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Song C, Zhou Y, Dong R, Li X, Dong D, Song X. Gut microbiota dynamics interacting with gastrointestinal evacuation of Apostichopus japonicus: novel insights into promising strategies for environmental improvement. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:9831-9843. [PMID: 38198086 DOI: 10.1007/s11356-023-31559-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
As an important input of environmental micropollutants into aquaculture environment, feed is now considered to be a critical factor in shaping gastrointestinal evacuation characteristics of animals. We analyzed the gastrointestinal evacuation characteristics and gut bacteria of Apostichopus japonicus within 30 h after feeding in recirculating aquaculture system (RAS) and explored the evacuation mechanism interacting by bacteria. The Gauss model was the most precise gastrointestinal evacuation curve, and 80% of gastrointestinal evacuation time was 27.81 h after feeding. Linear discriminant analysis effect size analysis revealed that gut microbial abundance associated significantly with time (P < 0.05), and 42 biomarkers that could predict gastrointestinal evacuation were totally detected, such as Lutibacter and Vibrio. Biomarkers at 25 h after feeding were related to harmful bacteria. A dynamic response between gastrointestinal content ratio and gut microbial abundance was detected. Taken together, we could discharge sewage about 25 h after feeding and carry out the next round of feeding activities.
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Affiliation(s)
- Chenyu Song
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Yijing Zhou
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Ruiguang Dong
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Xian Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Dengpan Dong
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Xiefa Song
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
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Zhong H, Zhang M, Chen L, Liu W, Tao Y. Development of Schizochytrium sp. strain HS01 with high-DHA and low-saturated fatty acids production by multi-pronged adaptive evolution. Biotechnol Lett 2023; 45:1147-1157. [PMID: 37341820 DOI: 10.1007/s10529-023-03378-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/18/2023] [Accepted: 04/04/2023] [Indexed: 06/22/2023]
Abstract
PURPOSE Docosahexaenoic acid (DHA) is an important omega-3 unsaturated fatty acid and has been widely applied in medicine, food additives, and feed ingredients. The fermentative production of DHA using microorganisms, including Schizochytrium sp., attracted much attention due to its high production efficiency and environment friendly properties. An efficient laboratory evolution approach was used to improve the strain's performance in this study. METHODS A multi-pronged laboratory evolution approach was applied to evolve high-yield DHA-producing Schizochytrium strain. We further employed comparative transcriptional analysis to identify transcriptional changes between the screened strain HS01 and its parent strain GS00. RESULTS After multiple generations of ALE, a strain HS01 with higher DHA content and lower saturated fatty acids content was obtained. Low nitrogen conditions were important for enhancing DHA biosynthesis in HS01. The comparative transcriptional analysis results indicated that during the fermentation process of HS01, the expression of key enzymes in the glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle were up-regulated, while the expression of polyketide synthase genes and fatty acid synthesis genes were similar to those in GS00. CONCLUSION The results suggest that the improved DHA production capacity of HS01 is not due to enhancement of the DHA biosynthesis pathway, but rather related to modulation of central metabolism pathways.
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Affiliation(s)
- Huichang Zhong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
- Xiamen Huison Biotech Co.,Ltd, Xiamen, 361100, China
| | - Meng Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liyi Chen
- Xiamen Huison Biotech Co.,Ltd, Xiamen, 361100, China.
| | - Weifeng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Guo P, Dong L, Wang F, Chen L, Zhang W. Deciphering and engineering the polyunsaturated fatty acid synthase pathway from eukaryotic microorganisms. Front Bioeng Biotechnol 2022; 10:1052785. [DOI: 10.3389/fbioe.2022.1052785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Polyunsaturated fatty acids (PUFAs) are important nutrients that play important roles in human health. In eukaryotes, PUFAs can be de novo synthesized through two independent biosynthetic pathways: the desaturase/elongase pathway and the PUFA synthase pathway. Among them, PUFAs synthesized through the PUFA synthase pathway typically have few byproducts and require fewer reduction equivalents. In the past 2 decades, numerous studies have been carried out to identify, analyze and engineer PUFA synthases from eukaryotes. These studies showed both similarities and differences between the eukaryotic PUFA synthase pathways and those well studied in prokaryotes. For example, eukaryotic PUFA synthases contain the same domain types as those in prokaryotic PUFA synthases, but the number and arrangement of several domains are different; the basic functions of same-type domains are similar, but the properties and catalytic activities of these domains are somewhat different. To further utilize the PUFA synthase pathway in microbial cell factories and improve the productivity of PUFAs, many challenges still need to be addressed, such as incompletely elucidated PUFA synthesis mechanisms and the difficult genetic manipulation of eukaryotic hosts. In this review, we provide an updated introduction to the eukaryotic PUFA synthase pathway, summarize the functions of domains and propose the possible mechanisms of the PUFA synthesis process, and then provide future research directions to further elucidate and engineer the eukaryotic PUFA synthase pathway for the maximal benefits of humans.
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Sanjulián L, Lamas A, Barreiro R, Cepeda A, Fente CA, Regal P. Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum. Nutrients 2021; 13:2414. [PMID: 34371924 PMCID: PMC8308733 DOI: 10.3390/nu13072414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/27/2022] Open
Abstract
The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.
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Affiliation(s)
| | - Alexandre Lamas
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Veterinary Science, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (L.S.); (R.B.); (A.C.); (C.A.F.)
| | | | | | | | - Patricia Regal
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Veterinary Science, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (L.S.); (R.B.); (A.C.); (C.A.F.)
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Genetic Suppression of Lethal Mutations in Fatty Acid Biosynthesis Mediated by a Secondary Lipid Synthase. Appl Environ Microbiol 2021; 87:e0003521. [PMID: 33837011 PMCID: PMC8174602 DOI: 10.1128/aem.00035-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis and incorporation of polyunsaturated fatty acids into phospholipid membranes are unique features of certain marine Gammaproteobacteria inhabiting high-pressure and/or low-temperature environments. In these bacteria, monounsaturated and saturated fatty acids are produced via the classical dissociated type II fatty acid synthase mechanism, while omega-3 polyunsaturated fatty acids such as eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) are produced by a hybrid polyketide/fatty acid synthase—encoded by the pfa genes—also referred to as the secondary lipid synthase mechanism. In this work, phenotypes associated with partial or complete loss of monounsaturated biosynthesis are shown to be compensated for by severalfold increased production of polyunsaturated fatty acids in the model marine bacterium Photobacterium profundum SS9. One route to suppression of these phenotypes could be achieved by transposition of insertion sequences within or upstream of the fabD coding sequence, which encodes malonyl coenzyme A (malonyl-CoA) acyl carrier protein transacylase. Genetic experiments in this strain indicated that fabD is not an essential gene, yet mutations in fabD and pfaA are synthetically lethal. Based on these results, we speculated that the malonyl-CoA transacylase domain within PfaA compensates for loss of FabD activity. Heterologous expression of either pfaABCD from P. profundum SS9 or pfaABCDE from Shewanella pealeana in Escherichia coli complemented the loss of the chromosomal copy of fabD in vivo. The co-occurrence of independent, yet compensatory, fatty acid biosynthetic pathways in selected marine bacteria may provide genetic redundancy to optimize fitness under extreme conditions. IMPORTANCE A defining trait among many cultured piezophilic and/or psychrophilic marine Gammaproteobacteria is the incorporation of both monounsaturated and polyunsaturated fatty acids into membrane phospholipids. The biosynthesis of these different classes of fatty acid molecules is linked to two genetically distinct co-occurring pathways that utilize the same pool of intracellular precursors. Using a genetic approach, new insights into the interactions between these two biosynthetic pathways have been gained. Specifically, core fatty acid biosynthesis genes previously thought to be essential were found to be nonessential in strains harboring both pathways due to functional overlap between the two pathways. These results provide new routes to genetically optimize long-chain omega-3 polyunsaturated fatty acid biosynthesis in bacteria and reveal a possible ecological role for maintaining multiple pathways for lipid synthesis in a single bacterium.
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Pilecky M, Závorka L, Arts MT, Kainz MJ. Omega-3 PUFA profoundly affect neural, physiological, and behavioural competences - implications for systemic changes in trophic interactions. Biol Rev Camb Philos Soc 2021; 96:2127-2145. [PMID: 34018324 DOI: 10.1111/brv.12747] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
In recent decades, much conceptual thinking in trophic ecology has been guided by theories of nutrient limitation and the flow of elements, such as carbon and nitrogen, within and among ecosystems. More recently, ecologists have also turned their attention to examining the value of specific dietary nutrients, in particular polyunsaturated fatty acids (PUFA), among which the omega-3 PUFA, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) play a central role as essential components of neuronal cell membranes in many organisms. This review focuses on a new neuro-ecological approach stemming from the biochemical (mechanistic) and physiological (functional) role of DHA in neuronal cell membranes, in particular in conjunction with G-protein coupled receptors (GPCRs). We link the co-evolution of these neurological functions to metabolic dependency on dietary omega-3 PUFA. We outline ways in which deficiencies in dietary DHA supply may affect, cognition, vision, and behaviour, and ultimately, the biological fitness of consumers. We then review emerging evidence that changes in access to dietary omega-3 PUFA may ultimately have profound impacts on trophic interactions leading to potential changes in community structure and ecosystem functioning that, in turn, may affect the supply of DHA within and across ecosystems, including the supply for human consumption.
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Affiliation(s)
- Matthias Pilecky
- WasserCluster Lunz - Biologische Station, Inter-University Center for Aquatic Ecosystem Research, Dr. Carl-Kupelwieser Promenade 5, Lunz am See, 3293, Austria.,Department of Biomedical Research, Donau-Universität Krems, Dr. Karl Dorrek-Straße 30, Krems, 3500, Austria
| | - Libor Závorka
- WasserCluster Lunz - Biologische Station, Inter-University Center for Aquatic Ecosystem Research, Dr. Carl-Kupelwieser Promenade 5, Lunz am See, 3293, Austria
| | - Michael T Arts
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St, Toronto, ON, M5B 2K3, Canada
| | - Martin J Kainz
- WasserCluster Lunz - Biologische Station, Inter-University Center for Aquatic Ecosystem Research, Dr. Carl-Kupelwieser Promenade 5, Lunz am See, 3293, Austria.,Department of Biomedical Research, Donau-Universität Krems, Dr. Karl Dorrek-Straße 30, Krems, 3500, Austria
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Carroll AR, Copp BR, Davis RA, Keyzers RA, Prinsep MR. Marine natural products. Nat Prod Rep 2021; 38:362-413. [PMID: 33570537 DOI: 10.1039/d0np00089b] [Citation(s) in RCA: 198] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review covers the literature published in 2019 for marine natural products (MNPs), with 719 citations (701 for the period January to December 2019) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1490 in 440 papers for 2019), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. Methods used to study marine fungi and their chemical diversity have also been discussed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. and Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia and School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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8
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Passarini MRZ, E Silva TR, Bernal SPF, Cecchet NL, Sartoratto A, Boroski M, Duarte AWF, Ottoni JR, Rosa LH, de Oliveira VM. Undecane production by cold-adapted bacteria from Antarctica. Extremophiles 2020; 24:863-873. [PMID: 32944821 DOI: 10.1007/s00792-020-01200-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 11/27/2022]
Abstract
In the last decades, efforts to reduce the use of fossil fuels have increased the search for alternative sustainable sources of renewable energy. In this scenario, hydrocarbons derived from fatty acids are among the compounds that have been drawing attention. The intracellular production of hydrocarbons by bacteria derived from cold environments such as the Antarctic continent is currently poorly investigated, as extremophilic microorganisms provide a great range of metabolic capabilities and may represent a key tool in the production of biofuels. The aim of this study was to explore the ability of bacterial cells derived from extreme environments to produce hydrocarbons with potential for further use as biofuels. Seven bacteria isolated from Antarctic samples were evaluated for hydrocarbon production using GC-MS approaches. Two isolates, identified as Arthrobacter livingstonensis 593 and Pseudoalteromonas arctica 628, were able to produce the hydrocarbon undecane (CH3-(CH2)9-CH3) in concentrations of 1.39 mg L-1 and 1.81 mg L-1, respectively. Results from the present work encourage further research focusing on the optimization of hydrocarbon production by the isolates identified as producers, which may be used in further aircraft biofuel production. This is the first report on the production of the undecane compound by bacteria isolated from waterlogged soil and sponge from Antarctica.
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Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
| | - Tiago Rodrigues E Silva
- CPQBA/UNICAMP-Divisão de Recursos Microbianos, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
| | - Suzan Prado Fernandes Bernal
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Nathália Luana Cecchet
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Adilson Sartoratto
- CPQBA/UNICAMP-Divisão de Química Orgânica e Farmacêutica, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
| | - Marcela Boroski
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Química, Av. Tancredo Neves 6731- Conjunto B, Foz do Iguaçu, PR, 85867-970, Brazil
| | - Alysson Wagner Fernandes Duarte
- UFAL-Universidade Federal de Alagoas, Av. Manoel Severino Barbosa-Rodovia AL-115, Bom Sucesso, Arapiraca, AL, 57309-005, Brazil
| | - Júlia Ronzella Ottoni
- UDC-Centro Universitário Dinâmica das Cataratas, Rua Castelo Branco, 349, Centro, Foz do Iguaçu, PR, Brazil
| | - Luiz Henrique Rosa
- UFMG-Departamento de Microbiologia, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Valéria Maia de Oliveira
- CPQBA/UNICAMP-Divisão de Recursos Microbianos, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
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Robinson SL, Terlouw BR, Smith MD, Pidot SJ, Stinear TP, Medema MH, Wackett LP. Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia. J Biol Chem 2020; 295:14826-14839. [PMID: 32826316 DOI: 10.1074/jbc.ra120.013528] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, Rochester, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA.
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Megan D Smith
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, Rochester, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA
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10
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Molecular mechanisms for biosynthesis and assembly of nutritionally important very long chain polyunsaturated fatty acids in microorganisms. Prog Lipid Res 2020; 79:101047. [DOI: 10.1016/j.plipres.2020.101047] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/29/2020] [Accepted: 06/09/2020] [Indexed: 12/23/2022]
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11
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Robinson SL, Smith MD, Richman JE, Aukema KG, Wackett LP. Machine learning-based prediction of activity and substrate specificity for OleA enzymes in the thiolase superfamily. Synth Biol (Oxf) 2020. [DOI: 10.1093/synbio/ysaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Abstract
Enzymes in the thiolase superfamily catalyze carbon–carbon bond formation for the biosynthesis of polyhydroxyalkanoate storage molecules, membrane lipids and bioactive secondary metabolites. Natural and engineered thiolases have applications in synthetic biology for the production of high-value compounds, including personal care products and therapeutics. A fundamental understanding of thiolase substrate specificity is lacking, particularly within the OleA protein family. The ability to predict substrates from sequence would advance (meta)genome mining efforts to identify active thiolases for the production of desired metabolites. To gain a deeper understanding of substrate scope within the OleA family, we measured the activity of 73 diverse bacterial thiolases with a library of 15 p-nitrophenyl ester substrates to build a training set of 1095 unique enzyme–substrate pairs. We then used machine learning to predict thiolase substrate specificity from physicochemical and structural features. The area under the receiver operating characteristic curve was 0.89 for random forest classification of enzyme activity, and our regression model had a test set root mean square error of 0.22 (R2 = 0.75) to quantitatively predict enzyme activity levels. Substrate aromaticity, oxygen content and molecular connectivity were the strongest predictors of enzyme–substrate pairing. Key amino acid residues A173, I284, V287, T292 and I316 in the Xanthomonas campestris OleA crystal structure lining the substrate binding pockets were important for thiolase substrate specificity and are attractive targets for future protein engineering studies. The predictive framework described here is generalizable and demonstrates how machine learning can be used to quantitatively understand and predict enzyme substrate specificity.
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Affiliation(s)
- Serina L Robinson
- Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, 111 S. Broadway, Suite 300, Rochester, MN 55904, USA
- Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, 689 23rd Ave SE, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Megan D Smith
- Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, 689 23rd Ave SE, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Jack E Richman
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Kelly G Aukema
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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12
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Hayashi S, Ogasawara Y, Satoh Y, Maruyama C, Hamano Y, Dairi T. Off-Loading Mechanism of Products in Polyunsaturated Fatty Acid Synthases. ACS Chem Biol 2020; 15:651-656. [PMID: 32105442 DOI: 10.1021/acschembio.0c00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Marine microorganisms de novo biosynthesize polyunsaturated fatty acids such as docosahexaenoic acid and eicosapentaenoic acid by polyunsaturated fatty acid (PUFA) synthases composed of three or four polypeptides in a manner similar to fatty acid synthases (FASs). FASs usually possess thioesterase (TE) domains to release free fatty acids from acyl carrier protein (ACP)-tethered intermediates. Here, we investigated the off-loading mechanism with microalgal and bacterial PUFA synthases through in vivo and in vitro experiments. The in vitro experiments with acyltransferase (AT)-like domains and acyl-ACP substrates clearly demonstrated that the AT-like domains catalyzed the hydrolysis of acyl-ACPs to yield free fatty acids.
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Affiliation(s)
- Shohei Hayashi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo 060-8628, Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo 060-8628, Japan
| | - Yasuharu Satoh
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo 060-8628, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, Fukui 910-1195, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, Fukui 910-1195, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo 060-8628, Japan
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