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Xie ZT, Mi BQ, Lu YJ, Chen MT, Ye ZW. Research progress on carotenoid production by Rhodosporidium toruloides. Appl Microbiol Biotechnol 2024; 108:7. [PMID: 38170311 DOI: 10.1007/s00253-023-12943-0] [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: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Carotenoids are natural lipophilic pigments, which have been proven to provide significant health benefits to humans, relying on their capacity to efficiently scavenge singlet oxygen and peroxyl radicals as antioxidants. Strains belonging to the genus Rhodosporidium represent a heterogeneous group known for a number of phenotypic traits including accumulation of carotenoids and lipids and tolerance to heavy metals and oxidative stress. As a representative of these yeasts, Rhodosporidium toruloides naturally produces carotenoids with high antioxidant activity and grows on a wide variety of carbon sources. As a result, R. toruloides is a promising host for the efficient production of more value-added lipophilic compound carotenoids, e.g., torulene and torularhodin. This review provides a comprehensive summary of the research progress on carotenoid biosynthesis in R. toruloides, focusing on the understanding of biosynthetic pathways and the regulation of key enzymes and genes involved in the process. Moreover, the relationship between the accumulation of carotenoids and lipid biosynthesis, as well as the stress from diverse abiotic factors, has also been discussed for the first time. Finally, several feasible strategies have been proposed to promote carotenoid production by R. toruloides. It is possible that R. toruloides may become a critical strain in the production of carotenoids or high-value terpenoids by genetic technologies and optimal fermentation processes. KEY POINTS: • Biosynthetic pathway and its regulation of carotenoids in Rhodosporidium toruloides were concluded • Stimulation of abiotic factors for carotenoid biosynthesis in R. toruloides was summarized • Feasible strategies for increasing carotenoid production by R. toruloides were proposed.
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Affiliation(s)
- Zhuo-Ting Xie
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510642, China
| | - Bing-Qian Mi
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yong-Jun Lu
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Mou-Tong Chen
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Zhi-Wei Ye
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China.
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510642, China.
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2
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Tiwari N, Tripathi AK. Biosynthesis of carotenoids in Azospirillum brasilense Cd is mediated via squalene (C30) route. Biochem Biophys Res Commun 2024; 722:150154. [PMID: 38795456 DOI: 10.1016/j.bbrc.2024.150154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/11/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
Azospirillum brasilense is a non-photosynthetic α-Proteobacteria, belongs to the family of Rhodospirillaceae and produces carotenoids to protect itself from photooxidative stress. In this study, we have used Resonance Raman Spectra to show similarity of bacterioruberins of Halobacterium salinarum to that of A. brasilense Cd. To navigate the role of genes involved in carotenoid biosynthesis, we used mutational analysis to inactivate putative genes predicted to be involved in carotenoid biosynthesis in A. brasilense Cd. We have shown that HpnCED enzymes are involved in the biosynthesis of squalene (C30), which is required for the synthesis of carotenoids in A. brasilense Cd. We also found that CrtI and CrtP desaturases were involved in the transformation of colorless squalene into the pink-pigmented carotenoids. This study elucidates role of some genes which constitute very pivotal role in biosynthetic pathway of carotenoid in A. brasilense Cd.
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Affiliation(s)
- Neha Tiwari
- Laboratory of Bacterial Genetics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Anil Kumar Tripathi
- Laboratory of Bacterial Genetics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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Kifle BA, Sime AM, Gemeda MT, Woldesemayat AA. Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil. Sci Rep 2024; 14:15096. [PMID: 38956049 PMCID: PMC11220033 DOI: 10.1038/s41598-024-63254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the "biosynthesis process". Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.
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Affiliation(s)
- Bezayit Amare Kifle
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Amsale Melkamu Sime
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Mesfin Tafesse Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Adugna Abdi Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
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4
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Akkewar AS, Mishra KA, Kamble MG, Kumar S, Dey J, Sethi KK. A mechanistic review on growing multiple therapeutic applications of lutein and its global market research. Phytother Res 2024; 38:3190-3217. [PMID: 38634408 DOI: 10.1002/ptr.8197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/22/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Lutein is a naturally occurring carotenoid synthesized by plants and algae that has a beneficial effect on several biological processes and associated ailments. Its immediate application is in ophthalmology, where it significantly lowers the incidences of age-related macular degeneration (AMD). It also has anti-inflammatory action, treatment of diabetic retinopathy, and cataracts, and enhancement of visual contrast. To critically assess lutein biosynthesis, therapeutic applicability, and market research literature. We have discussed its theoretical frameworks, experimental evidence, limitations, as well as clinical trial results, and future research prospects. The literature for this review article was mined and compiled by collecting and analyzing articles from several databases, including ScienceDirect, Google Scholar, PubMed, Wiley Online Library, Patentscope, and ClinicalTrials.gov published until March 30, 2022. Patent publications were identified using the search terms like IC:(C07C67/56) AND EN_AB:(lutein) OR EN_TI:(lutein) OR EN_AB:(extraction) OR EN_TI:(process). According to the literature, lutein is an essential nutrient given that it cannot be synthesized in the human body and acts as an antioxidant, affecting AMD, diabetic retinopathy, Rheumatic diseases, inflammation, and cancer. Due to inadequate production and laborious extraction, lutein is expensive despite its high demand and applicability. Market research predicts a 6.3% compound annual growth rate for lutein by 2032. Optimizing lutein extraction for high yield and purity is necessary. Lutein has proven applicability in various ailments as well as cosmetics that can be developed as a candidate drug for various diseases discussed in the review.
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Affiliation(s)
- Ashish Sunil Akkewar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Guwahati, Guwahati, India
| | - Km Abha Mishra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Guwahati, Guwahati, India
| | - Mahesh Gopichand Kamble
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Guwahati, Guwahati, India
| | - Sanjay Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Guwahati, Guwahati, India
| | - Juhi Dey
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Guwahati, Guwahati, India
| | - Kalyan Kumar Sethi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Guwahati, Guwahati, India
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Liu M, Wang Z, Qin C, Cao H, Kong L, Liu T, Jiang S, Ma L, Liu X, Ren W, Ma W. Cloning, Expression Characteristics of Farnesyl Pyrophosphate Synthase Gene from Platycodon grandiflorus and Functional Identification in Triterpenoid Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11429-11437. [PMID: 38738769 DOI: 10.1021/acs.jafc.3c09293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Platycodon grandiflorus is a medicinal plant whose main component is platycodins, which have a variety of pharmacological effects and nutritional values. The farnesyl pyrophosphate synthase (FPS) is a key enzyme in the isoprenoid biosynthesis pathway, which catalyzes the synthesis of farnesyl diphosphate (FPP). In this study, we cloned the FPS gene from P. grandiflorus (PgFPS) with an ORF of 1260 bp, encoding 419 amino acids with a deduced molecular weight and theoretical pI of 46,200.98 Da and 6.52, respectively. The squalene content of overexpressed PgFPS in tobacco leaves and yeast cells extract was 1.88-fold and 1.21-fold higher than that of the control group, respectively, and the total saponin content was also increased by 1.15 times in yeast cells extract, which verified the biological function of PgFPS in terpenoid synthesis. After 48 h of MeJA treatment and 6 h of ethephon treatment, the expression of the PgFPS gene in roots and stems reached its peak, showing a 3.125-fold and 3.236-fold increase compared to the untreated group, respectively. Interestingly, the expression of the PgFPS gene in leaves showed a decreasing trend after exogenous elicitors treatment. The discovery of this enzyme will provide a novel perspective for enhancing the efficient synthesis of platycodins.
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Affiliation(s)
- Meiqi Liu
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Zhen Wang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Chen Qin
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Huiyan Cao
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Lingyang Kong
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Tingxia Liu
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Shan Jiang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Lengleng Ma
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Xiubo Liu
- College of Jiamusi, Heilongjiang University of Chinese Medicine, Jiamusi 154002, China
| | - Weichao Ren
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Wei Ma
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin 150040, China
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6
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Zhang Z, Gao L, Tao L, Wu T, Suo J, Hu Y, Yu W, Wu J, Song L. Gas Chromatography-Mass Spectrometry Metabolites and Transcriptome Profiling Reveal Molecular Mechanisms and Differences in Terpene Biosynthesis in Two Torrya grandis Cultivars during Postharvest Ripening. Int J Mol Sci 2024; 25:5581. [PMID: 38891770 PMCID: PMC11171539 DOI: 10.3390/ijms25115581] [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: 03/30/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Terpene aroma compounds are key quality attributes of postharvest Torreya grandis nuts, contributing to their commercial value. However, terpene biosynthesis and regulatory networks in different T. grandis cvs. are still poorly understood. Here, chief cvs. 'Xi Fei' and 'Xiangya Fei' were investigated for their differences in terpene biosynthesis and gene expression levels during postharvest ripening using headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) and transcriptomic datasets. A total of 28 and 22 aroma compounds were identified in 'Xi Fei' and 'Xiangya Fei', respectively. Interestingly, differences in aroma composition between the two cvs. were mostly attributed to D-limonene and α-pinene levels as key determinants in Torreya nuts' flavor. Further, transcriptome profiling, correlation analysis, and RT-qPCR annotated two novel genes, TgTPS1 in 'Xi Fei' and TgTPS2 in 'Xiangya Fei', involved in terpene biosynthesis. In addition, six transcription factors (TFs) with comparable expression patterns to TgTPS1 and four TFs to TgTPS2 were identified via correlation analysis of a volatile and transcriptome dataset to be involved in terpene biosynthesis. Our study provides novel insight into terpene biosynthesis and its regulation at the molecular level in T. grandis nut and presents a valuable reference for metabolic engineering and aroma improvement in this less explored nut.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Z.Z.); (L.G.); (L.T.); (T.W.); (J.S.); (Y.H.); (W.Y.)
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Z.Z.); (L.G.); (L.T.); (T.W.); (J.S.); (Y.H.); (W.Y.)
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Li X, Xu M, Zhou K, Hao S, Li L, Wang L, Zhou W, Kai G. SmEIL1 transcription factor inhibits tanshinone accumulation in response to ethylene signaling in Salvia miltiorrhiza. FRONTIERS IN PLANT SCIENCE 2024; 15:1356922. [PMID: 38628367 PMCID: PMC11018959 DOI: 10.3389/fpls.2024.1356922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Among the bioactive compounds, lipid-soluble tanshinone is present in Salvia miltiorrhiza, a medicinal plant species. While it is known that ethephon has the ability to inhibit the tanshinones biosynthesis in the S. miltiorrhiza hairy root, however the underlying regulatory mechanism remains obscure. In this study, using the transcriptome dataset of the S. miltiorrhiza hairy root induced by ethephon, an ethylene-responsive transcriptional factor EIN3-like 1 (SmEIL1) was identified. The SmEIL1 protein was found to be localized in the nuclei, and confirmed by the transient transformation observed in tobacco leaves. The overexpression of SmEIL1 was able to inhibit the tanshinones accumulation to a large degree, as well as down-regulate tanshinones biosynthetic genes including SmGGPPS1, SmHMGR1, SmHMGS1, SmCPS1, SmKSL1 and SmCYP76AH1. These are well recognized participants in the tanshinones biosynthesis pathway. Further investigation on the SmEIL1 was observed to inhibit the transcription of the CPS1 gene by the Dual-Luciferase (Dual-LUC) and yeast one-hybrid (Y1H) assays. The data in this work will be of value regarding the involvement of EILs in regulating the biosynthesis of tanshinones and lay the foundation for the metabolic engineering of bioactive ingredients in S. miltiorrhiza.
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Affiliation(s)
- Xiujuan Li
- Zhejiang Provincial Traditional Chinese Medicine Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang Provincial International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Man Xu
- Zhejiang Provincial Traditional Chinese Medicine Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang Provincial International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ke Zhou
- Dermatology department, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Siyu Hao
- Zhejiang Provincial Traditional Chinese Medicine Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang Provincial International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Liqin Li
- Key Laboratory of Traditional Chinese Medicine for the Development and Clinical Transformation of Immunomodulatory Traditional Chinese Medicine in Zhejiang Province, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, Hangzhou, China
| | - Leran Wang
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wei Zhou
- Zhejiang Provincial Traditional Chinese Medicine Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang Provincial International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Guoyin Kai
- Zhejiang Provincial Traditional Chinese Medicine Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang Provincial International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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Zhu P, Hou J, Xiong Y, Xie R, Wang Y, Wang F. Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis. Microorganisms 2024; 12:707. [PMID: 38674651 PMCID: PMC11052028 DOI: 10.3390/microorganisms12040707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA's enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.
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Affiliation(s)
- Pengfei Zhu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Jialin Hou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Yixuan Xiong
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Ruize Xie
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Fengping Wang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Southern Marine Science and Engineering, Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
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Zhou J, Xu S, Li H, Xi H, Cheng W, Yang C. A Ribulose-5-phosphate Shunt from the Calvin-Benson Cycle to Methylerythritol Phosphate Pathway for Enhancing Photosynthetic Terpenoid Production. ACS Synth Biol 2024; 13:876-887. [PMID: 38362836 DOI: 10.1021/acssynbio.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cyanobacteria are attractive hosts for photosynthetic terpenoid production, using CO2 as the sole carbon source. Although the methylerythritol phosphate (MEP) pathway is superior to the mevalonate pathway for cyanobacterial terpenoid synthesis, the first reaction of the MEP pathway, which is catalyzed by 1-deoxy-d-xylulose-5-phosphate (DXP) synthase, involves complex regulation and carbon loss. Here, we constructed a direct route linking ribulose-5-phosphate (Ru5P) in the Calvin-Benson (CB) cycle with DXP in the MEP pathway in a cyanobacterium to increase the terpenoid yield from CO2 and bypass the DXS-targeted regulations. By employing the adaptive laboratory evolution, we identified new RibB variants including RibB 90-92del with a high activity of synthesizing DXP from Ru5P. These RibB variants were introduced into Synechococcus elongatus, resulting in the significantly increased photosynthetic production of isopentenol. The 13C tracer experiments demonstrated a direct carbon flow from Ru5P in the CB cycle to the MEP pathway; thus, this direct route was denoted as the Ru5P shunt. The strain harboring the Ru5P shunt produced 105.2 mg L-1 of isopentenol with an average rate of 17.5 mg L-1 d-1 under continuous light conditions, which is higher than those ever reported for five-carbon alcohol production by photoautotrophic microorganisms. Utilization of the Ru5P shunt in cyanobacterial cells also improved the pinene production, which demonstrates that this shunt can be used to enhance the photosynthetic production of diverse terpenoids.
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Affiliation(s)
- Jie Zhou
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suxian Xu
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Li
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huachao Xi
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Cheng
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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10
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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11
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Tamang A, Kaur A, Thakur D, Thakur A, Thakur BK, Shivani, Swarnkar M, Pal PK, Hallan V, Pandey SS. Unraveling endophytic diversity in dioecious Siraitia grosvenorii: implications for mogroside production. Appl Microbiol Biotechnol 2024; 108:247. [PMID: 38427084 PMCID: PMC10907472 DOI: 10.1007/s00253-024-13076-8] [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: 08/10/2023] [Revised: 01/04/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic composition of the targeted crop is essential, especially for the dioecious plants where the male and female plants are different. Here, efforts were made to understand the endophytic bacterial composition of the dioecious Siraitia grosvenorii plant using 16S rRNA amplicon sequencing. The present study revealed the association of distinct endophytic bacterial communities with different parts of male and female plants. Roots of male and female plants had a higher bacterial diversity than other parts of plants, and the roots of male plants had more bacterial diversity than the roots of female plants. Endophytes belonging to the phylum Proteobacteria were abundant in all parts of male and female plants except male stems and fruit pulp, where the Firmicutes were most abundant. Class Gammaproteobacteria predominated in both male and female plants, with the genus Acinetobacter as the most dominant and part of the core microbiome of the plant (present in all parts of both, male and female plants). The presence of distinct taxa specific to male and female plants was also identified. Macrococcus, Facklamia, and Propionibacterium were the distinct genera found only in fruit pulp, the edible part of S. grosvenorii. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite (especially mogroside) biosynthesis in the associated endophytic community with predominance in roots. The present study revealed bacterial endophytic communities of male and female S. grosvenorii plants that can be further explored for monk fruit cultivation, mogroside production, and early-stage identification of male and female plants. KEY POINTS: • Male and female Siraitia grosvenorii plants had distinct endophytic communities • The diversity of endophytic communities was specific to different parts of plants • S. grosvenorii-associated endophytes may be valuable for mogroside biosynthesis and monk fruit cultivation.
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Affiliation(s)
- Anish Tamang
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amanpreet Kaur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
| | - Deepali Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
| | - Ankita Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Babit Kumar Thakur
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shivani
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohit Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
| | - Probir K Pal
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vipin Hallan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shiv Shanker Pandey
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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12
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Son SH, Kang J, Shin Y, Lee C, Sung BH, Lee JY, Lee W. Sustainable production of natural products using synthetic biology: Ginsenosides. J Ginseng Res 2024; 48:140-148. [PMID: 38465212 PMCID: PMC10920010 DOI: 10.1016/j.jgr.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/23/2023] [Accepted: 12/30/2023] [Indexed: 03/12/2024] Open
Abstract
Synthetic biology approaches offer potential for large-scale and sustainable production of natural products with bioactive potency, including ginsenosides, providing a means to produce novel compounds with enhanced therapeutic properties. Ginseng, known for its non-toxic and potent qualities in traditional medicine, has been used for various medical needs. Ginseng has shown promise for its antioxidant and neuroprotective properties, and it has been used as a potential agent to boost immunity against various infections when used together with other drugs and vaccines. Given the increasing demand for ginsenosides and the challenges associated with traditional extraction methods, synthetic biology holds promise in the development of therapeutics. In this review, we discuss recent developments in microorganism producer engineering and ginsenoside production in microorganisms using synthetic biology approaches.
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Affiliation(s)
- So-Hee Son
- Research Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
| | - Jin Kang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea National University of Science and Technology (UST), Daejeon, Republic of Korea
| | - YuJin Shin
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - ChaeYoung Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea National University of Science and Technology (UST), Daejeon, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Ju Young Lee
- Research Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
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13
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Wang Y, Xue D, Chen X, Qiu Q, Chen H. Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands. MICROBIAL ECOLOGY 2024; 87:47. [PMID: 38407642 PMCID: PMC10896819 DOI: 10.1007/s00248-024-02355-6] [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: 10/10/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024]
Abstract
Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.
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Affiliation(s)
- Yue Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Xue
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China.
| | - Xuhui Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Qiu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
| | - Huai Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China.
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14
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Cheah LC, Sainsbury F, Vickers CE. Translational fusion of terpene synthases for metabolic engineering: Lessons learned and practical considerations. Methods Enzymol 2024; 699:121-161. [PMID: 38942501 DOI: 10.1016/bs.mie.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The step catalyzed by terpene synthases is a well-recognized and significant bottleneck in engineered terpenoid bioproduction. Consequently, substantial efforts have been devoted towards increasing metabolic flux catalyzed by terpene synthases, employing strategies such as gene overexpression and protein engineering. Notably, numerous studies have demonstrated remarkable titer improvements by applying translational fusion, typically by fusing the terpene synthase with a prenyl diphosphate synthase that catalyzes the preceding step in the pathway. The main appeal of the translational fusion approach lies in its simplicity and orthogonality to other metabolic engineering tools. However, there is currently limited understanding of the underlying mechanism of flux enhancement, owing to the unpredictable and often protein-specific effects of translational fusion. In this chapter, we discuss practical considerations when engineering translationally fused terpene synthases, drawing insights from our experience and existing literature. We also provide detailed experimental workflows and protocols based on our previous work in budding yeast (Saccharomyces cerevisiae). Our intention is to encourage further research into the translational fusion of terpene synthases, anticipating that this will contribute mechanistic insights not only into the activity, behavior, and regulation of terpene synthases, but also of other enzymes.
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Affiliation(s)
- Li Chen Cheah
- Australian Centre for Disease Preparedness, East Geelong, VIC, Australia.
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
| | - Claudia E Vickers
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia; School of Biological and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia; BioBuilt Solutions, Brisbane, QLD, Australia
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15
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Wang J, Wu W, Zhou Y, Han M, Zhou X, Sun Y, Zhang A. Design, synthesis and activity evaluation of pseudilin analogs against cyanobacteria as IspD inhibitors. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 199:105769. [PMID: 38458678 DOI: 10.1016/j.pestbp.2024.105769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 03/10/2024]
Abstract
The discovery of safe, effective, and selective chemical algicides is the stringent need for the algicides development, and it is also one of the effective routes to control cyanobacteria harmful algal blooms and to meet the higher requirements of environmental and ecological. In this work, a series of novel bromo-N-phenyl-5-o-hydroxyphenylpyrazole-3-carboxyamides were rationally designed as pseudilin analogs by bioisosteric replacement and molecular hybridization strategies, in which the pyrrole unit of pseudilin was replaced with pyrazole and further combined with the dominant structural fragments of algicide diuron. The synthesis was carried out by a facile four-step routeincluding cyclization, amidation, transanulation, and halogenation. The biological activity evaluation on AtIspD, EcIspD, Synechocystis sp. PCC6803 and Microcystis aeruginosa FACHB905 revealed that most compounds had good EcIspD and excellent cyanobacteria inhibitory activity. In particular, compound 6bb exhibited potent algicidal activity against PCC6803 and FACHB905 with EC50 = 1.28 μM and 0.37 μM, respectively, 1.4-fold and 4.0-fold enhancement compared to copper sulfate (EC50 = 1.79 and 1.49 μM, respectively), and it also showed the best inhibitory activity of EcIspD. The binding of 6bb to EcIspD was explored by molecular docking, and it was confirmed that 6bb could bind to the EcIspD active site. Compound 6bb was proven to be a potential structure for the further development of novel algicides that targets IspD in the MEP pathway.
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Affiliation(s)
- Jili Wang
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China
| | - Wenhai Wu
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China
| | - Yaqing Zhou
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China
| | - Mengying Han
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xin Zhou
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China
| | - Yong Sun
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China.
| | - Aidong Zhang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China.
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16
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Tai Y, Zhang J, Chen Y, Yuan Y, Wang H, Yu L, Li S, Yang L, Jin Y. Establishment and validation of a callus tissue transformation system for German chamomile (Matricaria chamomilla L.). BMC PLANT BIOLOGY 2023; 23:659. [PMID: 38124039 PMCID: PMC10731808 DOI: 10.1186/s12870-023-04680-3] [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: 09/26/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND German chamomile (Matricaria chamomilla L.) is an important medicinal plant, and the essential oils in the flowers have various biological activities. Genetic transformation systems are important for plant quality improvement and molecular research. To the best of our knowledge, a genetic transformation system has not yet been reported for German chamomile. RESULTS In this study, we developed Agrobacterium-mediated transformation protocols for German chamomile callus tissues. This involved optimizing key parameters, such as hygromycin and cefotaxime concentrations, bacterial density, and infection and co-culture durations. We also performed gas chromatography-mass spectrometry analysis to identify volatile compounds in non-transgenic and transgenic callus and hairy root tissues. Furthermore, to compare and verify the callus transformation system of German chamomile, we transferred McFPS to the hairy roots of German chamomile. The results showed that the optimal conditions for Agrobacterium-mediated callus tissue transformation were as follows: explant, petiole; cefotaxime concentration, 300 mg/L; hygromycin concentration, 10 mg/L; and bacterial solution concentration, OD600 = 0.6; callus transformation efficiency was the highest when the co-culture time was 3 days. CONCLUSIONS Establishment of a high-efficiency callus transformation system will lay the foundation for gene function identification in German chamomile.
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Affiliation(s)
- Yuling Tai
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Jie Zhang
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Youhui Chen
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Yi Yuan
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
| | - Honggang Wang
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Luyao Yu
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Shuangshuang Li
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Lu Yang
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Yifan Jin
- School of Life Science, Anhui Agricultural University, Hefei, 230036, People's Republic of China
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17
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Tamang A, Swarnkar M, Kumar P, Kumar D, Pandey SS, Hallan V. Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb. Microbiol Spectr 2023; 11:e0227923. [PMID: 37811959 PMCID: PMC10715050 DOI: 10.1128/spectrum.02279-23] [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: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro-generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants.
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Affiliation(s)
- Anish Tamang
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Mohit Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
| | - Pawan Kumar
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dinesh Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Shiv Shanker Pandey
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Vipin Hallan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
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18
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Du Z, Bhat WW, Poliner E, Johnson S, Bertucci C, Farre E, Hamberger B. Engineering Nannochloropsis oceanica for the production of diterpenoid compounds. MLIFE 2023; 2:428-437. [PMID: 38818264 PMCID: PMC10989085 DOI: 10.1002/mlf2.12097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/24/2023] [Accepted: 10/04/2023] [Indexed: 06/01/2024]
Abstract
Photosynthetic microalgae like Nannochloropsis hold enormous potential as sustainable, light-driven biofactories for the production of high-value natural products such as terpenoids. Nannochloropsis oceanica is distinguished as a particularly robust host with extensive genomic and transgenic resources available. Its capacity to grow in wastewater, brackish, and sea waters, coupled with advances in microalgal metabolic engineering, genome editing, and synthetic biology, provides an excellent opportunity. In the present work, we demonstrate how N. oceanica can be engineered to produce the diterpene casbene-an important intermediate in the biosynthesis of pharmacologically relevant macrocyclic diterpenoids. Casbene accumulated after stably expressing and targeting the casbene synthase from Daphne genkwa (DgTPS1) to the algal chloroplast. The engineered strains yielded production titers of up to 0.12 mg g-1 total dry cell weight (DCW) casbene. Heterologous overexpression and chloroplast targeting of two upstream rate-limiting enzymes in the 2-C-methyl- d-erythritol 4-phosphate pathway, Coleus forskohlii 1-deoxy- d-xylulose-5-phosphate synthase and geranylgeranyl diphosphate synthase genes, further enhanced the yield of casbene to a titer up to 1.80 mg g-1 DCW. The results presented here form a basis for further development and production of complex plant diterpenoids in microalgae.
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Affiliation(s)
- Zhi‐Yan Du
- Department of Molecular Biosciences and BioengineeringUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Wajid W. Bhat
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eric Poliner
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Sean Johnson
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
- Present address:
New England Biolabs Inc.240 County RoadIpswich01938MAUSA
| | - Conor Bertucci
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eva Farre
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Bjoern Hamberger
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
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Yu H, Chen B, Li J, Dong N, Chang X, Wang J, Peng H, Zha L, Gui S. Identification and functional characterization of two trans-isopentenyl diphosphate synthases and one squalene synthase involved in triterpenoid biosynthesis in Platycodon grandiflorus. PLANTA 2023; 258:115. [PMID: 37943378 DOI: 10.1007/s00425-023-04273-2] [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: 06/26/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
MAIN CONCLUSION Two trans-isopentenyl diphosphate synthase and one squalene synthase genes were identified and proved to be involved in the triterpenoid biosynthesis in Platycodon grandiflorus. Platycodon grandiflorus is a commonly used traditional Chinese medicine. The main bioactive compounds of P. grandiflorus are triterpenoid saponins. The biosynthetic pathway of triterpenoid saponins in P. grandiflorus has been preliminarily explored. However, limited functional information on related genes has been reported. A total of three trans-isopentenyl diphosphate synthases (trans-IDSs) genes (PgFPPS, PgGGPPS1 and PgGGPPS2) and one squalene synthase (SQS) gene (PgSQS) in P. grandiflorus were screened and identified from transcriptome dataset. Subcellular localization of the proteins was defined based on the analysis of GFP-tagged. The activity of genes was verified in Escherichia coli, demonstrating that recombinant PgFPPS catalysed the production of farnesyl diphosphate. PgGGPPS1 produced geranylgeranyl diphosphate, whereas PgGGPPS2 did not exhibit catalytic activity. By structural identification of encoding genes, a transmembrane region was found at the C-terminus of the PgSQS gene, which produced an insoluble protein when expressed in E. coli but showed no apparent effect on the enzyme function. Furthermore, some triterpenoid saponin synthesis-related genes were discovered by combining the component content and the gene expression assays at the five growth stages of P. grandiflorus seedlings. The accumulation of active components in P. grandiflorus was closely associated with the expression level of genes related to the synthesis pathway.
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Affiliation(s)
- Hanwen Yu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Bowen Chen
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Jing Li
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Nan Dong
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiangwei Chang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Jutao Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Huasheng Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU057), National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liangping Zha
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Conservation and Development of Traditional Chinese Medicine Resources, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China.
| | - Shuangying Gui
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Pharmaceutics, Anhui Academy of Chinese Medicine, Hefei, China.
- Anhui Province Key Laboratory of Pharmaceutical Technology and Application, Anhui University of Chinese Medicine, Hefei, China.
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China.
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Liu Y, Wang J, Huang JB, Li XF, Chen Y, Liu K, Zhao M, Huang XL, Gao XL, Luo YN, Tao W, Wu J, Xue ZL. Advances in regulating vitamin K 2 production through metabolic engineering strategies. World J Microbiol Biotechnol 2023; 40:8. [PMID: 37938463 DOI: 10.1007/s11274-023-03828-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
Vitamin K2 (menaquinone, VK2, MK) is an essential lipid-soluble vitamin that plays critical roles in inhibiting cell ferroptosis, improving blood clotting, and preventing osteoporosis. The increased global demand for VK2 has inspired interest in novel production strategies. In this review, various novel metabolic regulation strategies, including static and dynamic metabolic regulation, are summarized and discussed. Furthermore, the advantages and disadvantages of both strategies are analyzed in-depth to highlight the bottlenecks facing microbial VK2 production on an industrial scale. Finally, advanced metabolic engineering biotechnology for future microbial VK2 production will also be discussed. In summary, this review provides in-depth information and offers an outlook on metabolic engineering strategies for VK2 production.
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Affiliation(s)
- Yan Liu
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China.
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China.
| | - Jian Wang
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Jun-Bao Huang
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Xiang-Fei Li
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China
| | - Yu Chen
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China
| | - Kun Liu
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China
| | - Ming Zhao
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China.
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China.
| | - Xi-Lin Huang
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Xu-Li Gao
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Ya-Ni Luo
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Wei Tao
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Jing Wu
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Zheng-Lian Xue
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China
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21
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Marshall B, Amritkar K, Wolfe M, Kaçar B, Landick R. Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway. Front Microbiol 2023; 14:1286626. [PMID: 38029103 PMCID: PMC10663253 DOI: 10.3389/fmicb.2023.1286626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron-sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron-sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.
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Affiliation(s)
- Bailey Marshall
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Kaustubh Amritkar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Michael Wolfe
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
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22
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Fordjour E, Liu CL, Hao Y, Sackey I, Yang Y, Liu X, Li Y, Tan T, Bai Z. Engineering Escherichia coli BL21 (DE3) for high-yield production of germacrene A, a precursor of β-elemene via combinatorial metabolic engineering strategies. Biotechnol Bioeng 2023; 120:3039-3056. [PMID: 37309999 DOI: 10.1002/bit.28467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/31/2023] [Accepted: 06/03/2023] [Indexed: 06/14/2023]
Abstract
β-elemene is one of the most commonly used antineoplastic drugs in cancer treatment. As a plant-derived natural chemical, biologically engineering microorganisms to produce germacrene A to be converted to β-elemene harbors great expectations since chemical synthesis and plant isolation methods come with their production deficiencies. In this study, we report the design of an Escherichia coli cell factory for the de novo production of germacrene A to be converted to β-elemene from a simple carbon source. A series of systematic approaches of engineering the isoprenoid and central carbon pathways, translational and protein engineering of the sesquiterpene synthase, and exporter engineering yielded high-efficient β-elemene production. Specifically, deleting competing pathways in the central carbon pathway ensured the availability of acetyl-coA, pyruvate, and glyceraldehyde-3-phosphate for the isoprenoid pathways. Adopting lycopene color as a high throughput screening method, an optimized NSY305N was obtained via error-prone polymerase chain reaction mutagenesis. Further overexpression of key pathway enzymes, exporter genes, and translational engineering produced 1161.09 mg/L of β-elemene in a shake flask. Finally, we detected the highest reported titer of 3.52 g/L of β-elemene and 2.13 g/L germacrene A produced by an E. coli cell factory in a 4-L fed-batch fermentation. The systematic engineering reported here generally applies to microbial production of a broader range of chemicals. This illustrates that rewiring E. coli central metabolism is viable for producing acetyl-coA-derived and pyruvate-derived molecules cost-effectively.
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Affiliation(s)
- Eric Fordjour
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Chun-Li Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yunpeng Hao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Isaac Sackey
- Department of Biological Sciences, Faculty of Biosciences, University for Development Studies, Tamale, Ghana
| | - Yankun Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Ye Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Tianwei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zhonghu Bai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
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23
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Wang L, Patena W, Van Baalen KA, Xie Y, Singer ER, Gavrilenko S, Warren-Williams M, Han L, Harrigan HR, Hartz LD, Chen V, Ton VTNP, Kyin S, Shwe HH, Cahn MH, Wilson AT, Onishi M, Hu J, Schnell DJ, McWhite CD, Jonikas MC. A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways. Cell 2023; 186:3499-3518.e14. [PMID: 37437571 DOI: 10.1016/j.cell.2023.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/14/2023]
Abstract
Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.
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Affiliation(s)
- Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kelly A Van Baalen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yihua Xie
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Emily R Singer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Linqu Han
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Henry R Harrigan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Linnea D Hartz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vivian Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vinh T N P Ton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Saw Kyin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Henry H Shwe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Matthew H Cahn
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jianping Hu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Claire D McWhite
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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24
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Bhat S, Banerjee A, Alagesan S. AraC-Based Biosensor for the Detection of Isoprene in E. coli. ACS OMEGA 2023; 8:26806-26815. [PMID: 37546622 PMCID: PMC10399174 DOI: 10.1021/acsomega.3c01164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Isoprene is a valuable platform chemical, which is produced by engineered microorganisms, albeit in low quantities. The amount of isoprene produced is usually measured by gas chromatography, which can be time-consuming and expensive. Alternatively, biosensors have evolved as a powerful tool for real-time high-throughput screening and monitoring of product synthesis. The AraC-pBAD-inducible system has been widely studied, evolved, and engineered to develop biosensors for small molecules. In our preliminary studies, the AraC-pBAD system was mildly induced at higher isoprene concentrations when arabinose was also available. Hence, in the present study, we designed and constructed a synthetic biosensor based on the AraC-pBAD system, wherein the ligand-binding domain of AraC was replaced with IsoA. On introducing this chimeric AraC-IsoA (AcIa) transcription factor with the native PBAD promoter system regulating rfp gene expression, fluorescence output was observed only when wild-type Escherichia coli cells were induced with both isoprene and arabinose. The biosensor sensitivity and dynamic range were further enhanced by removing operator sequences and by substituting the native promoter (PAraC) with the strong tac promoter (Ptac). The chimeric sensor did not work in AraC knockout strains; however, functionality was restored by reintroducing AraC. Hence, AraC is essential for the functioning of our biosensor, while AcIa provides enhanced sensitivity and specificity for isoprene. However, insights into how AraC-AcIa interacts and the possible working mechanism remain to be explored. This study provides a prototype for developing chimeric AraC-based biosensors with proteins devoid of known dimerizing domains and opens a new avenue for further study and exploration.
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25
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Řezanka T, Kyselová L, Murphy DJ. Archaeal lipids. Prog Lipid Res 2023; 91:101237. [PMID: 37236370 DOI: 10.1016/j.plipres.2023.101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.
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Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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26
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Wilkens D, Simon J. Biosynthesis and function of microbial methylmenaquinones. Adv Microb Physiol 2023; 83:1-58. [PMID: 37507157 DOI: 10.1016/bs.ampbs.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The membranous quinone/quinol pool is essential for the majority of life forms and its composition has been widely used as a biomarker in microbial taxonomy. The most abundant quinone is menaquinone (MK), which serves as an essential redox mediator in various electron transport chains of aerobic and anaerobic respiration. Several methylated derivatives of MK, designated methylmenaquinones (MMKs), have been reported to be present in members of various microbial phyla possessing either the classical MK biosynthesis pathway (Men) or the futalosine pathway (Mqn). Due to their low redox midpoint potentials, MMKs have been proposed to be specifically involved in appropriate electron transport chains of anaerobic respiration. The class C radical SAM methyltransferases MqnK, MenK and MenK2 have recently been shown to catalyse specific MK methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesise 8-MMK, 7-MMK and 7,8-dimethylmenaquinone (DMMK). MqnK, MenK and MenK2 from organisms such as Wolinella succinogenes, Adlercreutzia equolifaciens, Collinsella tanakaei, Ferrimonas marina and Syntrophus aciditrophicus have been functionally produced in Escherichia coli, enabling extensive quinone/quinol pool engineering of the native MK and 2-demethylmenaquinone (DMK). Cluster and phylogenetic analyses of available MK and MMK methyltransferase sequences revealed signature motifs that allowed the discrimination of MenK/MqnK/MenK2 family enzymes from other radical SAM enzymes and the identification of C-7-specific menaquinone methyltransferases of the MenK2 subfamily. It is envisaged that this knowledge will help to predict the methylation status of the menaquinone/menaquinol pool of any microbial species (or even a microbial community) from its (meta)genome.
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Affiliation(s)
- Dennis Wilkens
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, Germany; Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
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27
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Zhang J, Gong X, Gan Q, Yan Y. Application of Metabolite-Responsive Biosensors for Plant Natural Products Biosynthesis. BIOSENSORS 2023; 13:633. [PMID: 37366998 DOI: 10.3390/bios13060633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023]
Abstract
Plant natural products (PNPs) have shown various pharmaceutical activities, possessing great potential in global markets. Microbial cell factories (MCFs) provide an economical and sustainable alternative for the synthesis of valuable PNPs compared with traditional approaches. However, the heterologous synthetic pathways always lack native regulatory systems, bringing extra burden to PNPs production. To overcome the challenges, biosensors have been exploited and engineered as powerful tools for establishing artificial regulatory networks to control enzyme expression in response to environments. Here, we reviewed the recent progress involved in the application of biosensors that are responsive to PNPs and their precursors. Specifically, the key roles these biosensors played in PNP synthesis pathways, including isoprenoids, flavonoids, stilbenoids and alkaloids, were discussed in detail.
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Affiliation(s)
- Jianli Zhang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Xinyu Gong
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Qi Gan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
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28
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Yahya RZ, Wellman GB, Overmans S, Lauersen KJ. Engineered production of isoprene from the model green microalga Chlamydomonas reinhardtii. Metab Eng Commun 2023; 16:e00221. [PMID: 37006831 PMCID: PMC10063407 DOI: 10.1016/j.mec.2023.e00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/23/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Isoprene is a clear, colorless, volatile 5-carbon hydrocarbon that is one monomer of all cellular isoprenoids and a platform chemical with multiple applications in industry. Many plants have evolved isoprene synthases (IspSs) with the capacity to liberate isoprene from dimethylallyl diphosphate (DMADP) as part of cellular thermotolerance mechanisms. Isoprene is hydrophobic and volatile, rapidly leaves plant tissues and is one of the main carbon emission sources from vegetation globally. The universality of isoprenoid metabolism allows volatile isoprene production from microbes expressing heterologous IspSs. Here, we compared heterologous overexpression from the nuclear genome and localization into the plastid of four plant terpene synthases (TPs) in the green microalga Chlamydomonas reinhardtii. Using sealed vial mixotrophic cultivation, direct quantification of isoprene production was achieved from the headspace of living cultures, with the highest isoprene production observed in algae expressing the Ipomoea batatas IspS. Perturbations of the downstream carotenoid pathway through keto carotenoid biosynthesis enhanced isoprene titers, which could be further enhanced by increasing flux towards DMADP through heterologous co-expression of a yeast isopentenyl-DP delta isomerase. Multiplexed controlled-environment testing revealed that cultivation temperature, rather than illumination intensity, was the main factor affecting isoprene yield from the engineered alga. This is the first report of heterologous isoprene production from a eukaryotic alga and sets a foundation for further exploration of carbon conversion to this commodity chemical.
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29
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Chen X, Wang MY, Deng CH, Beatson RA, Templeton KR, Atkinson RG, Nieuwenhuizen NJ. The hops (Humulus lupulus) genome contains a mid-sized terpene synthase family that shows wide functional and allelic diversity. BMC PLANT BIOLOGY 2023; 23:280. [PMID: 37231379 DOI: 10.1186/s12870-023-04283-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/14/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Hops (Humulus lupulus L.) are a dioecious climbing perennial, with the dried mature "cones" (strobili) of the pistillate/female inflorescences being widely used as both a bittering agent and to enhance the flavour of beer. The glandular trichomes of the bract and bracteole flowering structures of the cones produce an abundance of secondary metabolites, such as terpenoids, bitter acids and prenylated phenolics depending on plant genetics, developmental stage and environment. More knowledge is required on the functional and allelic diversity of terpene synthase (TPS) genes responsible for the biosynthesis of volatile terpenes to assist in flavour-directed hop breeding. RESULTS Major volatile terpene compounds were identified using gas chromatography-mass spectrometry (GC-MS) in the ripe cones of twenty-one hop cultivars grown in New Zealand. All cultivars produced the monoterpene β-myrcene and the sesquiterpenes α-humulene and β-caryophyllene, but the quantities varied broadly. Other terpenes were found in large quantities in only a smaller subset of cultivars, e.g. β-farnesene (in seven cultivars) and α-pinene (in four). In four contrasting cultivars (Wakatu™, Wai-iti™, Nelson Sauvin™, and 'Nugget'), terpene production during cone development was investigated in detail, with concentrations of some of the major terpenes increasing up to 1000-fold during development and reaching maximal levels from 50-60 days after flowering. Utilising the published H. lupulus genome, 87 putative full-length and partial terpene synthase genes were identified. Alleles corresponding to seven TPS genes were amplified from ripe cone cDNA from multiple cultivars and subsequently functionally characterised by transient expression in planta. Alleles of the previously characterised HlSTS1 produced humulene/caryophyllene as the major terpenes. HlRLS alleles produced (R)-(-)-linalool, whilst alleles of two sesquiterpene synthase genes, HlAFS1 and HlAFS2 produced α-farnesene. Alleles of HlMTS1, HlMTS2 and HlTPS1 were inactive in all the hop cultivars studied. CONCLUSIONS Alleles of four TPS genes were identified and shown to produce key aroma volatiles in ripe hop cones. Multiple expressed but inactive TPS alleles were also identified, suggesting that extensive loss-of-function has occurred during domestication and breeding of hops. Our results can be used to develop hop cultivars with novel/improved terpene profiles using marker-assisted breeding strategies to select for, or against, specific TPS alleles.
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Affiliation(s)
- Xiuyin Chen
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Mindy Y Wang
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ron A Beatson
- PFR, 55 Old Mill Road, RD 3, Motueka, 7198, New Zealand
| | | | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Niels J Nieuwenhuizen
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.
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Göttl VL, Pucker B, Wendisch VF, Henke NA. Screening of Structurally Distinct Lycopene β-Cyclases for Production of the Cyclic C40 Carotenoids β-Carotene and Astaxanthin by Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7765-7776. [PMID: 37162369 DOI: 10.1021/acs.jafc.3c01492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Lycopene β-cyclase (EC 5.5.1.19) is one of the key enzymes in the biosynthesis of β-carotene and derived carotenoids. It catalyzes isomerase reactions to form β-carotene from lycopene by β-cyclization of both of its ψ-ends. Lycopene β-cyclases are widespread in nature. We systematically analyzed the phylogeny of lycopene β-cyclases from all kingdoms of life and predicted their transmembrane structures. To this end, a collection of previously characterized lycopene β-cyclase polypeptide sequences served as bait sequences to identify their closest homologues in a range of bacteria, archaea, fungi, algae, and plant species. Furthermore, a DeepTMHMM scan was applied to search for the presence of transmembrane domains. A phylogenetic tree suggests at least five distinct clades, and the DeepTMHMM scan revealed that lycopene β-cyclases are a group of structurally different proteins: membrane-bound and cytosolic enzymes. Representative lycopene β-cyclases were screened in the lycopene-overproducing Corynebacterium glutamicum strain for β-carotene and astaxanthin production. This systematic screening facilitates the identification of new enzymes for carotenoid production. Higher astaxanthin production and less reduction of total carotenoids were achieved with the cytosolic lycopene β-cyclase CrtL from Synechococcus elongatus and the membrane-bound heterodimeric lycopene β-cyclase CrtYcd from Brevibacterium linens.
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Affiliation(s)
- Vanessa L Göttl
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Boas Pucker
- Institute of Plant Biology & BRICS, TU Braunschweig, 38106 Braunschweig, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Nadja A Henke
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
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Nguyen VH, Wemheuer B, Song W, Bennett H, Webster N, Thomas T. Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species. Syst Appl Microbiol 2023; 46:126426. [PMID: 37141831 DOI: 10.1016/j.syapm.2023.126426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Yang Q, Zheng Z, Wang P, Wang L, Wang H, Zhang M, Zhao G. Insights into Regulating Mechanism of Mutagenesis Strains of Elizabethkingia meningoseptica sp. F2 by Omics Analysis. Curr Microbiol 2023; 80:183. [PMID: 37055590 DOI: 10.1007/s00284-023-03270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/14/2023] [Indexed: 04/15/2023]
Abstract
Vitamin K2 plays an important role in electron transport, blood coagulation, and calcium homeostasis, and researchers have been trying to use microbes to produce it. Although our previous studies have shown that gradient radiation, breeding, and culture acclimation can improve vitamin K2 production in Elizabethkingia meningoseptica, the mechanism is still unclear. This study is the first which performs genome sequencing of E. meningoseptica sp. F2 as a basis for subsequent experiments and further comparative analyses with other strains. Comparative metabolic pathway analysis of E. meningoseptica sp. F2, E. coli, Bacillus subtilis, and other vitamin K2 product strains revealed that the mevalonate pathway of E. meningoseptica sp. F2 is different in bacteria at the system level. The expressions of menA, menD, menH, and menI in the menaquinone pathway and idi, hmgR, and ggpps in the mevalonate pathway were higher than those in the original strain. A total of 67 differentially expressed proteins involved in the oxidative phosphorylation metabolic pathway and citric acid cycle (TCA cycle) were identified. Our results reveal that combined gradient radiation breeding and culture acclimation can promote vitamin K2 accumulation probably by regulating the vitamin K2 pathway, oxidative phosphorylation metabolism pathway, and the citrate cycle (TCA cycle).
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Affiliation(s)
- Qiang Yang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Zhiming Zheng
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
| | - Peng Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Li Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Han Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Mengxue Zhang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Genhai Zhao
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
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Hu Y, Song A, Guan Z, Zhang X, Sun H, Wang Y, Yu Q, Fu X, Fang W, Chen F. CmWRKY41 activates CmHMGR2 and CmFPPS2 to positively regulate sesquiterpenes synthesis in Chrysanthemum morifolium. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:821-829. [PMID: 36868130 DOI: 10.1016/j.plaphy.2023.02.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Chrysanthemum morifolium is one of the most significant multipurpose crops with ornamental, medicinal, and edible value. Terpenoids, an essentials component of volatile oils, are abundant in chrysanthemum. However, the transcriptional regulation of terpenoid biosynthesis in chrysanthemums remains unclear. In the present investigation, we identified CmWRKY41, whose expression pattern is similar to that of terpenoid content in chrysanthemum floral scent, as a candidate gene that may promote terpenoid biosynthesis in chrysanthemum. Two structural genes 3-hydroxy-3-methylglutaryl-CoA reductase 2 (CmHMGR2) and farnesyl pyrophosphate synthase 2 (CmFPPS2), play key role in terpene biosynthesis in chrysanthemum. CmWRKY41 can directly bind to the promoters of CmHMGR2 or CmFPPS2 through GTGACA or CTGACG elements and activate its expression to promote sesquiterpene biosynthesis. In summary, these results indicate that CmWRKY41 targets CmHMGR2 and CmFPPS2 to positively regulate sesquiterpene biosynthesis in chrysanthemums. This study preliminarily revealed the molecular mechanism of terpenoid biosynthesis in chrysanthemum while enriching the secondary metabolism regulatory network.
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Affiliation(s)
- Yueheng Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Hainan Sun
- Jiangsu Academy of Forestry, Nanjing, 211153, China.
| | - Yuxi Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qi Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xianrong Fu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Liu X, Zhang P, Zhao Q, Huang AC. Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:417-443. [PMID: 35852486 DOI: 10.1111/jipb.13330] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant natural products have been extensively exploited in food, medicine, flavor, cosmetic, renewable fuel, and other industrial sectors. Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products. Compared with engineering microbes for the production of plant natural products, the potential of plants as chassis for producing these compounds is underestimated, largely due to challenges encountered in engineering plants. Knowledge in plant engineering is instrumental for enabling the effective and efficient production of valuable phytochemicals in plants, and also paves the way for a more sustainable future agriculture. In this manuscript, we briefly recap the biosynthesis of plant natural products, focusing primarily on industrially important terpenoids, alkaloids, and phenylpropanoids. We further summarize the plant hosts and strategies that have been used to engineer the production of natural products. The challenges and opportunities of using plant synthetic biology to achieve rapid and scalable production of high-value plant natural products are also discussed.
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Affiliation(s)
- Xinyu Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Peijun Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiao Zhao
- Shenzhen Institutes of Advanced Technology (SIAT), the Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
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35
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Bi Y, Guo P, Liu L, Chen L, Zhang W. Elucidation of sterol biosynthesis pathway and its co-regulation with fatty acid biosynthesis in the oleaginous marine protist Schizochytrium sp. Front Bioeng Biotechnol 2023; 11:1188461. [PMID: 37180050 PMCID: PMC10174431 DOI: 10.3389/fbioe.2023.1188461] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023] Open
Abstract
Sterols constitute vital structural and regulatory components of eukaryotic cells. In the oleaginous microorganism Schizochytrium sp. S31, the sterol biosynthetic pathway primarily produces cholesterol, stigmasterol, lanosterol, and cycloartenol. However, the sterol biosynthesis pathway and its functional roles in Schizochytrium remain unidentified. Through Schizochytrium genomic data mining and a chemical biology approach, we first in silico elucidated the mevalonate and sterol biosynthesis pathways of Schizochytrium. The results showed that owing to the lack of plastids in Schizochytrium, it is likely to use the mevalonate pathway as the terpenoid backbone pathway to supply isopentenyl diphosphate for the synthesis of sterols, similar to that in fungi and animals. In addition, our analysis revealed a chimeric organization of the Schizochytrium sterol biosynthesis pathway, which possesses features of both algae and animal pathways. Temporal tracking of sterol profiles reveals that sterols play important roles in Schizochytrium growth, carotenoid synthesis, and fatty acid synthesis. Furthermore, the dynamics of fatty acid and transcription levels of genes involved in fatty acid upon chemical inhibitor-induced sterol inhibition reveal possible co-regulation of sterol synthesis and fatty acid synthesis, as the inhibition of sterol synthesis could promote the accumulation of fatty acid in Schizochytrium. Sterol and carotenoid metabolisms are also found possibly co-regulated, as the inhibition of sterols led to decreased carotenoid synthesis through down-regulating the gene HMGR and crtIBY in Schizochytrium. Together, elucidation of the Schizochytrium sterol biosynthesis pathway and its co-regulation with fatty acid synthesis lay the essential foundation for engineering Schizochytrium for the sustainable production of lipids and high-value chemicals.
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Affiliation(s)
- Yali Bi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Pengfei Guo
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Liangsen Liu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
- *Correspondence: Weiwen Zhang,
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Carr S, Buan NR. Insights into the biotechnology potential of Methanosarcina. Front Microbiol 2022; 13:1034674. [PMID: 36590411 PMCID: PMC9797515 DOI: 10.3389/fmicb.2022.1034674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 12/23/2022] Open
Abstract
Methanogens are anaerobic archaea which conserve energy by producing methane. Found in nearly every anaerobic environment on earth, methanogens serve important roles in ecology as key organisms of the global carbon cycle, and in industry as a source of renewable biofuels. Environmentally, methanogenic archaea play an essential role in the reintroducing unavailable carbon to the carbon cycle by anaerobically converting low-energy, terminal metabolic degradation products such as one and two-carbon molecules into methane which then returns to the aerobic portion of the carbon cycle. In industry, methanogens are commonly used as an inexpensive source of renewable biofuels as well as serving as a vital component in the treatment of wastewater though this is only the tip of the iceberg with respect to their metabolic potential. In this review we will discuss how the efficient central metabolism of methanoarchaea could be harnessed for future biotechnology applications.
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Over 40 Years of Fosmidomycin Drug Research: A Comprehensive Review and Future Opportunities. Pharmaceuticals (Basel) 2022; 15:ph15121553. [PMID: 36559004 PMCID: PMC9782300 DOI: 10.3390/ph15121553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
To address the continued rise of multi-drug-resistant microorganisms, the development of novel drugs with new modes of action is urgently required. While humans biosynthesize the essential isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) via the established mevalonate pathway, pathogenic protozoa and certain pathogenic eubacteria use the less well-known methylerythritol phosphate pathway for this purpose. Important pathogens using the MEP pathway are, for example, Plasmodium falciparum, Mycobacterium tuberculosis, Pseudomonas aeruginosa and Escherichia coli. The enzymes of that pathway are targets for antiinfective drugs that are exempt from target-related toxicity. 2C-Methyl-D-erythritol 4-phosphate (MEP), the second enzyme of the non-mevalonate pathway, has been established as the molecular target of fosmidomycin, an antibiotic that has so far failed to be approved as an anti-infective drug. This review describes the development and anti-infective properties of a wide range of fosmidomycin derivatives synthesized over the last four decades. Here we discuss the DXR inhibitor pharmacophore, which comprises a metal-binding group, a phosphate or phosphonate moiety and a connecting linker. Furthermore, non-fosmidomycin-based DXRi, bisubstrate inhibitors and several prodrug concepts are described. A comprehensive structure-activity relationship (SAR) of nearly all inhibitor types is presented and some novel opportunities for further drug development of DXR inhibitors are discussed.
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Wang S, Wang A, Wang H, Jiang F, Xu D, Fan W. Chromosome-level genome of a leaf vegetable Glebionis coronaria provides insights into the biosynthesis of monoterpenoids contributing to its special aroma. DNA Res 2022; 29:dsac036. [PMID: 36197084 PMCID: PMC9724771 DOI: 10.1093/dnares/dsac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022] Open
Abstract
Glebionis coronaria is a popular vegetable with special aroma and a medical plant in East Asia and Mediterranean, but its biological studies and breeding have been hindered by the lack of reference genome. Here, we present a chromosome-level reference genome of G. coronaria, with assembled genome size of 6.8 Gb, which is the largest among all the published genomes of diploid Asteraceae species. The large genome size of G. coronaria is mainly caused by the recent widespread explosions of long-terminal-repeat retrotransposons. Analyses of macro-synteny and synonymous mutation rate distribution indicate that the G. coronaria genome experienced a whole-genome triplication at 40-45 million years ago, shared with all Asteraceae species. In subtribe Artemisiinae, Glebionis arose before the divergence of Chrysanthemum from Artemisia, and Glebionis species evolved much faster than Chrysanthemum and Artemisia species. In G. coronaria, the synthesis genes of monoterpenoids 8-oxocitronellyl enol and isopiperitenone were expanded, and the higher expressions of these expanded genes in leaves and stems may contribute to its special aroma. The G. coronaria genomic resources will promote the evolution studies of Asteraceae, the metabolism mechanism studies of bioactive compounds, and the breeding improvement of agronomic traits in G. coronaria.
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Affiliation(s)
- Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
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Zhang DC, Luo LL, Wang ZR, Xu WJ, Li JL, Tan ST, Wu JH, Li Y, Zhang C, Liang C, Wang XY. SmDXS5, acting as a molecular valve, plays a key regulatory role in the primary and secondary metabolism of tanshinones in Salvia miltiorrhiza. FRONTIERS IN PLANT SCIENCE 2022; 13:1043761. [PMID: 36438137 PMCID: PMC9685628 DOI: 10.3389/fpls.2022.1043761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Red sage, the dry root and rhizome of the herbaceous plant Salvia miltiorrhiza Bunge, is widely used for treating various diseases. The low content of tanshinones (terpenoids) has always restricted development of the S. miltiorrhiza industry. Here, we found that SmDXS5, a rate-limiting enzyme-coding gene located at the intersection of primary and secondary metabolism, can effectively change the transcription level and secondary metabolome profile of hairy roots of S. miltiorrhiza, and significantly increase the content of tanshinones. Agrobacterium rhizogenes was used to infuse S. miltiorrhiza explants, and hairy roots of S. miltiorrhiza expressing the SmDXS5 gene were obtained successfully. We identified 39 differentially accumulated metabolites (DAMs) by metabolomics based on ultra-high performance liquid chromatography quadrupole exactive mass spectrometry and multivariate statistics. These DAMs might be key metabolites of SmDXS5 gene regulation. RNA sequencing was used to compare gene expression between the hairy roots of the SmDXS5 overexpressing group and the blank control (BC) group. Compared with the BC group, 18,646 differentially expressed genes were obtained: 8994 were upregulated and 9,652 downregulated. The combined transcriptome and metabolome analyses revealed that the mevalonate and methylerythritol phosphate pathways and synthase gene expression levels in the SmDXS5 overexpressing group were upregulated significantly, and the accumulation of tanshinone components was increased significantly, which promoted the process of glycolysis and promoted the transformation of carbohydrates to secondary metabolism. Moreover, the expression of SmPAL, the first rate-limiting enzyme gene of the phenylpropane pathway, decreased, reducing the accumulation of phenolic acid, another secondary metabolite. Therefore, SmDXS5 can be defined as a 'valve' gene, mainly responsible for regulating the distribution of primary and secondary metabolic flow of tanshinones in S. miltiorrhiza, and for other secondary metabolic pathways. The discovery of SmDXS5 and its molecular valve function in regulating primary and secondary metabolism will provide a basis for the industrial production of tanshinone components, and cultivation of high quality S. miltiorrhiza.
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Nirati Y, Purushotham N, Alagesan S. Quantitative insight into the metabolism of isoprene-producing Synechocystis sp. PCC 6803 using steady state 13C-MFA. PHOTOSYNTHESIS RESEARCH 2022; 154:195-206. [PMID: 36070060 DOI: 10.1007/s11120-022-00957-0] [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] [Received: 05/13/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria are photosynthetic bacteria, widely studied for the conversion of atmospheric carbon dioxide to useful platform chemicals. Isoprene is one such industrially important chemical, primarily used for production of synthetic rubber and biofuels. Synechocystis sp. PCC 6803, a genetically amenable cyanobacterium, produces isoprene on heterologous expression of isoprene synthase gene, albeit in very low quantities. Rationalized metabolic engineering to re-route the carbon flux for enhanced isoprene production requires in-dept knowledge of the metabolic flux distribution in the cell. Hence, in the present study, we undertook steady state 13C-metabolic flux analysis of glucose-tolerant wild-type (GTN) and isoprene-producing recombinant (ISP) Synechocystis sp. to understand and compare the carbon flux distribution in the two strains. The R-values for amino acids, flux analysis predictions and gene expression profiles emphasized predominance of Calvin cycle and glycogen metabolism in GTN. Alternatively, flux analysis predicted higher activity of the anaplerotic pathway through phosphoenolpyruvate carboxylase and malic enzyme in ISP. The striking difference in the Calvin cycle, glycogen metabolism and anaplerotic pathway activity in GTN and ISP suggested a possible role of energy molecules (ATP and NADPH) in regulating the carbon flux distribution in GTN and ISP. This claim was further supported by the transcript level of selected genes of the electron transport chain. This study provides the first quantitative insight into the carbon flux distribution of isoprene-producing cyanobacterium, information critical for developing Synechocystis sp. as a single cell factory for isoprenoid/terpenoid production.
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Affiliation(s)
- Yasha Nirati
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India
| | - Nidhish Purushotham
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India
- Dayananda Sagar University, Bengaluru, India
| | - Swathi Alagesan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India.
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41
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Sleda MA, Li ZH, Behera R, Baierna B, Li C, Jumpathong J, Malwal SR, Kawamukai M, Oldfield E, Moreno SNJ. The Heptaprenyl Diphosphate Synthase (Coq1) Is the Target of a Lipophilic Bisphosphonate That Protects Mice against Toxoplasma gondii Infection. mBio 2022; 13:e0196622. [PMID: 36129297 PMCID: PMC9600589 DOI: 10.1128/mbio.01966-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Prenyldiphosphate synthases catalyze the reaction of allylic diphosphates with one or more isopentenyl diphosphate molecules to form compounds such as farnesyl diphosphate, used in, e.g., sterol biosynthesis and protein prenylation, as well as longer "polyprenyl" diphosphates, used in ubiquinone and menaquinone biosynthesis. Quinones play an essential role in electron transport and are associated with the inner mitochondrial membrane due to the presence of the polyprenyl group. In this work, we investigated the synthesis of the polyprenyl diphosphate that alkylates the ubiquinone ring precursor in Toxoplasma gondii, an opportunistic pathogen that causes serious disease in immunocompromised patients and the unborn fetus. The enzyme that catalyzes this early step of the ubiquinone synthesis is Coq1 (TgCoq1), and we show that it produces the C35 species heptaprenyl diphosphate. TgCoq1 localizes to the mitochondrion and is essential for in vitro T. gondii growth. We demonstrate that the growth defect of a T. gondii TgCoq1 mutant is rescued by complementation with a homologous TgCoq1 gene or with a (C45) solanesyl diphosphate synthase from Trypanosoma cruzi (TcSPPS). We find that a lipophilic bisphosphonate (BPH-1218) inhibits T. gondii growth at low-nanomolar concentrations, while overexpression of the TgCoq1 enzyme dramatically reduced growth inhibition by the bisphosphonate. Both the severe growth defect of the mutant and the inhibition by BPH-1218 were rescued by supplementation with a long-chain (C30) ubiquinone (UQ6). Importantly, BPH-1218 also protected mice against a lethal T. gondii infection. TgCoq1 thus represents a potential drug target that could be exploited for improved chemotherapy of toxoplasmosis. IMPORTANCE Millions of people are infected with Toxoplasma gondii, and the available treatment for toxoplasmosis is not ideal. Most of the drugs currently used are only effective for the acute infection, and treatment can trigger serious side effects requiring changes in the therapeutic approach. There is, therefore, a compelling need for safe and effective treatments for toxoplasmosis. In this work, we characterize an enzyme of the mitochondrion of T. gondii that can be inhibited by an isoprenoid pathway inhibitor. We present evidence that demonstrates that inhibition of the enzyme is linked to parasite death. In addition, the inhibitor can protect mice against a lethal dose of T. gondii. Our results thus reveal a promising chemotherapeutic target for the development of new medicines for toxoplasmosis.
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Affiliation(s)
- Melissa A. Sleda
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Zhu-Hong Li
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Ranjan Behera
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Baihetiya Baierna
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Catherine Li
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Jomkwan Jumpathong
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
| | - Satish R. Malwal
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Makoto Kawamukai
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Silvia N. J. Moreno
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
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42
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Braasch-Turi MM, Koehn JT, Crans DC. Chemistry of Lipoquinones: Properties, Synthesis, and Membrane Location of Ubiquinones, Plastoquinones, and Menaquinones. Int J Mol Sci 2022; 23:12856. [PMID: 36361645 PMCID: PMC9656164 DOI: 10.3390/ijms232112856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
Lipoquinones are the topic of this review and are a class of hydrophobic lipid molecules with key biological functions that are linked to their structure, properties, and location within a biological membrane. Ubiquinones, plastoquinones, and menaquinones vary regarding their quinone headgroup, isoprenoid sidechain, properties, and biological functions, including the shuttling of electrons between membrane-bound protein complexes within the electron transport chain. Lipoquinones are highly hydrophobic molecules that are soluble in organic solvents and insoluble in aqueous solution, causing obstacles in water-based assays that measure their chemical properties, enzyme activities and effects on cell growth. Little is known about the location and ultimately movement of lipoquinones in the membrane, and these properties are topics described in this review. Computational studies are particularly abundant in the recent years in this area, and there is far less experimental evidence to verify the often conflicting interpretations and conclusions that result from computational studies of very different membrane model systems. Some recent experimental studies have described using truncated lipoquinone derivatives, such as ubiquinone-2 (UQ-2) and menaquinone-2 (MK-2), to investigate their conformation, their location in the membrane, and their biological function. Truncated lipoquinone derivatives are soluble in water-based assays, and hence can serve as excellent analogs for study even though they are more mobile in the membrane than the longer chain counterparts. In this review, we will discuss the properties, location in the membrane, and syntheses of three main classes of lipoquinones including truncated derivatives. Our goal is to highlight the importance of bridging the gap between experimental and computational methods and to incorporate properties-focused considerations when proposing future studies relating to the function of lipoquinones in membranes.
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Affiliation(s)
| | - Jordan T. Koehn
- Chemistry Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Debbie C. Crans
- Chemistry Department, Colorado State University, Fort Collins, CO 80523, USA
- Cell & Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
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43
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Haywood J, Breese KJ, Zhang J, Waters MT, Bond CS, Stubbs KA, Mylne JS. A fungal tolerance trait and selective inhibitors proffer HMG-CoA reductase as a herbicide mode-of-action. Nat Commun 2022; 13:5563. [PMID: 36137996 PMCID: PMC9500038 DOI: 10.1038/s41467-022-33185-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/07/2022] [Indexed: 12/02/2022] Open
Abstract
Decades of intense herbicide use has led to resistance in weeds. Without innovative weed management practices and new herbicidal modes of action, the unabated rise of herbicide resistance will undoubtedly place further stress upon food security. HMGR (3-hydroxy-3-methylglutaryl-coenzyme A reductase) is the rate limiting enzyme of the eukaryotic mevalonate pathway successfully targeted by statins to treat hypercholesterolemia in humans. As HMGR inhibitors have been shown to be herbicidal, HMGR could represent a mode of action target for the development of herbicides. Here, we present the crystal structure of a HMGR from Arabidopsis thaliana (AtHMG1) which exhibits a wider active site than previously determined structures from different species. This plant conserved feature enables the rational design of specific HMGR inhibitors and we develop a tolerance trait through sequence analysis of fungal gene clusters. These results suggest HMGR to be a viable herbicide target modifiable to provide a tolerance trait. Managing herbicide resistance problem needs the identification of new herbicidal modes of action. Here, the authors solve the crystal structures of Arabidopsis HMGR and show HMGR as a potential new herbicide target by identifying plant-specific HMGR inhibitors and engineering tolerant trait in Arabidopsis.
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Affiliation(s)
- Joel Haywood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA, 6102, Australia. .,School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia.
| | - Karen J Breese
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Jingjing Zhang
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Mark T Waters
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Joshua S Mylne
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA, 6102, Australia. .,School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia.
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44
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Xu R, Ming Y, Li Y, Li S, Zhu W, Wang H, Guo J, Shi Z, Shu S, Xiong C, Cheng X, Wang L, You J, Wan D. Full-Length Transcriptomic Sequencing and Temporal Transcriptome Expression Profiling Analyses Offer Insights into Terpenoid Biosynthesis in Artemisia argyi. Molecules 2022; 27:molecules27185948. [PMID: 36144681 PMCID: PMC9501300 DOI: 10.3390/molecules27185948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/31/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Artemisiae argyi Folium is a traditional herbal medicine used for moxibustion heat therapy in China. The volatile oils in A.argyi leaves are closely related to its medicinal value. Records suggest that the levels of these terpenoids components within the leaves vary as a function of harvest time, with June being the optimal time for A. argyi harvesting, owing to the high levels of active ingredients during this month. However, the molecular mechanisms governing terpenoid biosynthesis and the time-dependent changes in this activity remain unclear. In this study, GC–MS analysis revealed that volatile oil levels varied across four different harvest months (April, May, June, and July) in A. argyi leaves, and the primarily terpenoids components (including both monoterpenes and sesquiterpenes) reached peak levels in early June. Through single-molecule real-time (SMRT) sequencing, corrected by Illumina RNA-sequencing (RNA-Seq), 44 full-length transcripts potentially involved in terpenoid biosynthesis were identified in this study. Differentially expressed genes (DEGs) exhibiting time-dependent expression patterns were divided into 12 coexpression clusters. Integrated chemical and transcriptomic analyses revealed distinct time-specific transcriptomic patterns associated with terpenoid biosynthesis. Subsequent hierarchical clustering and correlation analyses ultimately identified six transcripts that were closely linked to the production of these two types of terpenoid within A. argyi leaves, revealing that the structural diversity of terpenoid is related to the generation of the diverse terpene skeletons by prenyltransferase (TPS) family of enzymes. These findings can guide further studies of the molecular mechanisms underlying the quality of A. argyi leaves, aiding in the selection of optimal timing for harvests of A. argyi.
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Affiliation(s)
- Ran Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
| | - Yue Ming
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yongchang Li
- College of Osteopathic Medicine, Kansas City University of Medicine and Biosciences, Joplin, MO 64804, USA
| | - Shaoting Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Wenjun Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hongxun Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jie Guo
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China
| | - Zhaohua Shi
- Key Laboratory of Chinese Medicine Resources and Compound Formula, Ministry of Education, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiang Cheng
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Limei Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jingmao You
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
| | - Dingrong Wan
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
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45
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Dufossé L. Back to nature, microbial production of pigments and colorants for food use. ADVANCES IN FOOD AND NUTRITION RESEARCH 2022; 102:93-122. [PMID: 36064297 DOI: 10.1016/bs.afnr.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Pigments-producing microorganisms are quite common in Nature. However, there is a long journey from the Petri dish to the market place. Twenty-five years ago, scientists wondered if such productions would remain a scientific oddity or become an industrial reality. The answer is not straightforward as processes using fungi, bacteria or yeasts can now indeed provide carotenoids or phycocyanin at an industrial level. Another production factor to consider is peculiar as Monascus red colored food is consumed by more than one billion Asian people; however, still banned in many other countries. European and American consumers will follow as soon as "100%-guaranteed" toxin-free strains (molecular engineered strains, citrinin gene deleted strains) will be developed and commercialized at a world level. For other pigmented biomolecules, some laboratories and companies invested and continue to invest a lot of money as any combination of new source and/or new pigment requires a lot of experimental work, process optimization, toxicological studies, and regulatory approval. Time will tell whether investments in pigments such as azaphilones or anthraquinones were justified. Future trends involve combinatorial engineering, gene knock-out, and the production of niche pigments not found in plants such as C50 carotenoids or aryl carotenoids.
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Affiliation(s)
- Laurent Dufossé
- Laboratoire de Chimie et Biotechnologie des Produits Naturels (CHEMBIOPRO), Université de La Réunion, ESIROI Agroalimentaire, Ile de La Réunion, France.
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46
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Shao X, He W, Fan Y, Shen Q, Mao J, Li M, Hu G, Liu F, Wang C. Study on the differences in aroma components and formation mechanisms of “Nasmi” melon from different production areas. Food Sci Nutr 2022; 10:3608-3620. [DOI: 10.1002/fsn3.2958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/15/2022] [Accepted: 06/18/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Xupeng Shao
- Key Laboratory of Agro‐Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro‐Products (Urumqi), Institute of Quality Standards & Testing Technology for Agro‐Products, Xinjiang Academy of Agricultural Sciences Ministry of Agriculture and Rural Affairs Urumqi China
- College of Food Science and Pharmacy Xinjiang Agricultural University Urumqi China
| | - Weizhong He
- Key Laboratory of Agro‐Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro‐Products (Urumqi), Institute of Quality Standards & Testing Technology for Agro‐Products, Xinjiang Academy of Agricultural Sciences Ministry of Agriculture and Rural Affairs Urumqi China
- College of Food Science and Pharmacy Xinjiang Agricultural University Urumqi China
| | - Yingying Fan
- Key Laboratory of Agro‐Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro‐Products (Urumqi), Institute of Quality Standards & Testing Technology for Agro‐Products, Xinjiang Academy of Agricultural Sciences Ministry of Agriculture and Rural Affairs Urumqi China
| | - Qi Shen
- Key Laboratory of Agro‐Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro‐Products (Urumqi), Institute of Quality Standards & Testing Technology for Agro‐Products, Xinjiang Academy of Agricultural Sciences Ministry of Agriculture and Rural Affairs Urumqi China
- College of Food Science and Pharmacy Xinjiang Agricultural University Urumqi China
| | - Jiancai Mao
- Hami Melon Research Center Xinjiang Academy of Agricultural Sciences Urumqi China
| | - Meihua Li
- Hami Melon Research Center Xinjiang Academy of Agricultural Sciences Urumqi China
| | - Guozhi Hu
- Hami Melon Research Center Xinjiang Academy of Agricultural Sciences Urumqi China
| | - Fengjuan Liu
- Key Laboratory of Agro‐Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro‐Products (Urumqi), Institute of Quality Standards & Testing Technology for Agro‐Products, Xinjiang Academy of Agricultural Sciences Ministry of Agriculture and Rural Affairs Urumqi China
- College of Food Science and Pharmacy Xinjiang Agricultural University Urumqi China
| | - Cheng Wang
- Key Laboratory of Agro‐Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro‐Products (Urumqi), Institute of Quality Standards & Testing Technology for Agro‐Products, Xinjiang Academy of Agricultural Sciences Ministry of Agriculture and Rural Affairs Urumqi China
- Xinjiang Academy of Agricultural Sciences Urumqi China
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47
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Liang Z, Lin X, Liao Y, Tang T. Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing. Arch Microbiol 2022; 204:435. [PMID: 35763100 DOI: 10.1007/s00203-022-03043-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/27/2022] [Indexed: 11/02/2022]
Abstract
Panax notoginseng is a traditional Chinese medicinal herb with diverse properties that is cultivated in a narrow ecological range because of its sensitivity to high temperatures. Endophytic bacteria play a prominent role in plant response to climate warming. However, the endophytic bacterial structures in P. notoginseng at high temperatures are yet unclear. In the present study, the diversity and composition of the endophytic bacterial community, and their relationships with two P. notoginseng plants with different heat tolerance capacities were compared using the full-length 16S rRNA PacBio sequencing system. The results revealed that the diversity and richness of endophytic bacteria were negatively associated with the heat tolerance of P. notoginseng. Beneficial Cyanobacteria, Rhodanobacter and Sphingomonas may be recruited positively by heat-tolerant plants, while higher amounts of adverse Proteobacteria such as Cellvibrio fibrivorans derived from soil destructed the cellular protective barriers of heat-sensitive plants and caused influx of pathogenic bacteria Stenotrophomonas maltophilia. Harmonious and conflicting bacterial community was observed in heat-tolerant and heat-sensitive P. notoginseng, respectively, based on the co-occurrence network. Using functional gene prediction of metabolism, endophytic bacteria have been proposed to be symbiotic with host plants; the bacteria improved primary metabolic pathways and secondary metabolite production of plants, incorporated beneficial endophytes, and combated adverse endophytes to prompt the adaptation of P. notoginseng to a warming environment. These findings provided a new perspective on the function of endophytes in P. notoginseng adaptation to high temperatures, and could pave the way for expanding the cultivable range of P. notoginseng.
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Affiliation(s)
- Zhenting Liang
- School of Life and Health Sciences, Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Xianjing Lin
- School of Life and Health Sciences, Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Yiqun Liao
- School of Life and Health Sciences, Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Ting Tang
- School of Life and Health Sciences, Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils, Hunan University of Science and Technology, Xiangtan, 411201, China.
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48
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Wang JZ, van de Ven W, Xiao Y, He X, Ke H, Yang P, Dehesh K. Reciprocity between a retrograde signal and a putative metalloprotease reconfigures plastidial metabolic and structural states. SCIENCE ADVANCES 2022; 8:eabo0724. [PMID: 35658042 PMCID: PMC9166295 DOI: 10.1126/sciadv.abo0724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Reconfiguration of the plastidial proteome in response to environmental cues is central to tailoring adaptive responses. To define the underlying mechanisms and consequences of these reconfigurations, we performed a suppressor screen, using a mutant (ceh1) accumulating high levels of a plastidial retrograde signaling metabolite, MEcPP. We isolated a revertant partially suppressing the dwarf stature and high salicylic acid of ceh1 and identified the mutation in a putative plastidial metalloprotease (VIR3). Biochemical analyses showed increased VIR3 levels in ceh1, accompanied by reduced abundance of VIR3-target enzymes, ascorbate peroxidase, and glyceraldehyde 3-phophate dehydrogenase B. These proteomic shifts elicited increased H2O2, salicylic acid, and MEcPP levels, as well as stromule formation. High light recapitulated VIR3-associated reconfiguration of plastidial metabolic and structural states. These results establish a link between a plastidial stress-inducible retrograde signaling metabolite and a putative metalloprotease and reveal how the reciprocity between the two components modulates plastidial metabolic and structural states, shaping adaptive responses.
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Affiliation(s)
- Jin-Zheng Wang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Wilhelmina van de Ven
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Yanmei Xiao
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Xiang He
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Haiyan Ke
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Panyu Yang
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
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49
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Lin CC, Hoo SY, Ma LT, Lin C, Huang KF, Ho YN, Sun CH, Lee HJ, Chen PY, Shu LJ, Wang BW, Hsu WC, Ko TP, Yang YL. Integrated omics approach to unveil antifungal bacterial polyynes as acetyl-CoA acetyltransferase inhibitors. Commun Biol 2022; 5:454. [PMID: 35551233 PMCID: PMC9098870 DOI: 10.1038/s42003-022-03409-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/23/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial polyynes are highly active natural products with a broad spectrum of antimicrobial activities. However, their detailed mechanism of action remains unclear. By integrating comparative genomics, transcriptomics, functional genetics, and metabolomics analysis, we identified a unique polyyne resistance gene, masL (encoding acetyl-CoA acetyltransferase), in the biosynthesis gene cluster of antifungal polyynes (massilin A 1, massilin B 2, collimonin C 3, and collimonin D 4) of Massilia sp. YMA4. Crystallographic analysis indicated that bacterial polyynes serve as covalent inhibitors of acetyl-CoA acetyltransferase. Moreover, we confirmed that the bacterial polyynes disrupted cell membrane integrity and inhibited the cell viability of Candida albicans by targeting ERG10, the homolog of MasL. Thus, this study demonstrated that acetyl-CoA acetyltransferase is a potential target for developing antifungal agents. In a multi-omics analysis, bacterial polyynes are found to act as antifungal agents by inhibiting the Candida albicans polyyne resistance gene ERG10, the homolog of MasL encoding acetyl-CoA acetyltransferase.
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Affiliation(s)
- Ching-Chih Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan
| | - Sin Yong Hoo
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan
| | - Li-Ting Ma
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan
| | - Chih Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Ying-Ning Ho
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Jhongjheng Dist., Keelung, 202, Taiwan
| | - Chi-Hui Sun
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Han-Jung Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Pi-Yu Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Lin-Jie Shu
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Bo-Wei Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan.,Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Gushan Dist., Kaohsiung, 804, Taiwan
| | - Wei-Chen Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan. .,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan.
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50
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Sussmann RAC, Gabriel HB, Ríos AG, Menchaca Vega DS, Yamaguchi LF, Doménech-Carbó A, Cebrián-Torrejón G, Kimura EA, Kato MJ, Bofill Verdaguer I, Crispim M, Katzin AM. Presence of Phylloquinone in the Intraerythrocytic Stages of Plasmodium falciparum. Front Cell Infect Microbiol 2022; 12:869085. [PMID: 35531326 PMCID: PMC9069557 DOI: 10.3389/fcimb.2022.869085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria is one of the most widespread parasitic diseases, especially in Africa, Southeast Asia and South America. One of the greatest problems for control of the disease is the emergence of drug resistance, which leads to a need for the development of new antimalarial compounds. The biosynthesis of isoprenoids has been investigated as part of a strategy to identify new targets to obtain new antimalarial drugs. Several isoprenoid quinones, including menaquinone-4 (MK-4/vitamin K2), α- and γ-tocopherol and ubiquinone (UQ) homologs UQ-8 and UQ-9, were previously detected in in vitro cultures of Plasmodium falciparum in asexual stages. Herein, we described for the first time the presence of phylloquinone (PK/vitamin K1) in P. falciparum and discuss the possible origins of this prenylquinone. While our results in metabolic labeling experiments suggest a biosynthesis of PK prenylation via phytyl pyrophosphate (phytyl-PP) with phytol being phosphorylated, on the other hand, exogenous PK attenuated atovaquone effects on parasitic growth and respiration, showing that this metabolite can be transported from extracellular environment and that the mitochondrial electron transport system (ETS) of P. falciparum is capable to interact with PK. Although the natural role and origin of PK remains elusive, this work highlights the PK importance in plasmodial metabolism and future studies will be important to elucidate in seeking new targets for antimalarial drugs.
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Affiliation(s)
- Rodrigo A. C. Sussmann
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Center for Environmental Sciences, Institute of Humanities, Arts and Sciences, Federal University of Southern Bahia, Porto Seguro, Brazil
| | - Heloisa B. Gabriel
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alejandro García Ríos
- Laboratory of Environmental Chemistry and Metalopharmaceuticals, Institute of Chemistry at the University of São Paulo, São Paulo, Brazil
- Chemistry Program, Universidad del Quindio, Quindio, Colombia
| | - Danielle S. Menchaca Vega
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lydia F. Yamaguchi
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Antonio Doménech-Carbó
- Departament of Analytic Chemistry, Facultat de Química, Universitat de València, Valencia, Spain
| | - Gerardo Cebrián-Torrejón
- Laboratoire Connaissance et Valorisation Equipes d'Accueil (COVACHIM-M2E EA) 3592, Université des Antilles, Pointe-à-Pitre Cedex, Pointe-à-Pitre, Guadeloupe, France
| | - Emilia A. Kimura
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Massuo J. Kato
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Ignasi Bofill Verdaguer
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcell Crispim
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alejandro M. Katzin
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Alejandro M. Katzin,
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