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Wang H, Xiang Z. Structural insights into type III polyketide synthase CylI from cylindrocyclophane biosynthesis. Protein Sci 2024; 33:e5130. [PMID: 39302095 PMCID: PMC11413912 DOI: 10.1002/pro.5130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/06/2024] [Accepted: 07/14/2024] [Indexed: 09/22/2024]
Abstract
Type III polyketide synthases (PKSs) catalyze the formation of a variety of polyketide natural products with remarkable structural diversity and biological activities. Despite significant progress in structural and mechanistic studies of type III PKSs in bacteria, fungi, and plants, research on type III PKSs in cyanobacteria is lacking. Here, we report structural and mechanistic insights into CylI, a type III PKS that catalyzes the formation of the alkylresorcinol intermediate in cylindrocyclophane biosynthesis. The crystal structure of apo-CylI reveals a distinct arrangement of structural elements that are proximal to the active site. We further solved the crystal structures of CylI in complexes with two substrate analogues at resolutions of 1.9 Å. The complex structures indicate that N259 is the key residue that determines the substrate preference of CylI. We also solved the crystal structure of CylI complexed with the alkylresorcinol product at a resolution of 2.0 Å. Structural analysis and mutagenesis experiments suggested that S170 functions as a key residue that determines cyclization specificity. On the basis of this result, a double mutant was engineered to completely switch the cyclization of CylI from aldol condensation to lactonization. This work elucidates the molecular basis of type III PKS in cyanobacteria and lays the foundation for engineering CylI-like enzymes to generate new products.
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Affiliation(s)
- Hua‐Qi Wang
- State Key Laboratory of Chemical Oncogenomics, Shenzhen Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhenPR China
| | - Zheng Xiang
- State Key Laboratory of Chemical Oncogenomics, Shenzhen Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhenPR China
- Institute of Chemical Biology, Shenzhen Bay LaboratoryGaoke Innovation CenterShenzhenPR China
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2
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Grabski M, Gawor J, Cegłowska M, Gromadka R, Mazur-Marzec H, Węgrzyn G. Genome Mining of Pseudanabaena galeata CCNP1313 Indicates a New Scope in the Search for Antiproliferative and Antiviral Agents. Microorganisms 2024; 12:1628. [PMID: 39203471 PMCID: PMC11356792 DOI: 10.3390/microorganisms12081628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
Compounds derived from natural sources pave the way for novel drug development. Cyanobacteria is an ubiquitous phylum found in various habitats. The fitness of those microorganisms, within different biotopes, is partially dependent on secondary metabolite production. Their enhanced production under biotic/abiotic stress factors accounts for better survival rates of cells, and thereby cyanobacteria are as an enticing source of bioactive compounds. Previous studies have shown the potent activity of extracts and fractions from Pseudanabaena galeata (Böcher 1949) strain CCNP1313 against cancer cells and viruses. However, active agents remain unknown, as the selected peptides had no effect on the tested cell lines. Here, we present a bottom-up approach, pinpointing key structures involved in secondary metabolite production. Consisting of six replicons, a complete genome sequence of P. galeata strain CCNP1313 was found to carry genes for non-ribosomal peptide/polyketide synthetases embedded within chromosome spans (4.9 Mbp) and for a ribosomally synthesized peptide located on one of the plasmids (0.2 Mbp). Elucidation of metabolite synthesis pathways led to prediction of their structure. While none of the synthesis-predicted products were found in mass spectrometry analysis, unexplored synthetases are characterized by structural similarities to those producing potent bioactive compounds.
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Affiliation(s)
- Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland;
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822 Gdańsk, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Marta Cegłowska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland;
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Hanna Mazur-Marzec
- Department of Marine Biology and Biotechnology, University of Gdansk, Piłsudskiego 46, 81-378 Gdynia, Poland;
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
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3
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Yancey CE, Hart L, Hefferan S, Mohamed OG, Newmister SA, Tripathi A, Sherman DH, Dick GJ. Metabologenomics reveals strain-level genetic and chemical diversity of Microcystis secondary metabolism. mSystems 2024; 9:e0033424. [PMID: 38916306 PMCID: PMC11264947 DOI: 10.1128/msystems.00334-24] [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: 03/08/2024] [Accepted: 04/22/2024] [Indexed: 06/26/2024] Open
Abstract
Microcystis spp. are renowned for producing the hepatotoxin microcystin in freshwater cyanobacterial harmful algal blooms around the world, threatening drinking water supplies and public and environmental health. However, Microcystis genomes also harbor numerous biosynthetic gene clusters (BGCs) encoding the biosynthesis of other secondary metabolites, including many with toxic properties. Most of these BGCs are uncharacterized and currently lack links to biosynthesis products. However, recent field studies show that many of these BGCs are abundant and transcriptionally active in natural communities, suggesting potentially important yet unknown roles in bloom ecology and water quality. Here, we analyzed 21 xenic Microcystis cultures isolated from western Lake Erie to investigate the diversity of the biosynthetic potential of this genus. Through metabologenomic and in silico approaches, we show that these Microcystis strains contain variable BGCs, previously observed in natural populations, and encode distinct metabolomes across cultures. Additionally, we find that the majority of metabolites and gene clusters are uncharacterized, highlighting our limited understanding of the chemical repertoire of Microcystis spp. Due to the complex metabolomes observed in culture, which contain a wealth of diverse congeners as well as unknown metabolites, these results underscore the need to deeply explore and identify secondary metabolites produced by Microcystis beyond microcystins to assess their impacts on human and environmental health.IMPORTANCEThe genus Microcystis forms dense cyanobacterial harmful algal blooms (cyanoHABs) and can produce the toxin microcystin, which has been responsible for drinking water crises around the world. While microcystins are of great concern, Microcystis also produces an abundance of other secondary metabolites that may be of interest due to their potential for toxicity, ecological importance, or pharmaceutical applications. In this study, we combine genomic and metabolomic approaches to study the genes responsible for the biosynthesis of secondary metabolites as well as the chemical diversity of produced metabolites in Microcystis strains from the Western Lake Erie Culture Collection. This unique collection comprises Microcystis strains that were directly isolated from western Lake Erie, which experiences substantial cyanoHAB events annually and has had negative impacts on drinking water, tourism, and industry.
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Affiliation(s)
- Colleen E. Yancey
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Lauren Hart
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Sierra Hefferan
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology, and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Osama G. Mohamed
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Sean A. Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology, and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
- Cooperative Institute for Great Lakes Research (CIGLR), School for Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
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4
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Tan RY, Ilham Z, Wan-Mohtar WAAQI, Abdul Halim-Lim S, Ahmad Usuldin SR, Ahmad R, Adlim M. Mushroom oils: A review of their production, composition, and potential applications. Heliyon 2024; 10:e31594. [PMID: 38845934 PMCID: PMC11153096 DOI: 10.1016/j.heliyon.2024.e31594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
This review delves into the world of mushroom oils, highlighting their production, composition, and versatile applications. Despite mushrooms' overall low lipid content, their fatty acid composition, rich in essential fatty acids like linoleic acid and oleic acid, proves nutritionally significant. Variations in fatty acid profiles across mushroom species and the prevalence of unsaturated fats contribute to their cardiovascular health benefits. The exploration extends to mushroom essential oils, revealing diverse volatile compounds through extraction methods like hydrodistillation and solvent-assisted flavor evaporation (SAFE). The identification of 1-octen-3-ol as a key contributor to the distinct "mushroom flavor" adds a nuanced perspective. The focus broadens to applications, encompassing culinary and industrial uses with techniques like cold pressing and supercritical fluid extraction (SFE). Mushroom oils, with their unique nutritional and flavor profiles, enhance gastronomic experiences. Non-food applications in cosmetics and biofuels underscore the oils' versatility. The nutritional composition, enriched with essential fatty acids, bioactive compositions, and trace elements, is explored for potential health benefits. Bioactive compounds such as phenolic compounds and terpenes contribute to antioxidant and anti-inflammatory properties, positioning mushroom oils as nutritional powerhouses. In short, this concise review synthesizes the intricate world of mushroom oils, emphasizing their nutritional significance, extraction methodologies, and potential health benefits. The comprehensive overview underscores mushroom oils as a promising area for further exploration and utilization. The characteristics of mushroom biomass oil for the use in various industries are influenced by the mushroom species, chemical composition, biochemical synthesis of mushroom, and downstream processes including extraction, purification and characterization. Therefore, further research and exploration need to be done to achieve a circular bioeconomy with the integration of SDGs, waste reduction, and economic stimulation, to fully utilize the benefits of mushroom, a valuable gift of nature.
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Affiliation(s)
- Rui Yeong Tan
- Biomass Energy Laboratory, Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Functional Omics and Bioprocess Development Laboratory, Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Zul Ilham
- Biomass Energy Laboratory, Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Wan Abd Al Qadr Imad Wan-Mohtar
- Functional Omics and Bioprocess Development Laboratory, Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Sarina Abdul Halim-Lim
- Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Seri Kembangan, Selangor Darul Ehsan, Malaysia
| | - Siti Rokhiyah Ahmad Usuldin
- Agro-Biotechnology Institute, Malaysia (ABI), National Institutes of Biotechnology Malaysia (NIMB), HQ MARDI, 43400, Serdang, Selangor, Malaysia
| | - Rahayu Ahmad
- Halal Action Laboratory, Kolej GENIUS Insan, Universiti Sains Islam Malaysia, 71800, Nilai, Negeri Sembilan, Malaysia
| | - Muhammad Adlim
- Chemistry Department, FKIP, Universitas Syiah Kuala, Darussalam Banda Aceh, 23111, Indonesia
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Asmaey MA. Unravelling the Secrets of α-Pyrones from Aspergillus Fungi: A Comprehensive Review of Their Natural Sources, Biosynthesis, and Biological Activities. Chem Biodivers 2023; 20:e202301185. [PMID: 37823671 DOI: 10.1002/cbdv.202301185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
Aspergillus, one of the most product-rich and genetically robust genera, contains a diverse range of species with potential economic and ecological implications. Chemically, Aspergillus is one of the essential sources of polyketides, alkaloids, diphenyl ethers, diketopiperazines, and other miscellaneous compounds, displaying a variety of pharmacological activities. The α-pyrones are unsaturated six-membered lactones. Although α-pyrone has a small structure, it is responsible for the structural diversity of several natural and synthetic compounds and multiple biological activities. In this review, we have summarized approximately 178 α-pyrone containing metabolites derivatives identified/reported from terrestrial, marine, endophytic, and filamentous Aspergillus species, including their sources, biological properties, and biosynthetic pathways until mid-2023, for the first time. This review is the first to compile and analyze the available data on α-pyrone metabolites from Aspergillus, which could facilitate further research and innovation in this field. Additionally, it offers a valuable source of scaffolds for future bioactive drug development, as some of these metabolites have shown potent antimicrobial, anti-inflammatory, and anticancer effects. Therefore, this review has significant implications for the advancement of natural product chemistry, pharmacology, biotechnology, and medicine.
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Affiliation(s)
- Mostafa A Asmaey
- Department of Chemistry, Faculty of Science, Al-Azhar University, Assiut Branch, Assiut, 71524, Egypt
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Cai Z, Zhao X, Zhou C, Fang T, Liu G, Luo J. Genome-Wide Mining of the Tandem Duplicated Type III Polyketide Synthases and Their Expression, Structure Analysis of Senna tora. Int J Mol Sci 2023; 24:ijms24054837. [PMID: 36902267 PMCID: PMC10003783 DOI: 10.3390/ijms24054837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Senna tora is one of the homologous crops used as a medicinal food containing an abundance of anthraquinones. Type III polyketide synthases (PKSs) are key enzymes that catalyze polyketide formation; in particular, the chalcone synthase-like (CHS-L) genes are involved in anthraquinone production. Tandem duplication is a fundamental mechanism for gene family expansion. However, the analysis of the tandem duplicated genes (TDGs) and the identification and characterization of PKSs have not been reported for S. tora. Herein, we identified 3087 TDGs in the S. tora genome; the synonymous substitution rates (Ks) analysis indicated that the TDGs had recently undergone duplication. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the type III PKSs were the most enriched TDGs involved in the biosynthesis of the secondary metabolite pathways, as evidenced by 14 tandem duplicated CHS-L genes. Subsequently, we identified 30 type III PKSs with complete sequences in the S. tora genome. Based on the phylogenetic analysis, the type III PKSs were classified into three groups. The protein conserved motifs and key active residues showed similar patterns in the same group. The transcriptome analysis showed that the chalcone synthase (CHS) genes were more highly expressed in the leaves than in the seeds in S. tora. The transcriptome and qRT-PCR analysis showed that the CHS-L genes had a higher expression in the seeds than in other tissues, particularly seven tandem duplicated CHS-L2/3/5/6/9/10/13 genes. The key active-site residues and three-dimensional models of the CHS-L2/3/5/6/9/10/13 proteins showed slight variation. These results indicated that the rich anthraquinones in S. tora seeds might be ascribed to the PKSs' expansion from tandem duplication, and the seven key CHS-L2/3/5/6/9/10/13 genes provide candidate genes for further research. Our study provides an important basis for further research on the regulation of anthraquinones' biosynthesis in S. tora.
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Affiliation(s)
- Zeping Cai
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Xingkun Zhao
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Chaoye Zhou
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Ting Fang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
| | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
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7
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Chen Y, Wang Y, Liang C, Liu L, Song X, Zhao Y, Wang J, Niu J. Characterization of the Key Bibenzyl Synthase in Dendrobium sinense. Int J Mol Sci 2022; 23:ijms23126780. [PMID: 35743224 PMCID: PMC9223774 DOI: 10.3390/ijms23126780] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrobium sinense, an endemic medicinal herb in Hainan Island, is rich in bibenzyls. However, the key rate-limited enzyme involved in bibenzyl biosynthesis has yet to be identified in D. sinense. In this study, to explore whether there is a significant difference between the D. sinense tissues, the total contents of bibenzyls were determined in roots, pseudobulbs, and leaves. The results indicated that roots had higher bibenzyl content than pseudobulbs and leaves. Subsequently, transcriptomic sequencings were conducted to excavate the genes encoding type III polyketide synthase (PKS). A total of six D. sinense PKS (DsPKS) genes were identified according to gene function annotation. Phylogenetic analysis classified the type III DsPKS genes into three groups. Importantly, the c93636.graph_c0 was clustered into bibenzyl synthase (BBS) group, named as D. sinense BBS (DsBBS). The expression analysis by FPKM and RT-qPCR indicated that DsBBS showed the highest expression levels in roots, displaying a positive correlation with bibenzyl contents in different tissues. Thus, the recombinant DsBBS-HisTag protein was constructed and expressed to study its catalytic activity. The molecular weight of the recombinant protein was verified to be approximately 45 kDa. Enzyme activity analysis indicated that the recombinant DsBBS-HisTag protein could use 4-coumaryol-CoA and malonyl-CoA as substrates for resveratrol production in vitro. The Vmax of the recombinant protein for the resveratrol production was 0.88 ± 0.07 pmol s−1 mg−1. These results improve our understanding with respect to the process of bibenzyl biosynthesis in D. sinense.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Niu
- Correspondence: (J.W.); (J.N.)
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8
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Zhang XY, Li B, Huang BC, Wang FB, Zhang YQ, Zhao SG, Li M, Wang HY, Yu XJ, Liu XY, Jiang J, Wang ZP. Production, Biosynthesis, and Commercial Applications of Fatty Acids From Oleaginous Fungi. Front Nutr 2022; 9:873657. [PMID: 35694158 PMCID: PMC9176664 DOI: 10.3389/fnut.2022.873657] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/31/2022] [Indexed: 12/18/2022] Open
Abstract
Oleaginous fungi (including fungus-like protists) are attractive in lipid production due to their short growth cycle, large biomass and high yield of lipids. Some typical oleaginous fungi including Galactomyces geotrichum, Thraustochytrids, Mortierella isabellina, and Mucor circinelloides, have been well studied for the ability to accumulate fatty acids with commercial application. Here, we review recent progress toward fermentation, extraction, of fungal fatty acids. To reduce cost of the fatty acids, fatty acid productions from raw materials were also summarized. Then, the synthesis mechanism of fatty acids was introduced. We also review recent studies of the metabolic engineering strategies have been developed as efficient tools in oleaginous fungi to overcome the biochemical limit and to improve production efficiency of the special fatty acids. It also can be predictable that metabolic engineering can further enhance biosynthesis of fatty acids and change the storage mode of fatty acids.
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Affiliation(s)
- Xin-Yue Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Bing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Bei-Chen Huang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Feng-Biao Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Yue-Qi Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Shao-Geng Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Min Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Hai-Ying Wang
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xin-Jun Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiao-Yan Liu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, China
| | - Jing Jiang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Zhi-Peng Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
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9
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Chevrette MG, Gavrilidou A, Mantri S, Selem-Mojica N, Ziemert N, Barona-Gómez F. The confluence of big data and evolutionary genome mining for the discovery of natural products. Nat Prod Rep 2021; 38:2024-2040. [PMID: 34787598 DOI: 10.1039/d1np00013f] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review covers literature between 2003-2021The development and application of genome mining tools has given rise to ever-growing genetic and chemical databases and propelled natural products research into the modern age of Big Data. Likewise, an explosion of evolutionary studies has unveiled genetic patterns of natural products biosynthesis and function that support Darwin's theory of natural selection and other theories of adaptation and diversification. In this review, we aim to highlight how Big Data and evolutionary thinking converge in the study of natural products, and how this has led to an emerging sub-discipline of evolutionary genome mining of natural products. First, we outline general principles to best utilize Big Data in natural products research, addressing key considerations needed to provide evolutionary context. We then highlight successful examples where Big Data and evolutionary analyses have been combined to provide bioinformatic resources and tools for the discovery of novel natural products and their biosynthetic enzymes. Rather than an exhaustive list of evolution-driven discoveries, we highlight examples where Big Data and evolutionary thinking have been embraced for the evolutionary genome mining of natural products. After reviewing the nascent history of this sub-discipline, we discuss the challenges and opportunities of genomic and metabolomic tools with evolutionary foundations and/or implications and provide a future outlook for this emerging and exciting field of natural product research.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Athina Gavrilidou
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany.
| | - Shrikant Mantri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany. .,Computational Biology Laboratory, National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Nelly Selem-Mojica
- Laboratorio de Evolución de la Diversidad Metabólica, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico.
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany.
| | - Francisco Barona-Gómez
- Laboratorio de Evolución de la Diversidad Metabólica, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico.
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10
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Jin H, Wang Y, Zhao P, Wang L, Zhang S, Meng D, Yang Q, Cheong LZ, Bi Y, Fu Y. Potential of Producing Flavonoids Using Cyanobacteria As a Sustainable Chassis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12385-12401. [PMID: 34649432 DOI: 10.1021/acs.jafc.1c04632] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Numerous plant secondary metabolites have remarkable impacts on both food supplements and pharmaceuticals for human health improvement. However, higher plants can only generate small amounts of these chemicals with specific temporal and spatial arrangements, which are unable to satisfy the expanding market demands. Cyanobacteria can directly utilize CO2, light energy, and inorganic nutrients to synthesize versatile plant-specific photosynthetic intermediates and organic compounds in large-scale photobioreactors with outstanding economic merit. Thus, they have been rapidly developed as a "green" chassis for the synthesis of bioproducts. Flavonoids, chemical compounds based on aromatic amino acids, are considered to be indispensable components in a variety of nutraceutical, pharmaceutical, and cosmetic applications. In contrast to heterotrophic metabolic engineering pioneers, such as yeast and Escherichia coli, information about the biosynthesis flavonoids and their derivatives is less comprehensive than that of their photosynthetic counterparts. Here, we review both benefits and challenges to promote cyanobacterial cell factories for flavonoid biosynthesis. With increasing concerns about global environmental issues and food security, we are confident that energy self-supporting cyanobacteria will attract increasing attention for the generation of different kinds of bioproducts. We hope that the work presented here will serve as an index and encourage more scientists to join in the relevant research area.
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Affiliation(s)
- Haojie Jin
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yan Wang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Pengquan Zhao
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Litao Wang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Su Zhang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Dong Meng
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Qing Yang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Ling-Zhi Cheong
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China
| | - Yonghong Bi
- State Key Laboratory of Fresh Water Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, P.R. China
| | - Yujie Fu
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
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