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Barcia-Cruz R, Balboa S, Lema A, Romalde JL. Comparative genomics of Vibrio toranzoniae strains. RESEARCH SQUARE 2024:rs.3.rs-4360386. [PMID: 38826277 PMCID: PMC11142368 DOI: 10.21203/rs.3.rs-4360386/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade, originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at genome level among strains, as well as to determine their phylogeny. For this purpose, whole genomes were sequenced by different technologies and the resulting sequences corrected. Genomes were annotated and compared with different online tools. Furthermore, the study of core and pan genome was examined, and the phylogeny was inferred. The content of the core genome ranged from 2,953 to 2,766 genes and that of the pangenome from 6,278 to 6,132, depending on the tool used. The comparison revealed that although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI higher than 97%,notable differences were found related to motility, capsule synthesis, iron acquisition system or mobile genetic elements. The phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle, but that of the pangenome pointed out certain geographical isolation in the same growing area. The study led to a reclassification of some isolates formerly described as V. toranzoniae and manifested the importance of cured deposited sequences to proper phylogenetic assignment.
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Leunda-Esnaola A, Bunin E, Arrufat P, Pearman PB, Kaberdin VR. Harnessing the intragenomic variability of rRNA operons to improve differentiation of Vibrio species. Sci Rep 2024; 14:9908. [PMID: 38688963 PMCID: PMC11061105 DOI: 10.1038/s41598-024-60505-9] [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: 07/14/2023] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species, including those in the genus Vibrio. Here, we investigate whether inclusion and analysis of 23S rRNA sequence can help overcome the intrinsic weaknesses of 16S rRNA analyses for the differentiation of Vibrio species. We construct a maximum likelihood 16S rRNA gene tree to assess the use of this gene to identify clades of Vibrio species. Within the 16S rRNA tree, we identify the putative informative bases responsible for polyphyly, and demonstrate the association of these positions with tree topology. We demonstrate that concatenation of 16S and 23S rRNA genes increases the number of informative nucleotide positions, thereby overcoming ambiguities in 16S rRNA-based phylogenetic reconstructions. Finally, we experimentally demonstrate that this approach considerably improves the differentiation and identification of Vibrio species in environmental samples.
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Affiliation(s)
- Amaia Leunda-Esnaola
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Evgeni Bunin
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
- CBET Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
| | - Pablo Arrufat
- Department of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Peter B Pearman
- Department of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain.
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain.
- BC3 Basque Center for Climate Change, Scientific Campus of the University of the Basque Country, 48940, Leioa, Spain.
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain.
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain.
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain.
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Liu Y, Pei T, Du J, Zhu H. Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, Shewanella zhuhaiensis sp. nov., Isolated from a Tidal Flat Sediment. Microorganisms 2023; 11:2870. [PMID: 38138013 PMCID: PMC10745330 DOI: 10.3390/microorganisms11122870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
A new, facultatively anaerobic, light-yellow, and rod-shaped bacterium designated as 3B26T isolated from Qi'ao Island's tidal flat sediment was identified. Strain 3B26T can hydrolyze gelatin, aesculin, and skim milk. The major cellular fatty acids were identified as iso-C15:0, referred to as summed feature 3, and C16:0; the polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and phospholipid; and the quinones contained Q-7, Q-8, MK-7, and MMK7. The genomic size of strain 3B26T was 4,682,650 bp, and its genomic DNA G + C content was 54.8%. While a 16S rRNA gene-based phylogenetic analysis confirmed that strain 3B26T belongs to the genus Shewanella, both phylogenomic inference and genomic comparison revealed that strain 3B26T is distinguishable from its relatives, and digital DNA-DNA hybridization (dDDH) values of 24.4-62.6% and average nucleotide identities (ANIs) of 83.5-95.6% between them were below the 70% dDDH and 96% ANI thresholds for bacterial species delineation. Genomic functional analysis demonstrated that strain 3B26T possesses complete gene clusters of eicosapentaenoic acid biosynthesis and denitrification. Based on the evidence above, strain 3B26T is considered to represent a novel species of the genus Shewanella, and the name Shewanella zhuhaiensis sp. nov. (type strain 3B26T = GDMCC 1.2057T = KCTC 82339T) is proposed.
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Affiliation(s)
| | | | | | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (Y.L.); (T.P.); (J.D.)
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4
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Wei H, He P, Yu D, Liu S, Li C, Qiu D. Characterization of the Positive Transcription Regulator PfaR for Improving Eicosapentaenoic Acid Production in Shewanella putrefaciens W3-18-1. Appl Environ Microbiol 2023; 89:e0002123. [PMID: 36916911 PMCID: PMC10132093 DOI: 10.1128/aem.00021-23] [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: 01/05/2023] [Accepted: 02/17/2023] [Indexed: 03/15/2023] Open
Abstract
The biosynthetic pathway of eicosapentaenoic acid (EPA) has previously been reported in marine bacteria, while the regulatory mechanism remains poorly understood. In this study, a putative transcriptional regulator PfaR encoded adjacent to the PFA biosynthesis gene cluster (pfaEABCD) was computationally and experimentally characterized. Comparative analyses on the wild type (WT) strain, in-frame deletion, and overexpression mutants revealed that PfaR positively regulated EPA synthesis at low temperature. RNA-Seq and real-time quantitative PCR analyses demonstrated that PfaR stimulated the transcription of pfaABCD. The transcription start site of pfaR was mapped by using primer extension and highly conserved promoter motifs bound by the housekeeping Sigma 70 factor that were identified in the upstream of pfaR. Moreover, overexpression of PfaR in WT strain W3-18-1 at low temperature could improve EPA productivity from 0.07% to 0.13% (percentage of EPA to dry weight, mg/mg) of dry weight. Taken together, these findings could provide important implications into the transcriptional control and metabolic engineering in terms of EPA productivity for industrial strains. IMPORTANCE We have experimentally confirmed that PfaR is a positive transcription regulator that promotes EPA synthesis at low temperature in Shewanella putrefaciens W3-18-1. Overexpression of PfaR in WT strain W3-18-1 could lead to a 1.8-fold increase in EPA productivity at low temperature. It is further shown that PfaR may be regulated by housekeeping Sigma 70 factor at low temperature.
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Affiliation(s)
- Hehong Wei
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, China
| | - Penghui He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Dianzhen Yu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
| | - Shuangyuan Liu
- Eco-Environmental Monitoring and Research Center, Pearl River Valley and South China Sea Ecology and Environment Administration, Ministry of Ecology and Environment, Guangzhou, China
| | - Chengtao Li
- College of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, China
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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5
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Functional and Compositional Changes in the Fecal Microbiome of a Shorebird during Migratory Stopover. mSystems 2023; 8:e0112822. [PMID: 36786579 PMCID: PMC10134852 DOI: 10.1128/msystems.01128-22] [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: 02/15/2023] Open
Abstract
Shorebirds migrate long distances twice annually, which requires intense physiological and morphological adaptations, including the ability to rapidly gain weight via fat deposition at stopover locations. The role of the microbiome in weight gain in avian hosts is unresolved, but there is substantial evidence to support the hypothesis that the microbiome is involved with host weight from mammalian microbiome literature. Here, we collected 100 fecal samples of Ruddy Turnstones to investigate microbiome composition and function during stopover weight gain in Delaware Bay, USA. Using 16S rRNA sequencing on 90 of these samples and metatranscriptomic sequencing on 22, we show that taxonomic composition of the microbiome shifts during weight gain, as do functional aspects of the metatranscriptome. We identified 10 genes that are associated with weight class, and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds. IMPORTANCE Many animals migrate long distances annually, and these journeys require intense physiological and morphological adaptations. One such adaptation in shorebirds is the ability to rapidly gain weight at stopover locations in the middle of their migrations. The role of the microbiome in weight gain in birds is unresolved but is likely to play a role. Here, we collected 100 fecal samples from Ruddy Turnstones to investigate microbiome composition (who is there) and function (what they are doing) during stopover weight gain in Delaware Bay, USA. Using multiple molecular methods, we show that both taxonomic composition and function of the microbiome shifts during weight gain. We identified 10 genes that are associated with weight class, and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds.
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Tamby A, Sinninghe Damsté JS, Villanueva L. Microbial membrane lipid adaptations to high hydrostatic pressure in the marine environment. Front Mol Biosci 2023; 9:1058381. [PMID: 36685280 PMCID: PMC9853057 DOI: 10.3389/fmolb.2022.1058381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/29/2022] [Indexed: 01/09/2023] Open
Abstract
The deep-sea is characterized by extreme conditions, such as high hydrostatic pressure (HHP) and near-freezing temperature. Piezophiles, microorganisms adapted to high pressure, have developed key strategies to maintain the integrity of their lipid membrane at these conditions. The abundance of specific membrane lipids, such as those containing unsaturated and branched-chain fatty acids, rises with increasing HHP. Nevertheless, this strategy is not universal among piezophiles, highlighting the need to further understand the effects of HHP on microbial lipid membranes. Challenges in the study of lipid membrane adaptations by piezophiles also involve methodological developments, cross-adaptation studies, and insight into slow-growing piezophiles. Moreover, the effects of HHP on piezophiles are often difficult to disentangle from effects caused by low temperature that are often characteristic of the deep sea. Here, we review the knowledge of membrane lipid adaptation strategies of piezophiles, and put it into the perspective of marine systems, highlighting the future challenges of research studying the effects of HHP on the microbial lipid composition.
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Affiliation(s)
- Anandi Tamby
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands,*Correspondence: Anandi Tamby,
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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Ugwuodo CJ, Colosimo F, Adhikari J, Shen Y, Badireddy AR, Mouser PJ. Salinity and hydraulic retention time induce membrane phospholipid acyl chain remodeling in Halanaerobium congolense WG10 and mixed cultures from hydraulically fractured shale wells. Front Microbiol 2022; 13:1023575. [PMID: 36439785 PMCID: PMC9687094 DOI: 10.3389/fmicb.2022.1023575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2023] Open
Abstract
Bacteria remodel their plasma membrane lipidome to maintain key biophysical attributes in response to ecological disturbances. For Halanaerobium and other anaerobic halotolerant taxa that persist in hydraulically fractured deep subsurface shale reservoirs, salinity, and hydraulic retention time (HRT) are important perturbants of cell membrane structure, yet their effects remain poorly understood. Membrane-linked activities underlie in situ microbial growth kinetics and physiologies which drive biogeochemical reactions in engineered subsurface systems. Hence, we used gas chromatography-mass spectrometry (GC-MS) to investigate the effects of salinity and HRT on the phospholipid fatty acid composition of H. congolense WG10 and mixed enrichment cultures from hydraulically fractured shale wells. We also coupled acyl chain remodeling to membrane mechanics by measuring bilayer elasticity using atomic force microscopy (AFM). For these experiments, cultures were grown in a chemostat vessel operated in continuous flow mode under strict anoxia and constant stirring. Our findings show that salinity and HRT induce significant changes in membrane fatty acid chemistry of H. congolense WG10 in distinct and complementary ways. Notably, under nonoptimal salt concentrations (7% and 20% NaCl), H. congolense WG10 elevates the portion of polyunsaturated fatty acids (PUFAs) in its membrane, and this results in an apparent increase in fluidity (homeoviscous adaptation principle) and thickness. Double bond index (DBI) and mean chain length (MCL) were used as proxies for membrane fluidity and thickness, respectively. These results provide new insight into our understanding of how environmental and engineered factors might disrupt the physical and biogeochemical equilibria of fractured shale by inducing physiologically relevant changes in the membrane fatty acid chemistry of persistent microbial taxa. GRAPHICAL ABSTRACTSalinity significantly alters membrane bilayer fluidity and thickness in Halanaerobium congolense WG10.
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Affiliation(s)
- Chika Jude Ugwuodo
- Natural Resources and Earth Systems Science, University of New Hampshire, Durham, NH, United States
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, United States
| | | | - Jishnu Adhikari
- Sanborn, Head and Associates, Inc., Concord, NH, United States
| | - Yuxiang Shen
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Appala Raju Badireddy
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Paula J. Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, United States
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Wang XY, Xie J. Response to Cold Adaption in Acinetobacter johnsonii XY27 from Spoiled Bigeye Tuna ( Thunnus obesus): Membrane Protein Composition and Protein Biomarker Identification by Proteomics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10000-10010. [PMID: 35919963 DOI: 10.1021/acs.jafc.2c03303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Acinetobacter johnsonii is one of the major food-spoilage bacteria and can survive under cold stress. In this study, the membrane composition, membrane permeability, and energy transduction of A. johnsonii XY27 cultured at 4 and 30 °C were examined comparatively by flow cytometry combined with liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. The Na+/K+ATPase activity, alkaline phosphatase and ATPase activity, fluorescence intensity, and cell viability in A. johnsonii XY27 increased with the decrease in cultivation temperature. The polyunsaturated fatty acid and monounsaturated fatty acids have a higher content in A. johnsonii XY27 cultured at 4 °C compared to that cultured at 30 °C, in which the contents of methyl palmitoleate, methyl myristoleate, and methyl oleate increased dramatically with decreasing temperature. Comparative proteomics analysis revealed that 31 proteins were downregulated and 4 proteins were upregulated, in which catalase-peroxidase 1 and cold shock proteins as biomarker proteins could effectively control A. johnsonii during cold adaptation.
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Affiliation(s)
- Xin-Yun Wang
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai Ocean University, Shanghai 201306, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering Shanghai Ocean University, Shanghai Ocean University, Shanghai 201306, China
- College of Food Science & Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Jing Xie
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai Ocean University, Shanghai 201306, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering Shanghai Ocean University, Shanghai Ocean University, Shanghai 201306, China
- College of Food Science & Technology, Shanghai Ocean University, Shanghai 201306, China
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Shah AM, Yang W, Mohamed H, Zhang Y, Song Y. Microbes: A Hidden Treasure of Polyunsaturated Fatty Acids. Front Nutr 2022; 9:827837. [PMID: 35369055 PMCID: PMC8968027 DOI: 10.3389/fnut.2022.827837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/21/2022] [Indexed: 12/26/2022] Open
Abstract
Microbes have gained a lot of attention for their potential in producing polyunsaturated fatty acids (PUFAs). PUFAs are gaining scientific interest due to their important health-promoting effects on higher organisms including humans. The current sources of PUFAs (animal and plant) have associated limitations that have led to increased interest in microbial PUFAs as most reliable alternative source. The focus is on increasing the product value of existing oleaginous microbes or discovering new microbes by implementing new biotechnological strategies in order to compete with other sources. The multidisciplinary approaches, including metabolic engineering, high-throughput screening, tapping new microbial sources, genome-mining as well as co-culturing and elicitation for the production of PUFAs, have been considered and discussed in this review. The usage of agro-industrial wastes as alternative low-cost substrates in fermentation for high-value single-cell oil production has also been discussed. Multidisciplinary approaches combined with new technologies may help to uncover new microbial PUFA sources that may have nutraceutical and biotechnological importance.
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Affiliation(s)
- Aabid Manzoor Shah
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Wu Yang
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Hassan Mohamed
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Yingtong Zhang
- Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yuanda Song
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
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Jia YL, Geng SS, Du F, Xu YS, Wang LR, Sun XM, Wang QZ, Li Q. Progress of metabolic engineering for the production of eicosapentaenoic acid. Crit Rev Biotechnol 2021; 42:838-855. [PMID: 34779326 DOI: 10.1080/07388551.2021.1971621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Eicosapentaenoic Acid (EPA) is an essential ω-3 polyunsaturated fatty acid for human health. Currently, high-quality EPA production is largely dependent on the extraction of fish oil, but this unsustainable approach cannot meet its rising market demand. Biotechnological approaches for EPA production from microorganisms have received increasing attention due to their suitability for large-scale production and independence of the seasonal or climate restrictions. This review summarizes recent research on different microorganisms capable of producing EPA, such as microalgae, bacteria, and fungi, and introduces the different EPA biosynthesis pathways. Notably, some novel engineering strategies have been applied to endow and improve the abilities of microorganisms to synthesize EPA, including the construction and optimization of the EPA biosynthesis pathway, an increase in the acetyl-CoA pool supply, the increase of NADPH and the inhibition of competing pathways. This review aims to provide an updated summary of EPA production.
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Affiliation(s)
- Yu-Lei Jia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Shan-Shan Geng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Fei Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ying-Shuang Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Qing-Zhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, People's Republic of China
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11
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Clostridium butyricum MIYAIRI 588 Modifies Bacterial Composition under Antibiotic-Induced Dysbiosis for the Activation of Interactions via Lipid Metabolism between the Gut Microbiome and the Host. Biomedicines 2021; 9:biomedicines9081065. [PMID: 34440269 PMCID: PMC8391242 DOI: 10.3390/biomedicines9081065] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is closely related to gut metabolic functions, and the gut microbiome and host metabolic functions affect each other. Clostridium butyricum MIYAIRI 588 (CBM 588) upregulates protectin D1 production in host colon tissue following G protein-coupled receptor (GPR) 120 activation to protect gut epithelial cells under antibiotic-induced dysbiosis. However, how CBM 588 enhances polyunsaturated fatty acid (PUFA) metabolites remains unclear. Therefore, we focused on the metabolic function alterations of the gut microbiome after CBM 588 and protectin D1 administration to reveal the interaction between the host and gut microbiome through lipid metabolism during antibiotic-induced dysbiosis. Consequently, CBM 588 modified gut microbiome and increased the butyric acid and oleic acid content. These lipid metabolic modifications induced GPR activation, which is a trigger of ERK 1/2 signaling and directed differentiation of downstream immune cells in the host colon tissue. Moreover, endogenous protectin D1 modified the gut microbiome, similar to CBM 588. This is the first study to report that CBM 588 influences the interrelationship between colon tissue and the gut microbiome through lipid metabolism. These findings provide insights into the mechanisms of prevention and recovery from inflammation and the improvement of host metabolism by CBM 588.
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12
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Jovanovic S, Dietrich D, Becker J, Kohlstedt M, Wittmann C. Microbial production of polyunsaturated fatty acids - high-value ingredients for aquafeed, superfoods, and pharmaceuticals. Curr Opin Biotechnol 2021; 69:199-211. [PMID: 33540327 DOI: 10.1016/j.copbio.2021.01.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 01/01/2021] [Accepted: 01/10/2021] [Indexed: 12/26/2022]
Abstract
Polyunsaturated fatty acids (PUFAs), primarily docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), have received worldwide attention in recent years due to an increasing awareness of their uniqueness in improving diet and human health and their apparently inevitable shortage in global availability. Microbial cell factories are a major solution to supplying these precious molecules in sufficient amounts and providing PUFA-rich aquafeed, superfoods, and medical formulations. This review assesses the PUFA world markets and highlights recent advances in upgrading and streamlining microalgae, yeasts, fungi, and bacteria for high-level PUFA production and broadening of the PUFA spectrum.
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Affiliation(s)
- Sofija Jovanovic
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Demian Dietrich
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany.
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13
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Cavan EL, Kawaguchi S, Boyd PW. Implications for the mesopelagic microbial gardening hypothesis as determined by experimental fragmentation of Antarctic krill fecal pellets. Ecol Evol 2021; 11:1023-1036. [PMID: 33520184 PMCID: PMC7820144 DOI: 10.1002/ece3.7119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/08/2020] [Accepted: 11/12/2020] [Indexed: 11/26/2022] Open
Abstract
Detritivores need to upgrade their food to increase its nutritional value. One method is to fragment detritus promoting the colonization of nutrient-rich microbes, which consumers then ingest along with the detritus; so-called microbial gardening. Observations and numerical models of the detritus-dominated ocean mesopelagic zone have suggested microbial gardening by zooplankton is a fundamental process in the ocean carbon cycle leading to increased respiration of carbon-rich detritus. However, no experimental evidence exists to demonstrate that microbial respiration rates are higher on recently fragmented sinking detrital particles.Using aquaria-reared Antarctic krill fecal pellets, we showed fragmentation increased microbial particulate organic carbon (POC) turnover by 1.9×, but only on brown fecal pellets, formed from the consumption of other pellets. Microbial POC turnover on un- and fragmented green fecal pellets, formed from consuming fresh phytoplankton, was equal. Thus, POC content, fragmentation, and potentially nutritional value together drive POC turnover rates.Mesopelagic microbial gardening could be a risky strategy, as the dominant detrital food source is settling particles; even though fragmentation decreases particle size and sinking rate, it is unlikely that an organism would remain with the particle long enough to nutritionally benefit from attached microbes. We propose "communal gardening" occurs whereby additional mesopelagic organisms nearby or below the site of fragmentation consume the particle and the colonized microbes.To determine how fragmentation impacts the remineralization of sinking carbon-rich detritus and to parameterize microbial gardening in mesopelagic carbon models, three key metrics from further controlled experiments and observations are needed; how particle composition (here, pellet color/krill diet) impacts the response of microbes to the fragmentation of particles; the nutritional benefit to zooplankton from ingesting microbes after fragmentation along with identification of which essential nutrients are being targeted; how both these factors vary between physical (shear) and biological particle fragmentation.
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Affiliation(s)
- Emma L. Cavan
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaBattery PointTASAustralia
- Department of Life Sciences, Silwood Park CampusImperial College LondonAscotUK
| | - So Kawaguchi
- Australian Antarctic DivisionKingstonTASAustralia
| | - Philip W. Boyd
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaBattery PointTASAustralia
- Antarctic Climate and Ecosystems CRCUniversity of TasmaniaBattery PointTASAustralia
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14
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Tommonaro G, El-Hagrassi AM, Fayad W, Iodice C, Shaker KH, EL-Hady FKA. Fatty Acid Profile and In Vitro Anticancer Activity of Two Marine Sponge- Associated Bacteria. CURRENT BIOACTIVE COMPOUNDS 2020; 16:1273-1280. [DOI: 10.2174/1573407216666200214095114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 09/02/2023]
Abstract
Background:
Colorectal cancer represents one of the prominent causes of mortality worldwide
in men and women. The objective of this study was to search for new potential anticancer compounds,
both in prevention and treatment of colorectal cancer. The anticancer potential of marine bacterial
extracts against Human colorectal carcinoma cell line (HCT116) was evaluated as well as the partial
identification of bioactive metabolites.
Methods:
All bacterial extracts were tested for their cytotoxicity against HCT116 cell line by means of
MTT assay. The highly cytotoxic dichloromethane extracts of marine sponge-associated bacteria Vibrio
sp. and Bacillus sp. were analyzed by GC-MS.
Results:
Two fractions, Vib3 and Bac3, exhibited a very interesting cytotoxicity against human colorectal
carcinoma (HCT116) cell line, with a percentage of cytotoxicity of 96.04 % and 29.48 %, respectively.
Discussion:
The GC-MS analysis revealed the presence of two major fatty acids, palmitic and oleic
acids, in Vib3 fraction and fatty acid esters and phenolic compounds in Bac3 fraction.
Conclusion:
Based on previous literature, it may be hypothesized that the anticancer activity of
bacterial extracts could be, at least partially, to the fatty acids fraction.
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Affiliation(s)
- Giuseppina Tommonaro
- National Research Council of Italy (CNR), Institute of Biomolecular Chemistry, Via Campi Flegrei, 34 - 80078, Pozzuoli, Italy
| | - Ali M. El-Hagrassi
- Phytochemistry and Plant Systematics Department, National Research Centre, Giza, Egypt
| | - Walid Fayad
- Drug Bioassay- Cell Culture Laboratory, Pharmacognosy Department, National Research Centre, Giza, Egypt
| | - Carmine Iodice
- National Research Council of Italy (CNR), Institute of Biomolecular Chemistry, Via Campi Flegrei, 34 - 80078, Pozzuoli, Italy
| | - Kamel H. Shaker
- Chemistry of Natural Compounds Department, National Research Centre, Giza, Egypt
| | - Faten K. Abd EL-Hady
- Chemistry of Natural and Microbial Products Department, National Research Centre, Giza, Egypt
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15
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Nachtschatt M, Okada S, Speight R. Integral Membrane Fatty Acid Desaturases: A Review of Biochemical, Structural, and Biotechnological Advances. EUR J LIPID SCI TECH 2020. [DOI: 10.1002/ejlt.202000181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthias Nachtschatt
- Commonwealth Scientific and Industrial Research Organisation Clunies Ross St. Canberra ACT 2601 Australia
- Queensland University of Technology 2 George St. Brisbane QLD 4000 Australia
| | - Shoko Okada
- Commonwealth Scientific and Industrial Research Organisation Clunies Ross St. Canberra ACT 2601 Australia
| | - Robert Speight
- Queensland University of Technology 2 George St. Brisbane QLD 4000 Australia
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16
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Wang S, Lan C, Wang Z, Wan W, Zhang H, Cui Q, Song X. Optimizing Eicosapentaenoic Acid Production by Grafting a Heterologous Polyketide Synthase Pathway in the Thraustochytrid Aurantiochytrium. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11253-11260. [PMID: 32829640 DOI: 10.1021/acs.jafc.0c04299] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Eicosapentaenoic acid (EPA) is an essential nutritional supplement for human health. The most prominent dietary source of EPA is fish oil, which is unsustainable because of the decline in fishery resources and serious environmental pollution. Alternatively, a heterologous polyketide synthase pathway for EPA biosynthesis was assembled in Thraustochytrid Aurantiochytrium. A 2A peptide-based facile assembly platform that can achieve multigene expression as a polycistron was first established. The platform was then applied to express the EPA biosynthetic gene cluster from Shewanella japonica in Aurantiochytrium. In the shake flask fermentation, the lipid and PUFA yields of the mutant were increased by 26.9 and 36.0%, respectively, and led to about 5-fold increase of the EPA yield. The final EPA titer reached 2.7 g/L in fed-batch fermentation. This study provides a novel metabolic engineering strategy to regulate the EPA ratio in microalgal oil for human nutritional supplementation.
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Affiliation(s)
- Sen Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
| | - Chuanzeng Lan
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuojun Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijian Wan
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
| | - Huidan Zhang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
| | - Xiaojin Song
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
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17
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Wang S, Lan C, Wang Z, Wan W, Cui Q, Song X. PUFA-synthase-specific PPTase enhanced the polyunsaturated fatty acid biosynthesis via the polyketide synthase pathway in Aurantiochytrium. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:152. [PMID: 32874202 PMCID: PMC7457351 DOI: 10.1186/s13068-020-01793-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/22/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Phosphopantetheinyl transferase (PPTase) can change the acyl-carrier protein (ACP) from an inactive apo-ACP to an active holo-ACP that plays a key role in fatty acids biosynthesis. Currently, the PPTase has been proved to be involved in the biosynthesis of polyunsaturated fatty acids (PUFAs) via a polyketide synthase (PKS) pathway in Thraustochytrids, while its characteristics are not clarified. RESULTS Here, the heterologous PPTase gene (pfaE) from bacteria was first co-expressed with the PKS system (orfA-orfC) from Thraustochytrid Aurantiochytrium. Then, a new endogenous PPTase (ppt_a) in Aurantiochytrium was identified by homologous alignment and its function was verified in E. coli. Moreover, the endogenous ppt_a was then overexpressed in Aurantiochytrium, and results showed that the production and proportion of PUFAs, especially docosahexaenoic acid (DHA), in the transformant SD116::PPT_A were increased by 35.5% and 17.6%, respectively. Finally, higher DHA and PUFA proportion (53.9% and 64.5% of TFA, respectively) were obtained in SD116::PPT_A using a cerulenin feeding strategy. CONCLUSIONS This study has illustrated a PUFAs-synthase-specific PPTase in PKS system and provided a new strategy to improve the PUFA production in Thraustochytrids.
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Affiliation(s)
- Sen Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 Shandong China
| | - Chuanzeng Lan
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhuojun Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Weijian Wan
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 Shandong China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 Shandong China
| | - Xiaojin Song
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 Shandong China
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18
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Romano R, Raddadi N, Fava F. Mediterranean Sea bacteria as a potential source of long-chain polyunsaturated fatty acids. FEMS Microbiol Lett 2020; 367:5884861. [PMID: 32766759 DOI: 10.1093/femsle/fnaa132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/05/2020] [Indexed: 12/26/2022] Open
Abstract
Long-chain polyunsaturated fatty acids (LC-PUFAs), including EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid) are important nutritional ingredients in fish feed. So far, fish oil has been used as a main source of LC-PUFAs; however, the limited global supply of fish oil is not able to meet the demand of the growing aquaculture sector. Hence, sustainability of aquaculture industry could be supported by searching alternative sources of these compounds. Marine microorganisms represent a sustainable and stable supply source of LC-PUFAs. A collection of 209 bacterial isolates obtained from sediment samples recovered in the Mediterranean Sea was screened in order to select new LC-PUFAs producers. Among 95 putative producers selected based on colourimetric screening, 31 quickly growing were selected for further studies. The detection of LC-PUFAs was confirmed from 15 isolates belonging to the genera Marinobacter, Halomonas and Thalassospira by GC-FID analysis. Among them, the isolate Marinobacter sp. G16.20 was found to be a potentially high LC-PUFA producer exhibiting relatively high levels of DHA in particular (maximum productivity of 1.85 ± 0.371 mg/g, representing 45.89% of the total fatty acids detected and identified). Microorganisms belonging to the genera reported in this study showed biotechnological traits interesting for their potential future application in aquaculture.
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Affiliation(s)
- Roberta Romano
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Noura Raddadi
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Fabio Fava
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, Via Terracini 28, 40131 Bologna, Italy
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19
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Blevins MS, James VK, Herrera CM, Purcell AB, Trent MS, Brodbelt JS. Unsaturation Elements and Other Modifications of Phospholipids in Bacteria: New Insight from Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2020; 92:9146-9155. [PMID: 32479092 PMCID: PMC7384744 DOI: 10.1021/acs.analchem.0c01449] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Glycerophospholipids (GPLs), one of the main components of bacterial cell membranes, exhibit high levels of structural complexity that are directly correlated with biophysical membrane properties such as permeability and fluidity. This structural complexity arises from the substantial variability in the individual GPL structural components such as the acyl chain length and headgroup type and is further amplified by the presence of modifications such as double bonds and cyclopropane rings. Here we use liquid chromatography coupled to high-resolution and high-mass-accuracy ultraviolet photodissociation mass spectrometry for the most in-depth study of bacterial GPL modifications to date. In doing so, we unravel a diverse array of unexplored GPL modifications, ranging from acyl chain hydroxyl groups to novel headgroup structures. Along with characterizing these modifications, we elucidate general trends in bacterial GPL unsaturation elements and thus aim to decipher some of the biochemical pathways of unsaturation incorporation in bacterial GPLs. Finally, we discover aminoacyl-PGs not only in Gram-positive bacteria but also in Gram-negative C. jejuni, advancing our knowledge of the methods of surface charge modulation that Gram-negative organisms may adopt for antibiotic resistance.
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Affiliation(s)
- Molly S Blevins
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Virginia K James
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carmen M Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - Alexandria B Purcell
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - M Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
- Department of Microbiology, College of Arts and Sciences, University of Georgia, Athens, Georgia 30602, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia 30602, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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20
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Role of acyl-CoA dehydrogenases from Shewanella livingstonensis Ac10 in docosahexaenoic acid conversion. Biochem Biophys Res Commun 2020; 528:453-458. [DOI: 10.1016/j.bbrc.2020.05.185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/25/2020] [Indexed: 11/21/2022]
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21
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Estupiñán M, Hernández I, Saitua E, Bilbao ME, Mendibil I, Ferrer J, Alonso-Sáez L. Novel Vibrio spp. Strains Producing Omega-3 Fatty Acids Isolated from Coastal Seawater. Mar Drugs 2020; 18:E99. [PMID: 32024040 PMCID: PMC7074563 DOI: 10.3390/md18020099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/26/2022] Open
Abstract
Omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs), such as eicosapentaenoic acid (EPA) (20:5n-3) and docosahexaenoic acid (DHA) (22:6n-3), are considered essential for human health. Microorganisms are the primary producers of omega-3 fatty acids in marine ecosystems, representing a sustainable source of these lipids, as an alternative to the fish industry. Some marine bacteria can produce LC-PUFAs de novo via the Polyunsaturated Fatty Acid (Pfa) synthase/ Polyketide Synthase (PKS) pathway, which does not require desaturation and elongation of saturated fatty acids. Cultivation-independent surveys have revealed that the diversity of microorganisms harboring a molecular marker of the pfa gene cluster (i.e., pfaA-KS domain) is high and their potential distribution in marine systems is widespread, from surface seawater to sediments. However, the isolation of PUFA producers from marine waters has been typically restricted to deep or cold environments. Here, we report a phenotypic and genotypic screening for the identification of omega-3 fatty acid producers in free-living bacterial strains isolated from 5, 500, and 1000 m deep coastal seawater from the Bay of Biscay (Spain). We further measured EPA production in pelagic Vibrio sp. strains collected at the three different depths. Vibrio sp. EPA-producers and non-producers were simultaneously isolated from the same water samples and shared a high percentage of identity in their 16S rRNA genes, supporting the view that the pfa gene cluster can be horizontally transferred. Within a cluster of EPA-producers, we found intraspecific variation in the levels of EPA synthesis for isolates harboring different genetic variants of the pfaA-KS domain. The maximum production of EPA was found in a Vibrio sp. strain isolated from a 1000 m depth (average 4.29% ± 1.07 of total fatty acids at 10 °C, without any optimization of culturing conditions).
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Affiliation(s)
- Mónica Estupiñán
- AZTI, Marine Research Division, Txatxarramendi Irla s/n, 48395 Sukarrieta, Spain; (M.E.); (M.E.B.); (I.M.)
| | - Igor Hernández
- AZTI, Food Research Division, Astondo Bidea, Building 609, 48160 Derio, Spain; (I.H.); (E.S.); (J.F.)
| | - Eduardo Saitua
- AZTI, Food Research Division, Astondo Bidea, Building 609, 48160 Derio, Spain; (I.H.); (E.S.); (J.F.)
| | - M. Elisabete Bilbao
- AZTI, Marine Research Division, Txatxarramendi Irla s/n, 48395 Sukarrieta, Spain; (M.E.); (M.E.B.); (I.M.)
| | - Iñaki Mendibil
- AZTI, Marine Research Division, Txatxarramendi Irla s/n, 48395 Sukarrieta, Spain; (M.E.); (M.E.B.); (I.M.)
| | - Jorge Ferrer
- AZTI, Food Research Division, Astondo Bidea, Building 609, 48160 Derio, Spain; (I.H.); (E.S.); (J.F.)
| | - Laura Alonso-Sáez
- AZTI, Marine Research Division, Txatxarramendi Irla s/n, 48395 Sukarrieta, Spain; (M.E.); (M.E.B.); (I.M.)
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22
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Complete Genome Sequence of the Deep-Sea Bacterium Moritella marina MP-1 (ATCC 15381). Microbiol Resour Announc 2020; 9:9/4/e01321-19. [PMID: 31974151 PMCID: PMC6979300 DOI: 10.1128/mra.01321-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, the complete assembly of the
Moritella marina
MP-1 (ATCC 15381) genome, combining Illumina and long Nanopore reads, is presented. The gapless assembly consists of a 4.7-Mb circular chromosome and a 26-kb plasmid, with a G+C content of 40.7%, and will assist in further studies of the molecular pathways in this biotechnologically significant organism.
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23
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Roslan NN, Ngalimat MS, Leow ATC, Oslan SN, Baharum SN, Sabri S. Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15. Microbiol Res 2020; 233:126410. [PMID: 31945517 DOI: 10.1016/j.micres.2020.126410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/29/2019] [Accepted: 01/09/2020] [Indexed: 11/18/2022]
Abstract
Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15.
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Affiliation(s)
- Noordiyanah Nadhirah Roslan
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohamad Syazwan Ngalimat
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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24
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Lemaire ON, Méjean V, Iobbi-Nivol C. The Shewanella genus: ubiquitous organisms sustaining and preserving aquatic ecosystems. FEMS Microbiol Rev 2020; 44:155-170. [DOI: 10.1093/femsre/fuz031] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
ABSTRACT
The Gram-negative Shewanella bacterial genus currently includes about 70 species of mostly aquatic γ-proteobacteria, which were isolated around the globe in a multitude of environments such as surface freshwater and the deepest marine trenches. Their survival in such a wide range of ecological niches is due to their impressive physiological and respiratory versatility. Some strains are among the organisms with the highest number of respiratory systems, depending on a complex and rich metabolic network. Implicated in the recycling of organic and inorganic matter, they are important components of organism-rich oxic/anoxic interfaces, but they also belong to the microflora of a broad group of eukaryotes from metazoans to green algae. Examples of long-term biological interactions like mutualism or pathogeny have been described, although molecular determinants of such symbioses are still poorly understood. Some of these bacteria are key organisms for various biotechnological applications, especially the bioremediation of hydrocarbons and metallic pollutants. The natural ability of these prokaryotes to thrive and detoxify deleterious compounds explains their use in wastewater treatment, their use in energy generation by microbial fuel cells and their importance for resilience of aquatic ecosystems.
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Affiliation(s)
- Olivier N Lemaire
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402 Marseille, France
| | - Vincent Méjean
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402 Marseille, France
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402 Marseille, France
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Sekova VY, Dergacheva DI, Isakova EP, Gessler NN, Tereshina VM, Deryabina YI. Soluble Sugar and Lipid Readjustments in the Yarrowia lipolytica Yeast at Various Temperatures and pH. Metabolites 2019; 9:metabo9120307. [PMID: 31861165 PMCID: PMC6950712 DOI: 10.3390/metabo9120307] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Microorganisms cope with a wide range of environmental challenges using different mechanisms. Their ability to prosper at extreme ambient pH and high temperatures has been well reported, but the adaptation mechanism often remains unrevealed. In this study, we addressed the dynamics of lipid and sugar profiles upon different cultivation conditions. The results showed that the cells grown at various pH and optimal temperature contained mannitol as the major cytosol sugar alcohol. The elevated temperature of 38 °C led to a two- to three-fold increase in total cytosol sugars with concurrent substitution of mannitol for trehalose. Lipid composition in the cells at optimal temperature changed insignificantly at any pH tested. The increase in the temperature caused some drop in the storage and membrane lipid levels, remarkable changes in their composition, and the degree of unsaturated fatty acids. It was shown that the fatty acid composition of some membrane phospholipids varied considerably at changing pH and temperature values. The data showed a pivotal role and flexibility of the sugar and lipid composition of Y. lipolytica W29 in adaptation to unfavorable environmental conditions.
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Affiliation(s)
- Varvara Yu Sekova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, bld 33-2, Leninsly Prospect, Moscow 119071, Russia; (D.I.D.); (N.N.G.); (Y.I.D.)
- Correspondence: (V.Y.S.); (E.P.I.)
| | - Daria I. Dergacheva
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, bld 33-2, Leninsly Prospect, Moscow 119071, Russia; (D.I.D.); (N.N.G.); (Y.I.D.)
| | - Elena P. Isakova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, bld 33-2, Leninsly Prospect, Moscow 119071, Russia; (D.I.D.); (N.N.G.); (Y.I.D.)
- Correspondence: (V.Y.S.); (E.P.I.)
| | - Natalya N. Gessler
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, bld 33-2, Leninsly Prospect, Moscow 119071, Russia; (D.I.D.); (N.N.G.); (Y.I.D.)
| | - Vera M. Tereshina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia;
| | - Yulia I. Deryabina
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, bld 33-2, Leninsly Prospect, Moscow 119071, Russia; (D.I.D.); (N.N.G.); (Y.I.D.)
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Lee-Sarwar KA, Kelly RS, Lasky-Su J, Zeiger RS, O'Connor GT, Sandel MT, Bacharier LB, Beigelman A, Laranjo N, Gold DR, Weiss ST, Litonjua AA. Integrative analysis of the intestinal metabolome of childhood asthma. J Allergy Clin Immunol 2019; 144:442-454. [PMID: 30914378 DOI: 10.1016/j.jaci.2019.02.032] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/14/2019] [Accepted: 02/20/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND The intestinal metabolome reflects the biological consequences of diverse exposures and might provide insight into asthma pathophysiology. OBJECTIVE We sought to perform an untargeted integrative analysis of the intestinal metabolome of childhood asthma in this ancillary study of the Vitamin D Antenatal Asthma Reduction Trial. METHODS Metabolomic profiling was performed by using mass spectrometry on fecal samples collected from 361 three-year-old subjects. Adjusted logistic regression analyses identified metabolites and modules of highly correlated metabolites associated with asthma diagnosis by age 3 years. Sparse canonical correlation analysis identified associations relevant to asthma between the intestinal metabolome and other "omics": the intestinal microbiome as measured by using 16S rRNA sequencing, the plasma metabolome as measured by using mass spectrometry, and diet as measured by using food frequency questionnaires. RESULTS Several intestinal metabolites were associated with asthma at age 3 years, including inverse associations between asthma and polyunsaturated fatty acids (adjusted logistic regression β = -6.3; 95% CI, -11.3 to -1.4; P = .01) and other lipids. Asthma-associated intestinal metabolites were significant mediators of the inverse relationship between exclusive breast-feeding for the first 4 months of life and asthma (P for indirect association = .04) and the positive association between a diet rich in meats and asthma (P = .03). Specific intestinal bacterial taxa, including the family Christensenellaceae, and plasma metabolites, including γ-tocopherol/β-tocopherol, were positively associated with asthma and asthma-associated intestinal metabolites. CONCLUSION Integrative analyses revealed significant interrelationships between the intestinal metabolome and the intestinal microbiome, plasma metabolome, and diet in association with childhood asthma. These findings require replication in future studies.
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Affiliation(s)
- Kathleen A Lee-Sarwar
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Robert S Zeiger
- Departments of Allergy and Research and Evaluation, Kaiser Permanente Southern California, San Diego and Pasadena, Calif
| | - George T O'Connor
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Mass
| | - Megan T Sandel
- Department of Pediatrics, Boston Medical Center, Boston, Mass
| | - Leonard B Bacharier
- Division of Pediatric Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, and St Louis Children's Hospital, St Louis, Mo
| | - Avraham Beigelman
- Division of Pediatric Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, and St Louis Children's Hospital, St Louis, Mo
| | - Nancy Laranjo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Diane R Gold
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Augusto A Litonjua
- Division of Pediatric Pulmonary Medicine, Golisano Children's Hospital at Strong, University of Rochester Medical Center, Rochester, NY.
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Li H, Ma L, Hu Z, Tu Y, Jiang C, Wu Q, Han J, Zeng B, He B. Heterologous expression of AoD9D enhances salt tolerance with increased accumulation of unsaturated fatty acid in transgenic Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2019; 46:231-239. [PMID: 30604237 DOI: 10.1007/s10295-018-02123-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022]
Abstract
Salt stress can trigger several physiological responses in microorganisms such as the increasing accumulation of unsaturated fatty acid, which was biosynthesized by delta-9 fatty acid desaturases (D9D) at the first step. In the present study, two D9D genes, designated AoD9D1 and AoD9D2, were isolated from Aspergillus oryzae. The expression analysis showed that AoD9D1 and AoD9D2 were upregulated under salt stress. To investigate the function of AoD9D, transgenic Saccharomyces cerevisiae strains that heterologously expressed AoD9D were exposed to salinity condition. These transgenic strains exhibited greater tolerance to salt stress than wild-type strains, and the heterologous expression of AoD9D increased the content in unsaturated fatty acids as compared to control cells. Moreover, AoD9D1 and AoD9D2 both contained fatty acid desaturase (FAD) and cytochrome b5-like Heme/Steroid-binding domains (Cyt-b5). S. cerevisiae separately transformed with the gene fragments coding for the FAD and Cyt-b5 domains in the AoD9D1 protein grew better and accumulated a higher concentration of unsaturated FAs than the control. Altogether, the heterologous expression of AoD9D enhanced the tolerance of transgenic S. cerevisiae to high salinity stress with increased accumulation of unsaturated fatty acid. The results provide some practical basis for the successful development of salt-tolerant fermentation microorganisms.
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Affiliation(s)
- Haoran Li
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Long Ma
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Zhihong Hu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Qinqin Wu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Jizhong Han
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
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Cordova LT, Alper HS. Production of α-linolenic acid in Yarrowia lipolytica using low-temperature fermentation. Appl Microbiol Biotechnol 2018; 102:8809-8816. [DOI: 10.1007/s00253-018-9349-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 08/16/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
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