseudomonadales (specifically genus Acinetobacter) in oiled sediment and Methylococcales in oiled water outnumbered the relative abundance of Alcanivorax in response to hydrocarbon contamination. Overall enhancement of xenobiotic degradation was suggested by metabolomic analysis in sediment and water post the spill event and varying quantitative assemblage of enzymes were found to be involved in hydrocarbon utilization. Laboratory enrichments revealed the competitive advantage of sediment communities over the water communities although unique taxa belonging to the later were also found to be enriched under in vitro conditions. Simultaneous analysis of sediment and water in the study provided explicit evidences on existence of differential microbial community dynamics, offering insight into possibilities of formulating nature identical solutions for hydrocarbon pollution.
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Affiliation(s)
- C S Neethu
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India
| | - C Saravanakumar
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India.
| | - R Purvaja
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India.
| | - R S Robin
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India
| | - R Ramesh
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India.
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50
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Tong X, Oh EK, Lee BH, Lee JK. Production of long-chain free fatty acids from metabolically engineered Rhodobacter sphaeroides heterologously producing periplasmic phospholipase A2 in dodecane-overlaid two-phase culture. Microb Cell Fact 2019; 18:20. [PMID: 30704481 PMCID: PMC6357386 DOI: 10.1186/s12934-019-1070-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/22/2019] [Indexed: 12/03/2022] Open
Abstract
Background Long-chain free fatty acids (FFAs) are a type of backbone molecule that can react with alcohol to produce biodiesels. Various microorganisms have become potent producers of FFAs. Efforts have focused on increasing metabolic flux to the synthesis of either neutral fat or fatty acyl intermediates attached to acyl carrier protein (ACP), which are the source of FFAs. Membrane lipids are also a source of FFAs. As an alternative way of producing FFAs, exogenous phospholipase may be used after heterologous production and localization in the periplasmic space. In this work, we examined whether Rhodobacter sphaeroides, which forms an intracytoplasmic membrane, can be used for long-chain FFA production using phospholipase. Results The recombinant R. sphaeroides strain Rs-A2, which heterologously produces Arabidopsis thaliana phospholipase A2 (PLA2) in the periplasm, excretes FFAs during growth. FFA productivity under photoheterotrophic conditions is higher than that observed under aerobic or semiaerobic conditions. When the biosynthetic enzymes for FA (β-ketoacyl-ACP synthase, FabH) and phosphatidate (1-acyl-sn-glycerol-3-phosphate acyltransferase, PlsC) were overproduced in Rs-A2, the FFA productivity of the resulting strain Rs-HCA2 was elevated, and the FFAs produced mainly consisted of long-chain FAs of cis-vaccenate, stearate, and palmitate in an approximately equimolar ratio. The high-cell-density culture of Rs-HCA2 with DMSO in two-phase culture with dodecane resulted in an increase of overall carbon substrate consumption, which subsequently leads to a large increase in FFA productivity of up to 2.0 g L−1 day−1. Overexpression of the genes encoding phosphate acyltransferase (PlsX) and glycerol-3-phosphate acyltransferase (PlsY), which catalyze the biosynthetic steps immediately upstream from PlsC, in Rs-HCA2 generated Rs-HXYCA2, which grew faster than Rs-HCA2 and showed an FFA productivity of 2.8 g L−1 day−1 with an FFA titer of 8.5 g L−1. Conclusion We showed that long-chain FFAs can be produced from metabolically engineered R. sphaeroides heterologously producing PLA2 in the periplasm. The FFA productivity was greatly increased by high-cell-density culture in two-phase culture with dodecane. This approach provides highly competitive productivity of long-chain FFAs by R. sphaeroides compared with other bacteria. This method may be applied to FFA production by other photosynthetic bacteria with similar differentiated membrane systems. Electronic supplementary material The online version of this article (10.1186/s12934-019-1070-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaomeng Tong
- Department of Life Science, Sogang University, Mapo, Shinsu 1, Seoul, 121-742, South Korea
| | - Eun Kyoung Oh
- Department of Life Science, Sogang University, Mapo, Shinsu 1, Seoul, 121-742, South Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Mapo, Shinsu 1, Seoul, 121-742, South Korea
| | - Jeong K Lee
- Department of Life Science, Sogang University, Mapo, Shinsu 1, Seoul, 121-742, South Korea.
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