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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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2
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Lam M, Leung KM, Lai GKK, Leung FCC, Griffin SDJ. Complete genome sequence of Gluconobacter frateurii ML.ISBL3, an endophytic strain isolated from aerial roots of Syngonium podophyllum. Microbiol Resour Announc 2024; 13:e0110623. [PMID: 38470266 PMCID: PMC11008163 DOI: 10.1128/mra.01106-23] [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: 11/16/2023] [Accepted: 03/02/2024] [Indexed: 03/13/2024] Open
Abstract
The endophytic strain Gluconobacter frateurii ML.ISBL3 was isolated from aerial roots of Syngonium podophyllum in Hong Kong. Its complete genome, established through hybrid assembly, comprises a single chromosome of 3,309,710 bp (56.30% G+C).
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Affiliation(s)
- M. Lam
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - K. M. Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - G. K. K. Lai
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - F. C. C. Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - S. D. J. Griffin
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
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3
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Ma Y, Shang Y, Stephanopoulos G. Engineering peroxisomal biosynthetic pathways for maximization of triterpene production in Yarrowia lipolytica. Proc Natl Acad Sci U S A 2024; 121:e2314798121. [PMID: 38261612 PMCID: PMC10835042 DOI: 10.1073/pnas.2314798121] [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: 08/25/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Constructing efficient cell factories for product synthesis is frequently hampered by competing pathways and/or insufficient precursor supply. This is particularly evident in the case of triterpenoid biosynthesis in Yarrowia lipolytica, where squalene biosynthesis is tightly coupled to cytosolic biosynthesis of sterols essential for cell viability. Here, we addressed this problem by reconstructing the complete squalene biosynthetic pathway, starting from acetyl-CoA, in the peroxisome, thus harnessing peroxisomal acetyl-CoA pool and sequestering squalene synthesis in this organelle from competing cytosolic reactions. This strategy led to increasing the squalene levels by 1,300-fold relatively to native cytosolic synthesis. Subsequent enhancement of the peroxisomal acetyl-CoA supply by two independent approaches, 1) converting cellular lipid pool to peroxisomal acetyl-CoA and 2) establishing an orthogonal acetyl-CoA shortcut from CO2-derived acetate in the peroxisome, further significantly improved local squalene accumulation. Using these approaches, we constructed squalene-producing strains capable of yielding 32.8 g/L from glucose, and 31.6 g/L from acetate by employing a cofeeding strategy, in bioreactor fermentations. Our findings provide a feasible strategy for protecting intermediate metabolites that can be claimed by multiple reactions by engineering peroxisomes in Y. lipolytica as microfactories for the production of such intermediates and in particular acetyl-CoA-derived metabolites.
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Affiliation(s)
- Yongshuo Ma
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, Chinese Academy of Agricultural Sciences (CAAS)-Yunnan Normal University (YNNU)-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming650500, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy (Ministry of Education), Yunnan Normal University, Kunming650500, China
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
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4
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Oshkin IY, Tikhonova EN, Suleimanov RZ, Ashikhmin AA, Ivanova AA, Pimenov NV, Dedysh SN. All Kinds of Sunny Colors Synthesized from Methane: Genome-Encoded Carotenoid Production by Methylomonas Species. Microorganisms 2023; 11:2865. [PMID: 38138009 PMCID: PMC10745290 DOI: 10.3390/microorganisms11122865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Carotenoids are secondary metabolites that exhibit antioxidant properties and are characterized by a striking range of colorations from red to yellow. These natural pigments are synthesized by a wide range of eukaryotic and prokaryotic organisms. Among the latter, carotenoid-producing methanotrophic bacteria, which display fast growth on methane or natural gas, are of particular interest as potential producers of a feed protein enriched with carotenoids. Until recently, Methylomonas strain 16a and Methylomonas sp. ZR1 remained the only representatives of the genus for which detailed carotenoid profile was determined. In this study, we analyzed the genome sequences of five strains of Methylomonas species whose pigmentation varied from white and yellow to orange and red, and identified carotenoids produced by these bacteria. Carotenoids synthesized using four pigmented strains included C30 fraction, primarily composed of 4,4'-diaplycopene-4,4'-dioic acid and 4,4'-diaplycopenoic acid, as well as C40 fraction with the major compound represented by 1,1'-dihydroxy-3,4-didehydrolycopene. The genomes of studied Methylomonas strains varied in size between 4.59 and 5.45 Mb and contained 4201-4735 protein-coding genes. These genomes and 35 reference Methylomonas genomes available in the GenBank were examined for the presence of genes encoding carotenoid biosynthesis. Genomes of all pigmented Methylomonas strains harbored genes necessary for the synthesis of 4,4'-diaplycopene-4,4'-dioic acid. Non-pigmented "Methylomonas montana" MW1T lacked the crtN gene required for carotenoid production. Nearly all strains possessed phytoene desaturases, which explained their ability to naturally synthesize lycopene. Thus, members of the genus Methylomonas can potentially be considered as producers of C30 and C40 carotenoids from methane.
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Affiliation(s)
- Igor Y. Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Ekaterina N. Tikhonova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Ruslan Z. Suleimanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Aleksandr A. Ashikhmin
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia
| | - Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Nikolai V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
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5
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Akone S, Hug JJ, Kaur A, Garcia R, Müller R. Structure Elucidation and Biosynthesis of Nannosterols A and B, Myxobacterial Sterols from Nannocystis sp. MNa10993. JOURNAL OF NATURAL PRODUCTS 2023; 86:915-923. [PMID: 37011180 PMCID: PMC10152446 DOI: 10.1021/acs.jnatprod.2c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Indexed: 05/04/2023]
Abstract
Myxobacteria represent an underinvestigated source of chemically diverse and biologically active secondary metabolites. Here, we report the discovery, isolation, structure elucidation, and biological evaluation of two new bacterial sterols, termed nannosterols A and B (1, 2), from the terrestrial myxobacterium Nannocystis sp. (MNa10993). Nannosterols feature a cholestanol core with numerous modifications including a secondary alcohol at position C-15, a terminal vicinal diol side chain at C-24-C-25 (1, 2), and a hydroxy group at the angular methyl group at C-18 (2), which is unprecedented for bacterial sterols. Another rare chemical feature of bacterial triterpenoids is a ketone group at position C-7, which is also displayed by 1 and 2. The combined exploration based on myxobacterial high-resolution secondary metabolome data and genomic in silico investigations exposed the nannosterols as frequently produced sterols within the myxobacterial suborder of Nannocystineae. The discovery of the nannosterols provides insights into the biosynthesis of these new myxobacterial sterols, with implications in understanding the evolution of sterol production by prokaryotes.
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Affiliation(s)
- Sergi
H. Akone
- Helmholtz-Institute
for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for
Infection Research (HZI), Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German
Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz
International Laboratories, Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Department
of Chemistry, Faculty of Science, University
of Douala, P.O. Box 24157, Douala, Cameroon
| | - Joachim J. Hug
- Helmholtz-Institute
for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for
Infection Research (HZI), Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German
Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz
International Laboratories, Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Amninder Kaur
- Helmholtz-Institute
for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for
Infection Research (HZI), Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German
Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz
International Laboratories, Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Ronald Garcia
- Helmholtz-Institute
for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for
Infection Research (HZI), Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German
Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz
International Laboratories, Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz-Institute
for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for
Infection Research (HZI), Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German
Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz
International Laboratories, Department of Microbial Natural Products, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
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6
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Bioassay-Guided Fractionation Leads to the Detection of Cholic Acid Generated by the Rare Thalassomonas sp. Mar Drugs 2022; 21:md21010002. [PMID: 36662175 PMCID: PMC9860883 DOI: 10.3390/md21010002] [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: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial symbionts of marine invertebrates are rich sources of novel, pharmaceutically relevant natural products that could become leads in combatting multidrug-resistant pathogens and treating disease. In this study, the bioactive potential of the marine invertebrate symbiont Thalassomonas actiniarum was investigated. Bioactivity screening of the strain revealed Gram-positive specific antibacterial activity as well as cytotoxic activity against a human melanoma cell line (A2058). The dereplication of the active fraction using HPLC-MS led to the isolation and structural elucidation of cholic acid and 3-oxo cholic acid. T. actiniarum is one of three type species belonging to the genus Thalassomonas. The ability to generate cholic acid was assessed for all three species using thin-layer chromatography and was confirmed by LC-MS. The re-sequencing of all three Thalassomonas type species using long-read Oxford Nanopore Technology (ONT) and Illumina data produced complete genomes, enabling the bioinformatic assessment of the ability of the strains to produce cholic acid. Although a complete biosynthetic pathway for cholic acid synthesis in this genus could not be determined based on sequence-based homology searches, the identification of putative penicillin or homoserine lactone acylases in all three species suggests a mechanism for the hydrolysis of conjugated bile acids present in the growth medium, resulting in the generation of cholic acid and 3-oxo cholic acid. With little known currently about the bioactivities of this genus, this study serves as the foundation for future investigations into their bioactive potential as well as the potential ecological role of bile acid transformation, sterol modification and quorum quenching by Thalassomonas sp. in the marine environment.
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7
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Structure-guided product determination of the bacterial type II diterpene synthase Tpn2. Commun Chem 2022; 5:146. [PMID: 36698006 PMCID: PMC9814783 DOI: 10.1038/s42004-022-00765-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
Abstract
A grand challenge in terpene synthase (TS) enzymology is the ability to predict function from protein sequence. Given the limited number of characterized bacterial TSs and significant sequence diversities between them and their eukaryotic counterparts, this is currently impossible. To contribute towards understanding the sequence-structure-function relationships of type II bacterial TSs, we determined the structure of the terpentedienyl diphosphate synthase Tpn2 from Kitasatospora sp. CB02891 by X-ray crystallography and made structure-guided mutants to probe its mechanism. Substitution of a glycine into a basic residue changed the product preference from the clerodane skeleton to a syn-labdane skeleton, resulting in the first syn-labdane identified from a bacterial TS. Understanding how a single residue can dictate the cyclization pattern in Tpn2, along with detailed bioinformatics analysis of bacterial type II TSs, sets the stage for the investigation of the functional scope of bacterial type II TSs and the discovery of novel bacterial terpenoids.
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8
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Secondary Metabolites and Biosynthetic Gene Clusters Analysis of Deep-Sea Hydrothermal Vent-Derived Streptomyces sp. SCSIO ZS0520. Mar Drugs 2022; 20:md20060393. [PMID: 35736196 PMCID: PMC9228677 DOI: 10.3390/md20060393] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 01/27/2023] Open
Abstract
Streptomyces sp. SCSIO ZS0520 is a deep-sea hydrothermal vent-derived actinomycete. Our previous metabolism investigation showed that Streptomyces sp. SCSIO ZS0520 is a producer of cytotoxic actinopyrones. Here, another four types of secondary metabolites were identified, including six salinomycin isomers (2–7), the macrolide elaiophylin (8), the triterpene N-acetyl-aminobacteriohopanetriol (9), and the pyrone minipyrone (10). Among them, compounds 2–6 and 10 are new compounds. To understand the biosynthetic pathway of these compounds, a bioinformatic analysis of the whole genome was carried out, which identified 34 secondary metabolite biosynthetic gene clusters. Next, the biosynthetic pathways responsive to four types of products were deduced on the basis of gene function predictions and structure information. Taken together, these findings prove the metabolite potential of ZS0520 and lay the foundations to solve the remaining biosynthetic issues in four types of marine natural products.
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Borcik C, Eason IR, Vanderloop B, Wylie BJ. 2H, 13C-Cholesterol for Dynamics and Structural Studies of Biological Membranes. ACS OMEGA 2022; 7:17151-17160. [PMID: 35647452 PMCID: PMC9134247 DOI: 10.1021/acsomega.2c00796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/08/2022] [Indexed: 05/19/2023]
Abstract
We present a cost-effective means of 2H and 13C enrichment of cholesterol. This method exploits the metabolism of 2H,13C-acetate into acetyl-CoA, the first substrate in the mevalonate pathway. We show that growing the cholesterol producing strain RH6827 of Saccharomyces cerevisiae in 2H,13C-acetate-enriched minimal media produces a skip-labeled pattern of deuteration. We characterize this cholesterol labeling pattern by mass spectrometry and solid-state nuclear magnetic resonance spectroscopy. It is confirmed that most 2H nuclei retain their original 2H-13C bonds from acetate throughout the biosynthetic pathway. We then quantify the changes in 13C chemical shifts brought by deuteration and the impact upon 13C-13C spin diffusion. Finally, using adiabatic rotor echo short pulse irradiation cross-polarization (RESPIRATIONCP), we acquire the 2H-13C correlation spectra to site specifically quantify cholesterol dynamics in two model membranes as a function of temperature. These measurements show that cholesterol acyl chains at physiological temperatures in mixtures of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), sphingomyelin, and cholesterol are more dynamic than cholesterol in POPC. However, this overall change in motion is not uniform across the cholesterol molecule. This result establishes that this cholesterol labeling pattern will have great utility in reporting on cholesterol dynamics and orientation in a variety of environments and with different membrane bilayer components, as well as monitoring the mevalonate pathway product interactions within the bilayer. Finally, the flexibility and universality of acetate labeling will allow this technique to be widely applied to a large range of lipids and other natural products.
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Nagata R, Suemune H, Kobayashi M, Shinada T, Shin‐ya K, Nishiyama M, Hino T, Sato Y, Kuzuyama T, Nagano S. Structural Basis for the Prenylation Reaction of Carbazole‐Containing Natural Products Catalyzed by Squalene Synthase‐Like Enzymes. Angew Chem Int Ed Engl 2022; 61:e202117430. [DOI: 10.1002/anie.202117430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Ryuhei Nagata
- Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Hironori Suemune
- Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Masaya Kobayashi
- Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Tetsuro Shinada
- Graduate School of Science Osaka City University Sugimoto, Sumiyoshi-ku Osaka 558-8585 Japan
| | - Kazuo Shin‐ya
- National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ku Tokyo 135-0064 Japan
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM) The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Tomoya Hino
- Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Yusuke Sato
- Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM) The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Shingo Nagano
- Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
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11
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Recent advances in the microbial production of squalene. World J Microbiol Biotechnol 2022; 38:91. [PMID: 35426523 PMCID: PMC9010451 DOI: 10.1007/s11274-022-03273-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/30/2022] [Indexed: 11/06/2022]
Abstract
Squalene is a triterpene hydrocarbon, a biochemical precursor for all steroids in plants and animals. It is a principal component of human surface lipids, in particular of sebum. Squalene has several applications in the food, pharmaceutical, and medical sectors. It is essentially used as a dietary supplement, vaccine adjuvant, moisturizer, cardio-protective agent, anti-tumor agent and natural antioxidant. With the increased demand for squalene along with regulations on shark-derived squalene, there is a need to find alternatives for squalene production which are low-cost as well as sustainable. Microbial platforms are being considered as a potential option to meet such challenges. Considerable progress has been made using both wild-type and engineered microbial strains for improved productivity and yields of squalene. Native strains for squalene production are usually limited by low growth rates and lesser titers. Metabolic engineering, which is a rational strain engineering tool, has enabled the development of microbial strains such as Saccharomyces cerevisiae and Yarrowia lipolytica, to overproduce the squalene in high titers. This review focuses on key strain engineering strategies involving both in-silico and in-vitro techniques. Emphasis is made on gene manipulations for improved precursor pool, enzyme modifications, cofactor regeneration, up-regulation of limiting reactions, and downregulation of competing reactions during squalene production. Process strategies and challenges related to both upstream and downstream during mass cultivation are detailed.
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12
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Nagata R, Suemune H, Kobayashi M, Shinada T, Shin‐ya K, Nishiyama M, Hino T, Sato Y, Kuzuyama T, Nagano S. Structural Basis for the Prenylation Reaction of Carbazole‐Containing Natural Products Catalyzed by Squalene Synthase‐Like Enzymes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ryuhei Nagata
- Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Hironori Suemune
- Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Masaya Kobayashi
- Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Tetsuro Shinada
- Graduate School of Science Osaka City University Sugimoto, Sumiyoshi-ku Osaka 558-8585 Japan
| | - Kazuo Shin‐ya
- National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ku Tokyo 135-0064 Japan
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM) The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Tomoya Hino
- Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Yusuke Sato
- Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM) The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Shingo Nagano
- Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
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13
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From Sharks to Yeasts: Squalene in the Development of Vaccine Adjuvants. Pharmaceuticals (Basel) 2022; 15:ph15030265. [PMID: 35337064 PMCID: PMC8951290 DOI: 10.3390/ph15030265] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
Squalene is a natural linear triterpene that can be found in high amounts in certain fish liver oils, especially from deep-sea sharks, and to a lesser extent in a wide variety of vegeTable oils. It is currently used for numerous vaccine and drug delivery emulsions due to its stability-enhancing properties and biocompatibility. Squalene-based vaccine adjuvants, such as MF59 (Novartis), AS03 (GlaxoSmithKline Biologicals), or AF03 (Sanofi) are included in seasonal vaccines against influenza viruses and are presently being considered for inclusion in several vaccines against SARS-CoV-2 and future pandemic threats. However, harvesting sharks for this purpose raises serious ecological concerns that the exceptional demand of the pandemic has exacerbated. In this line, the use of plants to obtain phytosqualene has been seen as a more sustainable alternative, yet the lower yields and the need for huge investments in infrastructures and equipment makes this solution economically ineffective. More recently, the enormous advances in the field of synthetic biology provided innovative approaches to make squalene production more sustainable, flexible, and cheaper by using genetically modified microbes to produce pharmaceutical-grade squalene. Here, we review the biological mechanisms by which squalene-based vaccine adjuvants boost the immune response, and further compare the existing sources of squalene and their environmental impact. We propose that genetically engineered microbes are a sustainable alternative to produce squalene at industrial scale, which are likely to become the sole source of pharmaceutical-grade squalene in the foreseeable future.
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Srivastava AK, Srivastava R, Bharati AP, Singh AK, Sharma A, Das S, Tiwari PK, Srivastava AK, Chakdar H, Kashyap PL, Saxena AK. Analysis of Biosynthetic Gene Clusters, Secretory, and Antimicrobial Peptides Reveals Environmental Suitability of Exiguobacterium profundum PHM11. Front Microbiol 2022; 12:785458. [PMID: 35185816 PMCID: PMC8851196 DOI: 10.3389/fmicb.2021.785458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
Halotolerant bacteria produce a wide range of bioactive compounds with important applications in agriculture for abiotic stress amelioration and plant growth promotion. In the present study, 17 biosynthetic gene clusters (BGCs) were identified in Exiguobacterium profundum PHM11 belonging to saccharides, desmotamide, pseudaminic acid, dipeptide aldehydes, and terpene biosynthetic pathways representing approximately one-sixth of genomes. The terpene biosynthetic pathway was conserved in Exiguobacterium spp. while the E. profundum PHM11 genome confirms the presence of the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway for the isopentenyl diphosphate (IPP) synthesis. Further, 2,877 signal peptides (SPs) were identified using the PrediSi server, out of which 592 proteins were prophesied for the secretion having a transmembrane helix (TMH). In addition, antimicrobial peptides (AMPs) were also identified using BAGEL4. The transcriptome analysis of PHM11 under salt stress reveals the differential expression of putative secretion and transporter genes having SPs and TMH. Priming of the rice, wheat and maize seeds with PHM11 under salt stress led to improvement in the root length, root diameters, surface area, number of links and forks, and shoot length. The study shows that the presence of BGCs, SPs, and secretion proteins constituting TMH and AMPs provides superior competitiveness in the environment and make E. profundum PHM11 a suitable candidate for plant growth promotion under salt stress.
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Affiliation(s)
- Alok Kumar Srivastava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
- Alok Kumar Srivastava,
| | - Ruchi Srivastava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Akhilendra Pratap Bharati
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Alok Kumar Singh
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Anjney Sharma
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Sudipta Das
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Praveen Kumar Tiwari
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Anchal Kumar Srivastava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Hillol Chakdar
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Prem Lal Kashyap
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, India
- *Correspondence: Prem Lal Kashyap, ;
| | - Anil Kumar Saxena
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
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15
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Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes. Microbiol Spectr 2021; 9:e0166921. [PMID: 34704787 PMCID: PMC8549736 DOI: 10.1128/spectrum.01669-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The aerodigestive tract (ADT) is the primary portal through which pathogens and other invading microbes enter the body. As the direct interface with the environment, we hypothesize that the ADT microbiota possess biosynthetic gene clusters (BGCs) for antibiotics and other specialized metabolites to compete with both endogenous and exogenous microbes. From 1,214 bacterial genomes, representing 136 genera and 387 species that colonize the ADT, we identified 3,895 BGCs. To determine the distribution of BGCs and bacteria in different ADT sites, we aligned 1,424 metagenomes, from nine different ADT sites, onto the predicted BGCs. We show that alpha diversity varies across the ADT and that each site is associated with distinct bacterial communities and BGCs. We identify specific BGC families enriched in the buccal mucosa, external naris, gingiva, and tongue dorsum despite these sites harboring closely related bacteria. We reveal BGC enrichment patterns indicative of the ecology at each site. For instance, aryl polyene and resorcinol BGCs are enriched in the gingiva and tongue, which are colonized by many anaerobes. In addition, we find that streptococci colonizing the tongue and cheek possess different ribosomally synthesized and posttranslationally modified peptide BGCs. Finally, we highlight bacterial genera with BGCs but are underexplored for specialized metabolism and demonstrate the bioactivity of Actinomyces against other bacteria, including human pathogens. Together, our results demonstrate that specialized metabolism in the ADT is extensive and that by exploring these microbiomes further, we will better understand the ecology and biogeography of this system and identify new bioactive natural products. IMPORTANCE Bacteria produce specialized metabolites to compete with other microbes. Though the biological activities of many specialized metabolites have been determined, our understanding of their ecology is limited, particularly within the human microbiome. As the aerodigestive tract (ADT) faces the external environment, bacteria colonizing this tract must compete both among themselves and with invading microbes, including human pathogens. We analyzed the genomes of ADT bacteria to identify biosynthetic gene clusters (BGCs) for specialized metabolites. We found that the majority of ADT BGCs are uncharacterized and the metabolites they encode are unknown. We mapped the distribution of BGCs across the ADT and determined that each site is associated with its own distinct bacterial community and BGCs. By further characterizing these BGCs, we will inform our understanding of ecology and biogeography across the ADT, and we may uncover new specialized metabolites, including antibiotics.
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16
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Heath RS, Ruscoe RE, Turner NJ. The beauty of biocatalysis: sustainable synthesis of ingredients in cosmetics. Nat Prod Rep 2021; 39:335-388. [PMID: 34879125 DOI: 10.1039/d1np00027f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2015 up to July 2021The market for cosmetics is consumer driven and the desire for green, sustainable and natural ingredients is increasing. The use of isolated enzymes and whole-cell organisms to synthesise these products is congruent with these values, especially when combined with the use of renewable, recyclable or waste feedstocks. The literature of biocatalysis for the synthesis of ingredients in cosmetics in the past five years is herein reviewed.
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Affiliation(s)
- Rachel S Heath
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Rebecca E Ruscoe
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nicholas J Turner
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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17
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Rizk S, Henke P, Santana-Molina C, Martens G, Gnädig M, Nguyen NA, Devos DP, Neumann-Schaal M, Saenz JP. Functional diversity of isoprenoid lipids in Methylobacterium extorquens PA1. Mol Microbiol 2021; 116:1064-1078. [PMID: 34387371 DOI: 10.1111/mmi.14794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/29/2021] [Accepted: 08/10/2021] [Indexed: 11/29/2022]
Abstract
Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate the role of isoprenoid lipids in surface membrane function and cellular fitness. By genetically knocking out hpnE, and crtB we disrupted the production of squalene, and phytoene in Methylobacterium extorquens PA1, which are the presumed precursors for hopanoids and carotenoids, respectively. Deletion of hpnE revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in pigmentation with a C30 backbone, rather than the previously predicted canonical C40 phytoene-derived pathway. Phylogenetic analysis suggested that M. extorquens may have acquired the C30 pathway through lateral gene transfer from Planctomycetes. Surprisingly, disruption of carotenoid synthesis did not generate any major growth or membrane biophysical phenotypes, but slightly increased sensitivity to oxidative stress. We further demonstrated that hopanoids but not carotenoids are essential for growth at higher temperatures, membrane permeability and tolerance of low divalent cation concentrations. These observations show that hopanoids and carotenoids serve diverse roles in the outer membrane of M. extorquens PA1.
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Affiliation(s)
- Sandra Rizk
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Petra Henke
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carlos Santana-Molina
- Centro Andaluz de Biologıa del Desarrollo (CABD)-CSIC, Junta de Andalucıa, Universidad Pablo de Olavide, Seville, Spain
| | - Gesa Martens
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marén Gnädig
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | | | - Damien P Devos
- Centro Andaluz de Biologıa del Desarrollo (CABD)-CSIC, Junta de Andalucıa, Universidad Pablo de Olavide, Seville, Spain
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - James P Saenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
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18
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Abstract
Steroids are one of three major lipid components of the eukaryotic cellular membrane, along with glycerophospolipids and sphingolipids. Steroids have critical roles in eukaryotic endocytosis and thus may have been structural prerequisites for the endocytic acquisition of mitochondria during eukaryogenesis. The evolutionary history of the eukaryotic cellular membrane is poorly understood and, as such, has limited our understanding of eukaryogenesis. We address the evolution of steroid biosynthesis by combining ancestral sequence reconstruction and phylogenetic analyses of steroid biosynthesis genes. Our results indicate that steroid biosynthesis evolved within bacteria in response to the rise of oxygen and was later horizontally transferred to eukaryotes. Membrane properties of early eukaryotes are inferred to have been different than that of modern eukaryotes. Steroids are components of the eukaryotic cellular membrane and have indispensable roles in the process of eukaryotic endocytosis by regulating membrane fluidity and permeability. In particular, steroids may have been a structural prerequisite for the acquisition of mitochondria via endocytosis during eukaryogenesis. While eukaryotes are inferred to have evolved from an archaeal lineage, there is little similarity between the eukaryotic and archaeal cellular membranes. As such, the evolution of eukaryotic cellular membranes has limited our understanding of eukaryogenesis. Despite evolving from archaea, the eukaryotic cellular membrane is essentially a fatty acid bacterial-type membrane, which implies a substantial bacterial contribution to the evolution of the eukaryotic cellular membrane. Here, we address the evolution of steroid biosynthesis in eukaryotes by combining ancestral sequence reconstruction and comprehensive phylogenetic analyses of steroid biosynthesis genes. Contrary to the traditional assumption that eukaryotic steroid biosynthesis evolved within eukaryotes, most steroid biosynthesis genes are inferred to be derived from bacteria. In particular, aerobic deltaproteobacteria (myxobacteria) seem to have mediated the transfer of key genes for steroid biosynthesis to eukaryotes. Analyses of resurrected steroid biosynthesis enzymes suggest that the steroid biosynthesis pathway in early eukaryotes may have been similar to the pathway seen in modern plants and algae. These resurrected proteins also experimentally demonstrate that molecular oxygen was required to establish the modern eukaryotic cellular membrane during eukaryogenesis. Our study provides unique insight into relationships between early eukaryotes and other bacteria in addition to the well-known endosymbiosis with alphaproteobacteria.
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Abstract
Fungal pathogens, among other stressors, negatively impact the productivity and population size of honey bees, one of our most important pollinators (1, 2), in particular their brood (larvae and pupae) (3, 4). Understanding the factors that influence disease incidence and prevalence in brood may help us improve colony health and productivity. Here, we examined the capacity of a honey bee-associated bacterium, Bombella apis, to suppress the growth of fungal pathogens and ultimately protect bee brood from infection. Our results showed that strains of B. apis inhibit the growth of two insect fungal pathogens, Beauveria bassiana and Aspergillus flavus, in vitro. This phenotype was recapitulated in vivo; bee broods supplemented with B. apis were significantly less likely to be infected by A. flavus. Additionally, the presence of B. apis reduced sporulation of A. flavus in the few bees that were infected. Analyses of biosynthetic gene clusters across B. apis strains suggest antifungal candidates, including a type 1 polyketide, terpene, and aryl polyene. Secreted metabolites from B. apis alone were sufficient to suppress fungal growth, supporting the hypothesis that fungal inhibition is mediated by an antifungal metabolite. Together, these data suggest that B. apis can suppress fungal infections in bee brood via secretion of an antifungal metabolite.
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20
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Willdigg JR, Helmann JD. Mini Review: Bacterial Membrane Composition and Its Modulation in Response to Stress. Front Mol Biosci 2021; 8:634438. [PMID: 34046426 PMCID: PMC8144471 DOI: 10.3389/fmolb.2021.634438] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Antibiotics and other agents that perturb the synthesis or integrity of the bacterial cell envelope trigger compensatory stress responses. Focusing on Bacillus subtilis as a model system, this mini-review summarizes current views of membrane structure and insights into how cell envelope stress responses remodel and protect the membrane. Altering the composition and properties of the membrane and its associated proteome can protect cells against detergents, antimicrobial peptides, and pore-forming compounds while also, indirectly, contributing to resistance against compounds that affect cell wall synthesis. Many of these regulatory responses are broadly conserved, even where the details of regulation may differ, and can be important in the emergence of antibiotic resistance in clinical settings.
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Affiliation(s)
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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21
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Shen H, Huang L, Dou H, Yang Y, Wu H. Effect of Trilobatin from Lithocarpus polystachyus Rehd on Gut Microbiota of Obese Rats Induced by a High-Fat Diet. Nutrients 2021; 13:nu13030891. [PMID: 33801901 PMCID: PMC8001797 DOI: 10.3390/nu13030891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/12/2022] Open
Abstract
Trilobatin was identified as the primary bioactive component in the Lithocarpus polystachyus Rehd (LPR) leaves. This study explored the antiobesity effect of trilobatin from LPR leaves and its influence on gut microbiota in obese rats. Results showed that trilobatin could significantly reduce body and liver weight gain induced by a high-fat diet, and the accumulation of perirenal fat, epididymal fat, and brown fat of SD (Male Sprague–Dawley) obese rats in a dose-independent manner. Short-chain fatty acids (SCFAs) concentrations increased, especially the concentration of butyrate. Trilobatin supplementation could significantly increase the relative abundance of Lactobacillus, Prevotella, CF231, Bacteroides, and Oscillospira, and decrease greatly the abundance of Blautia, Allobaculum, Phascolarctobacterium, and Coprococcus, resulting in an increase of the ratio of Bacteroidetes to Firmicutes (except the genera of Lactobacillus and Oscillospira). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway predicted by the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated the different relative metabolic pathways after trilobatin supplementation. This study may reveal the contribution of gut microbiota to the antiobesity effect of trilobatin from LPR leaves and predict the potential regulatory mechanism for obesity induced by a high-fat diet.
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Affiliation(s)
- Hailiang Shen
- Citrus Research Institute, Southwest University, Chongqing 400000, China; (H.S.); (L.H.); (H.D.)
- Citrus Research Institute, Chinese Academy of Agricultural Science, Chongqing 400000, China
| | - Linhua Huang
- Citrus Research Institute, Southwest University, Chongqing 400000, China; (H.S.); (L.H.); (H.D.)
- Citrus Research Institute, Chinese Academy of Agricultural Science, Chongqing 400000, China
| | - Huating Dou
- Citrus Research Institute, Southwest University, Chongqing 400000, China; (H.S.); (L.H.); (H.D.)
- Citrus Research Institute, Chinese Academy of Agricultural Science, Chongqing 400000, China
| | - Yali Yang
- Department of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an 710000, China;
- National Research and Development Center of Apple Processing Technology, Xi’an 710000, China
| | - Houjiu Wu
- Citrus Research Institute, Southwest University, Chongqing 400000, China; (H.S.); (L.H.); (H.D.)
- Citrus Research Institute, Chinese Academy of Agricultural Science, Chongqing 400000, China
- Correspondence: ; Tel./Fax: +86-023-68349701
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22
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Wolter LA, Wietz M, Ziesche L, Breider S, Leinberger J, Poehlein A, Daniel R, Schulz S, Brinkhoff T. Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle. Syst Appl Microbiol 2021; 44:126166. [PMID: 33310406 DOI: 10.1016/j.syapm.2020.126166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/23/2022]
Abstract
The genus Pseudooceanicola from the alphaproteobacterial Roseobacter group currently includes ten validated species. We herein describe strain Lw-13eT, the first Pseudooceanicola species from marine macroalgae, isolated from the brown alga Fucus spiralis abundant at European and North American coasts. Physiological and pangenome analyses of Lw-13eT showed corresponding adaptive features. Adaptations to the tidal environment include a broad salinity tolerance, degradation of macroalgae-derived substrates (mannitol, mannose, proline), and resistance to several antibiotics and heavy metals. Notably, Lw-13eT can degrade oligomeric alginate via PL15 alginate lyase encoded in a polysaccharide utilization locus (PUL), rarely described for roseobacters to date. Plasmid localization of the PUL strengthens the importance of mobile genetic elements for evolutionary adaptations within the Roseobacter group. PL15 homologs were primarily detected in marine plant-associated metagenomes from coastal environments but not in the open ocean, corroborating its adaptive role in algae-rich habitats. Exceptional is the tolerance of Lw-13eT against the broad-spectrum antibiotic tropodithietic acid, produced by Phaeobacter spp. co-occurring in coastal habitats. Furthermore, Lw-13eT exhibits features resembling terrestrial plant-bacteria associations, i.e. biosynthesis of siderophores, terpenes and volatiles, which may contribute to mutual bacteria-algae interactions. Closest described relative of Lw-13eT is Pseudopuniceibacterium sediminis CY03T with 98.4% 16S rRNA gene sequence similarity. However, protein sequence-based core genome phylogeny and average nucleotide identity indicate affiliation of Lw-13eT with the genus Pseudooceanicola. Based on phylogenetic, physiological and (chemo)taxonomic distinctions, we propose strain Lw-13eT (=DSM 29013T=LMG 30557T) as a novel species with the name Pseudooceanicola algae.
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Affiliation(s)
- Laura A Wolter
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany; JST ERATO Nomura Project, Faculty of Life and Environmental Sciences, Tsukuba, Japan.
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Lisa Ziesche
- Institute of Organic Chemistry, Technische Universität Braunschweig, Germany
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, Genomic and Applied Microbiology, and Göttingen Genomics Laboratory, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Genomic and Applied Microbiology, and Göttingen Genomics Laboratory, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.
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23
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Willdigg JR, Helmann JD. Mini Review: Bacterial Membrane Composition and Its Modulation in Response to Stress. Front Mol Biosci 2021. [PMID: 34046426 DOI: 10.3389/fmolb.2021.634438/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Antibiotics and other agents that perturb the synthesis or integrity of the bacterial cell envelope trigger compensatory stress responses. Focusing on Bacillus subtilis as a model system, this mini-review summarizes current views of membrane structure and insights into how cell envelope stress responses remodel and protect the membrane. Altering the composition and properties of the membrane and its associated proteome can protect cells against detergents, antimicrobial peptides, and pore-forming compounds while also, indirectly, contributing to resistance against compounds that affect cell wall synthesis. Many of these regulatory responses are broadly conserved, even where the details of regulation may differ, and can be important in the emergence of antibiotic resistance in clinical settings.
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Affiliation(s)
- Jessica R Willdigg
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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24
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Chang HY, Cheng TH, Wang AHJ. Structure, catalysis, and inhibition mechanism of prenyltransferase. IUBMB Life 2020; 73:40-63. [PMID: 33246356 PMCID: PMC7839719 DOI: 10.1002/iub.2418] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/02/2020] [Accepted: 11/14/2020] [Indexed: 12/31/2022]
Abstract
Isoprenoids, also known as terpenes or terpenoids, represent a large family of natural products composed of five‐carbon isopentenyl diphosphate or its isomer dimethylallyl diphosphate as the building blocks. Isoprenoids are structurally and functionally diverse and include dolichols, steroid hormones, carotenoids, retinoids, aromatic metabolites, the isoprenoid side‐chain of ubiquinone, and isoprenoid attached signaling proteins. Productions of isoprenoids are catalyzed by a group of enzymes known as prenyltransferases, such as farnesyltransferases, geranylgeranyltransferases, terpenoid cyclase, squalene synthase, aromatic prenyltransferase, and cis‐ and trans‐prenyltransferases. Because these enzymes are key in cellular processes and metabolic pathways, they are expected to be potential targets in new drug discovery. In this review, six distinct subsets of characterized prenyltransferases are structurally and mechanistically classified, including (1) head‐to‐tail prenyl synthase, (2) head‐to‐head prenyl synthase, (3) head‐to‐middle prenyl synthase, (4) terpenoid cyclase, (5) aromatic prenyltransferase, and (6) protein prenylation. Inhibitors of those enzymes for potential therapies against several diseases are discussed. Lastly, recent results on the structures of integral membrane enzyme, undecaprenyl pyrophosphate phosphatase, are also discussed.
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Affiliation(s)
- Hsin-Yang Chang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Tien-Hsing Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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25
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Kim M, Cha IT, Lee KE, Lee EY, Park SJ. Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea. Microorganisms 2020; 8:microorganisms8091412. [PMID: 32937826 PMCID: PMC7564069 DOI: 10.3390/microorganisms8091412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/11/2020] [Indexed: 11/16/2022] Open
Abstract
Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea;
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (I.-T.C.); (K.-E.L.)
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (I.-T.C.); (K.-E.L.)
| | - Eun-Young Lee
- Exhibition & Education Division, National Institute of Biological Resources, Incheon 22689, Korea;
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea;
- Correspondence: ; Tel.: +82-64-753-3524; Fax: +82-64-756-3541
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26
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Meng Y, Shao X, Wang Y, Li Y, Zheng X, Wei G, Kim S, Wang C. Extension of cell membrane boosting squalene production in the engineered
Escherichia coli. Biotechnol Bioeng 2020; 117:3499-3507. [DOI: 10.1002/bit.27511] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/10/2020] [Accepted: 07/19/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Yunhe Meng
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Xixi Shao
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Yan Wang
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Yumei Li
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Xiaojian Zheng
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Gongyuan Wei
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Seon‐Won Kim
- Division of Applied Life Science (BK21 Plus) PMBBRC, Gyeongsang National University Jinju Republic of Korea
| | - Chonglong Wang
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
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Santana-Molina C, Rivas-Marin E, Rojas AM, Devos DP. Origin and Evolution of Polycyclic Triterpene Synthesis. Mol Biol Evol 2020; 37:1925-1941. [PMID: 32125435 PMCID: PMC7306690 DOI: 10.1093/molbev/msaa054] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Polycyclic triterpenes are members of the terpene family produced by the cyclization of squalene. The most representative polycyclic triterpenes are hopanoids and sterols, the former are mostly found in bacteria, whereas the latter are largely limited to eukaryotes, albeit with a growing number of bacterial exceptions. Given their important role and omnipresence in most eukaryotes, contrasting with their scant representation in bacteria, sterol biosynthesis was long thought to be a eukaryotic innovation. Thus, their presence in some bacteria was deemed to be the result of lateral gene transfer from eukaryotes. Elucidating the origin and evolution of the polycyclic triterpene synthetic pathways is important to understand the role of these compounds in eukaryogenesis and their geobiological value as biomarkers in fossil records. Here, we have revisited the phylogenies of the main enzymes involved in triterpene synthesis, performing gene neighborhood analysis and phylogenetic profiling. Squalene can be biosynthesized by two different pathways containing the HpnCDE or Sqs proteins. Our results suggest that the HpnCDE enzymes are derived from carotenoid biosynthesis ones and that they assembled in an ancestral squalene pathway in bacteria, while remaining metabolically versatile. Conversely, the Sqs enzyme is prone to be involved in lateral gene transfer, and its emergence is possibly related to the specialization of squalene biosynthesis. The biosynthesis of hopanoids seems to be ancestral in the Bacteria domain. Moreover, no triterpene cyclases are found in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages.
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Affiliation(s)
- Carlos Santana-Molina
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Ana M Rojas
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
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Song Y, Guan Z, van Merkerk R, Pramastya H, Abdallah II, Setroikromo R, Quax WJ. Production of Squalene in Bacillus subtilis by Squalene Synthase Screening and Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4447-4455. [PMID: 32208656 PMCID: PMC7168599 DOI: 10.1021/acs.jafc.0c00375] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Squalene synthase (SQS) catalyzes the conversion of two farnesyl pyrophosphates to squalene, an important intermediate in between isoprene and valuable triterpenoids. In this study, we have constructed a novel biosynthesis pathway for squalene in Bacillus subtilis and performed metabolic engineering aiming at facilitating further exploitation and production of squalene-derived triterpenoids. Therefore, systematic studies and analysis were performed including selection of multiple SQS candidates from various organisms, comparison of expression vectors, optimization of cultivation temperatures, and examination of rate-limiting factors within the synthetic pathway. We were, for the first time, able to obtain squalene synthesis in B. subtilis. Furthermore, we achieved a 29-fold increase of squalene yield (0.26-7.5 mg/L) by expressing SQS from Bacillus megaterium and eliminating bottlenecks within the upstream methylerythritol-phosphate pathway. Moreover, our findings showed that also ispA could positively affect the production of squalene.
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Affiliation(s)
- Yafeng Song
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Zheng Guan
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ronald van Merkerk
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hegar Pramastya
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Pharmaceutical
Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, 40132 Bandung, Indonesia
| | - Ingy I. Abdallah
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department
of Pharmacognosy, Faculty of Pharmacy, Alexandria
University, Alexandria 21521, Egypt
| | - Rita Setroikromo
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J. Quax
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- . Phone: +31 (0) 50 363 2558, (0) 50 363 8174. Fax: +31 (0) 50 363 3000
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Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus. Genes (Basel) 2020; 11:genes11040389. [PMID: 32260256 PMCID: PMC7231039 DOI: 10.3390/genes11040389] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 02/01/2023] Open
Abstract
Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.
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Abstract
This review covers newly isolated triterpenoids that have been reported during 2015.
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31
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Sato S, Kudo F, Rohmer M, Eguchi T. Characterization of Radical SAM Adenosylhopane Synthase, HpnH, which Catalyzes the 5
′
‐Deoxyadenosyl Radical Addition to Diploptene in the Biosynthesis of C
35
Bacteriohopanepolyols. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Shusuke Sato
- Department of Chemistry Tokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
| | - Fumitaka Kudo
- Department of Chemistry Tokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
| | - Michel Rohmer
- Institut Le Bel Université de Strasbourg/CNRS 4 rue Blaise Pascal 67070 Strasbourg Cedex France
| | - Tadashi Eguchi
- Department of Chemistry Tokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
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32
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Sato S, Kudo F, Rohmer M, Eguchi T. Characterization of Radical SAM Adenosylhopane Synthase, HpnH, which Catalyzes the 5
′
‐Deoxyadenosyl Radical Addition to Diploptene in the Biosynthesis of C
35
Bacteriohopanepolyols. Angew Chem Int Ed Engl 2019; 59:237-241. [DOI: 10.1002/anie.201911584] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/15/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Shusuke Sato
- Department of Chemistry Tokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
| | - Fumitaka Kudo
- Department of Chemistry Tokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
| | - Michel Rohmer
- Institut Le Bel Université de Strasbourg/CNRS 4 rue Blaise Pascal 67070 Strasbourg Cedex France
| | - Tadashi Eguchi
- Department of Chemistry Tokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
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Liu X, Zhao K, Yang X, Zhao Y. Gut Microbiota and Metabolome Response of Decaisnea insignis Seed Oil on Metabolism Disorder Induced by Excess Alcohol Consumption. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10667-10677. [PMID: 31483636 DOI: 10.1021/acs.jafc.9b04792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This study investigated the modulatory effects of Decaisnea insignis seed oil (DISO), which was rich in palmitoleic acid (55.25%), palmitic acid (12.25%), and oleic acid (28.74%), on alcohol-induced metabolism disorder in mice. Fifty mice were orally administered with 38% alcohol (0.4 mL/day) and without or with DISO (3, 6, and 12 g/kg) for consecutive 12 weeks. DISO inhibited the alcohol-induced weight loss and liver function abnormality (p < 0.01) and shifted the profiles of cecal microbiome: elevating the abundance of Lactobacillus, Ruminoccoceae_UCG_004 (p < 0.05) and decreasing abundance of Parabacteroides (p < 0.05). This treatment also regulated metabolome response of amino acid and lipid metabolism in cecal content: upregulating 5-hydroxyindole-3-acetic acid (p < 0.05), 6-hydroxynicotinic acid, 5-methoxytryptamine, nicotinamide, and nicotinic acid (p < 0.1) and downregulating androsterone, tryptophan, and indole-3-acetamide (p < 0.05). DISO protected against alcoholic liver injury and gut microbiota dysbiosis by enriching the relative abundance of Lactobacillus, which was positively associated with the improvement of intestinal permeability and tryptophan metabolism.
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Gohil N, Bhattacharjee G, Khambhati K, Braddick D, Singh V. Corrigendum: Engineering Strategies in Microorganisms for the Enhanced Production of Squalene: Advances, Challenges and Opportunities. Front Bioeng Biotechnol 2019; 7:114. [PMID: 31192199 PMCID: PMC6547300 DOI: 10.3389/fbioe.2019.00114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/07/2019] [Indexed: 01/05/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fbioe.2019.00050.].
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Affiliation(s)
- Nisarg Gohil
- School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
| | - Gargi Bhattacharjee
- School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
| | - Khushal Khambhati
- School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
| | - Darren Braddick
- Department of R&D, Cementic S. A. S., Genopole, Paris, France
| | - Vijai Singh
- School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
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35
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Fleitas Martínez O, Cardoso MH, Ribeiro SM, Franco OL. Recent Advances in Anti-virulence Therapeutic Strategies With a Focus on Dismantling Bacterial Membrane Microdomains, Toxin Neutralization, Quorum-Sensing Interference and Biofilm Inhibition. Front Cell Infect Microbiol 2019; 9:74. [PMID: 31001485 PMCID: PMC6454102 DOI: 10.3389/fcimb.2019.00074] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance constitutes one of the major challenges facing humanity in the Twenty-First century. The spread of resistant pathogens has been such that the possibility of returning to a pre-antibiotic era is real. In this scenario, innovative therapeutic strategies must be employed to restrict resistance. Among the innovative proposed strategies, anti-virulence therapy has been envisioned as a promising alternative for effective control of the emergence and spread of resistant pathogens. This review presents some of the anti-virulence strategies that are currently being developed, it will cover strategies focused on quench pathogen quorum sensing (QS) systems, disassemble of bacterial functional membrane microdomains (FMMs), disruption of biofilm formation and bacterial toxin neutralization.
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Affiliation(s)
- Osmel Fleitas Martínez
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Marlon Henrique Cardoso
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Suzana Meira Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Octavio Luiz Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
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36
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Gohil N, Bhattacharjee G, Khambhati K, Braddick D, Singh V. Engineering Strategies in Microorganisms for the Enhanced Production of Squalene: Advances, Challenges and Opportunities. Front Bioeng Biotechnol 2019; 7:50. [PMID: 30968019 PMCID: PMC6439483 DOI: 10.3389/fbioe.2019.00050] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/01/2019] [Indexed: 12/20/2022] Open
Abstract
The triterpene squalene is a natural compound that has demonstrated an extraordinary diversity of uses in pharmaceutical, nutraceutical, and personal care industries. Emboldened by this range of uses, novel applications that can gain profit from the benefits of squalene as an additive or supplement are expanding, resulting in its increasing demand. Ever since its discovery, the primary source has been the deep-sea shark liver, although recent declines in their populations and justified animal conservation and protection regulations have encouraged researchers to identify a novel route for squalene biosynthesis. This renewed scientific interest has profited from immense developments in synthetic biology, which now allows fine-tuning of a wider range of plants, fungi, and microorganisms for improved squalene production. There are numerous naturally squalene producing species and strains; although they generally do not make commercially viable yields as primary shark liver sources can deliver. The recent advances made toward improving squalene output from natural and engineered species have inspired this review. Accordingly, it will cover in-depth knowledge offered by the studies of the natural sources, and various engineering-based strategies that have been used to drive the improvements in the pathways toward large-scale production. The wide uses of squalene are also discussed, including the notable developments in anti-cancer applications and in augmenting influenza vaccines for greater efficacy.
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Affiliation(s)
- Nisarg Gohil
- School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
| | - Gargi Bhattacharjee
- School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
| | - Khushal Khambhati
- School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
| | - Darren Braddick
- Department of R&D, Cementic S. A. S., Genopole, Paris, France
| | - Vijai Singh
- School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
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37
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Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, Poehlein A, Ziemert N, König GM, Schäberle TF. Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites. Sci Rep 2018; 8:16600. [PMID: 30413766 PMCID: PMC6226438 DOI: 10.1038/s41598-018-34954-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/29/2018] [Indexed: 01/14/2023] Open
Abstract
Comparative genomic/metabolomic analysis is a powerful tool to disclose the potential of microbes for the biosynthesis of novel specialized metabolites. In the group of marine myxobacteria only a limited number of isolated species and sequenced genomes is so far available. However, the few compounds isolated thereof so far show interesting bioactivities and even novel chemical scaffolds; thereby indicating a huge potential for natural product discovery. In this study, all marine myxobacteria with accessible genome data (n = 5), including Haliangium ochraceum DSM 14365, Plesiocystis pacifica DSM 14875, Enhygromyxa salina DSM 15201 and the two newly sequenced species Enhygromyxa salina SWB005 and SWB007, were analyzed. All of these accessible genomes are large (~10 Mb), with a relatively small core genome and many unique coding sequences in each strain. Genome analysis revealed a high variety of biosynthetic gene clusters (BGCs) between the strains and several resistance models and essential core genes indicated the potential to biosynthesize antimicrobial molecules. Polyketides (PKs) and terpenes represented the majority of predicted specialized metabolite BGCs and contributed to the highest share between the strains. BGCs coding for non-ribosomal peptides (NRPs), PK/NRP hybrids and ribosomally synthesized and post-translationally modified peptides (RiPPs) were mostly strain specific. These results were in line with the metabolomic analysis, which revealed a high diversity of the chemical features between the strains. Only 6-11% of the metabolome was shared between all the investigated strains, which correlates to the small core genome of these bacteria (13-16% of each genome). In addition, the compound enhygrolide A, known from E. salina SWB005, was detected for the first time and structurally elucidated from Enhygromyxa salina SWB006. The here acquired data corroborate that these microorganisms represent a most promising source for the detection of novel specialized metabolites.
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Affiliation(s)
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Mohammad Alanjary
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Henrik Harms
- German Center for Infection Research (DZIF) Partner Site Cologne/Bonn, Bonn, Germany.,Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anja Poehlein
- Department of Genomics and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August-University Göttingen, Göttingen, Germany
| | - Nadine Ziemert
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.
| | - Till F Schäberle
- German Center for Infection Research (DZIF) Partner Site Cologne/Bonn, Bonn, Germany. .,Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany. .,Department of Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.
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38
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Draft Genome Sequence of Methylovulum psychrotolerans Sph1 T, an Obligate Methanotroph from Low-Temperature Environments. GENOME ANNOUNCEMENTS 2018; 6:6/11/e01488-17. [PMID: 29545306 PMCID: PMC5854766 DOI: 10.1128/genomea.01488-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Methylovulum psychrotolerans Sph1T is an aerobic, obligate methanotroph, which was isolated from cold methane seeps in West Siberia. This bacterium possesses only a particulate methane monooxygenase and is widely distributed in low-temperature environments. Strain Sph1T has the genomic potential for biosynthesis of hopanoids required for the maintenance of intracytoplasmic membranes.
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39
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Mao X, Liu Z, Sun J, Lee SY. Metabolic engineering for the microbial production of marine bioactive compounds. Biotechnol Adv 2017; 35:1004-1021. [DOI: 10.1016/j.biotechadv.2017.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/01/2017] [Accepted: 03/01/2017] [Indexed: 01/22/2023]
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40
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Park YK, Nicaud JM, Ledesma-Amaro R. The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications. Trends Biotechnol 2017; 36:304-317. [PMID: 29132754 DOI: 10.1016/j.tibtech.2017.10.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/30/2022]
Abstract
Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism. This review focuses on recent engineering approaches in R. toruloides for bioproduction and explores its potential as a biotechnological chassis.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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41
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Xie Y, Sen B, Wang G. Mining terpenoids production and biosynthetic pathway in thraustochytrids. BIORESOURCE TECHNOLOGY 2017; 244:1269-1280. [PMID: 28549813 DOI: 10.1016/j.biortech.2017.05.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 05/26/2023]
Abstract
Terpenoids are major bioactive compounds produced by microalgae and other eukaryotic microorganisms. Mining metabolic potential of marine microalgae for commercial production of terpenoids suggest thraustochytrids as one of the promising cell factories. The identification of potential thraustochytrid strains and relevant laboratory scale bioprocesses has been pursued largely. Further investigations in the improvement of terpenoids biosynthesis expect relevant molecular mechanisms to be understood directing metabolic engineering of the pathways. In this review, fermentative and mechanistic studies to identify key enzymes and pathways that are associated to terpenoids biosynthesis in thraustochytrids are discussed. Exploration of biosynthesis mechanisms in other model organisms facilitated identification of potential molecular targets for engineering terpenoids biosynthetic pathway in thraustochytrids. In addition, the preliminary genetic manipulation and in silico analysis in this review provides a platform for system-level metabolic engineering towards thraustochytrid strains improvement. Overall, the review contributes comprehensive information to allow better terpenoids productivity in thraustochytrids.
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Affiliation(s)
- Yunxuan Xie
- Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China.
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42
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Lee JS, Pan JJ, Ramamoorthy G, Poulter CD. Structure–Function Studies of Artemisia tridentata Farnesyl Diphosphate Synthase and Chrysanthemyl Diphosphate Synthase by Site-Directed Mutagenesis and Morphogenesis. J Am Chem Soc 2017; 139:14556-14567. [DOI: 10.1021/jacs.7b07608] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Scott Lee
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Jian-Jung Pan
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Gurusankar Ramamoorthy
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - C. Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
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43
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Melton ED, Sorokin DY, Overmars L, Lapidus AL, Pillay M, Ivanova N, Del Rio TG, Kyrpides NC, Woyke T, Muyzer G. Draft genome sequence of Dethiobacter alkaliphilus strain AHT1 T, a gram-positive sulfidogenic polyextremophile. Stand Genomic Sci 2017; 12:57. [PMID: 28943998 PMCID: PMC5609068 DOI: 10.1186/s40793-017-0268-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/08/2017] [Indexed: 12/01/2022] Open
Abstract
Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.
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Affiliation(s)
- Emily Denise Melton
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, RAS, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Lex Overmars
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Alla L Lapidus
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State, University, St. Petersburg, Russia
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | - Nikos C Kyrpides
- Joint Genome Institute, Walnut Creek, CA USA.,Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA USA
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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44
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Abstract
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The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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45
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Damsté JSS, Rijpstra WIC, Dedysh SN, Foesel BU, Villanueva L. Pheno- and Genotyping of Hopanoid Production in Acidobacteria. Front Microbiol 2017; 8:968. [PMID: 28642737 PMCID: PMC5462960 DOI: 10.3389/fmicb.2017.00968] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/15/2017] [Indexed: 11/28/2022] Open
Abstract
Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only "Ca. K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-, and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.
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Affiliation(s)
- Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
- Department of Earth Sciences, Geochemistry, Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of SciencesMoscow, Russia
| | - Bärbel U. Foesel
- Department of Microbial Ecology and Diversity Research, German Collection of Microorganisms and Cell Cultures (LG)Braunschweig, Germany
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
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46
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Sandoval-Calderón M, Guan Z, Sohlenkamp C. Knowns and unknowns of membrane lipid synthesis in streptomycetes. Biochimie 2017; 141:21-29. [PMID: 28522365 DOI: 10.1016/j.biochi.2017.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/12/2017] [Indexed: 11/16/2022]
Abstract
Bacteria belonging to the genus Streptomyces are among the most prolific producers of antibiotics. Research on cellular membrane biosynthesis and turnover is lagging behind in Streptomyces compared to related organisms like Mycobacterium tuberculosis. While natural products discovery in Streptomyces is evidently a priority in order to discover new antibiotics to combat the increase in antibiotic resistant pathogens, a better understanding of this cellular compartment should provide insights into the interplay between core and secondary metabolism. However, some of the pathways for membrane lipid biosynthesis are still incomplete. In addition, while it has become clear that remodelling of the membrane is necessary for coping with environmental stress and for morphological differentiation, the detailed mechanisms of these adaptations remain elusive. Here, we aim to provide a summary of what is known about the polar lipid composition in Streptomyces, the biosynthetic pathways of polar lipids, and to highlight current gaps in understanding function, dynamics and biosynthesis of these essential molecules.
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Affiliation(s)
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
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47
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Schwalen CJ, Feng X, Liu W, O-Dowd B, Ko TP, Shin CJ, Guo RT, Mitchell DA, Oldfield E. Head-to-Head Prenyl Synthases in Pathogenic Bacteria. Chembiochem 2017; 18:985-991. [PMID: 28340291 DOI: 10.1002/cbic.201700099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Indexed: 11/07/2022]
Abstract
Many organisms contain head-to-head isoprenoid synthases; we investigated three such types of enzymes from the pathogens Neisseria meningitidis, Neisseria gonorrhoeae, and Enterococcus hirae. The E. hirae enzyme was found to produce dehydrosqualene, and we solved an inhibitor-bound structure that revealed a fold similar to that of CrtM from Staphylococcus aureus. In contrast, the homologous proteins from Neisseria spp. carried out only the first half of the reaction, yielding presqualene diphosphate (PSPP). Based on product analyses, bioinformatics, and mutagenesis, we concluded that the Neisseria proteins were HpnDs (PSPP synthases). The differences in chemical reactivity to CrtM were due, at least in part, to the presence of a PSPP-stabilizing arginine in the HpnDs, decreasing the rate of dehydrosqualene biosynthesis. These results show that not only S. aureus but also other bacterial pathogens contain head-to-head prenyl synthases, although their biological functions remain to be elucidated.
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Affiliation(s)
- Christopher J Schwalen
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Xinxin Feng
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Bing O-Dowd
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei, 11529, Taiwan
| | - Christopher J Shin
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA.,Department of Microbiology, University of Illinois, 601 South Goodwin Avenue, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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48
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Production of squalene by microbes: an update. World J Microbiol Biotechnol 2016; 32:195. [DOI: 10.1007/s11274-016-2155-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/06/2016] [Indexed: 01/24/2023]
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49
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Xu W, Chai C, Shao L, Yao J, Wang Y. Metabolic engineering of Rhodopseudomonas palustris for squalene production. ACTA ACUST UNITED AC 2016; 43:719-25. [DOI: 10.1007/s10295-016-1745-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/03/2016] [Indexed: 10/22/2022]
Abstract
Abstract
Squalene is a strong antioxidant used extensively in the food, cosmetic and medicine industries. Rhodopseudomonas palustris TIE-1 was used as the host because of its ability to grow photosynthetically using solar energy and carbon dioxide from atmosphere. The deletion of the shc gene resulted in a squalene production of 3.8 mg/g DCW, which was 27-times higher than that in the wild type strain. For constructing a substrate channel to elevate the conversion efficiency, we tried to fuse crtE gene with hpnD gene. By fusing the two genes, squalene content was increased to 12.6 mg/g DCW, which was 27.4 % higher than that resulted from the co-expression method. At last, the titer of squalene reached 15.8 mg/g DCW by co-expressing the dxs gene, corresponding to 112-fold increase relative to that for wild-type strain. This study provided novel strategies for improving squalene yield and demonstrated the potential of producing squalene by Rhodopseudomonas palustris.
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Affiliation(s)
- Wen Xu
- grid.43169.39 0000000105991243 Department of Pathogen Biology, School of Basic Medical Science Xi’an Medical University 710021 Xi’an Shaanxi China
| | - Changbin Chai
- grid.43169.39 0000000105991243 Department of Pathogen Biology, School of Basic Medical Science Xi’an Medical University 710021 Xi’an Shaanxi China
| | - Lingqiao Shao
- grid.43169.39 0000000105991243 Department of Pathogen Biology, School of Basic Medical Science Xi’an Medical University 710021 Xi’an Shaanxi China
| | - Jia Yao
- grid.43169.39 0000000105991243 Department of Pathogen Biology, School of Basic Medical Science Xi’an Medical University 710021 Xi’an Shaanxi China
| | - Yang Wang
- grid.43169.39 0000000105991243 Department of Pathogen Biology, School of Basic Medical Science Xi’an Medical University 710021 Xi’an Shaanxi China
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50
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Thapa HR, Naik MT, Okada S, Takada K, Molnár I, Xu Y, Devarenne TP. A squalene synthase-like enzyme initiates production of tetraterpenoid hydrocarbons in Botryococcus braunii Race L. Nat Commun 2016; 7:11198. [PMID: 27050299 PMCID: PMC4823828 DOI: 10.1038/ncomms11198] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/29/2016] [Indexed: 12/24/2022] Open
Abstract
The green microalga Botryococcus braunii is considered a promising biofuel feedstock producer due to its prodigious accumulation of hydrocarbon oils that can be converted into fuels. B. braunii Race L produces the C40 tetraterpenoid hydrocarbon lycopadiene via an uncharacterized biosynthetic pathway. Structural similarities suggest this pathway follows a biosynthetic mechanism analogous to that of C30 squalene. Confirming this hypothesis, the current study identifies C20 geranylgeranyl diphosphate (GGPP) as a precursor for lycopaoctaene biosynthesis, the first committed intermediate in the production of lycopadiene. Two squalene synthase (SS)-like complementary DNAs are identified in race L with one encoding a true SS and the other encoding an enzyme with lycopaoctaene synthase (LOS) activity. Interestingly, LOS uses alternative C15 and C20 prenyl diphosphate substrates to produce combinatorial hybrid hydrocarbons, but almost exclusively uses GGPP in vivo. This discovery highlights how SS enzyme diversification results in the production of specialized tetraterpenoid oils in race L of B. braunii. The green microalga Botryococcus braunii is a promising biofuel producer due to its ability to produce large amounts of hydrocarbon oils that can be converted into fuels. Here the authors implicate lycopaoctaene synthase, a squalene synthases-like enzyme, in the first step towards the biosynthesis of the C40 tetraterpenoid hydrocarbon lycopadiene.
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Affiliation(s)
- Hem R Thapa
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Mandar T Naik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA.,Biomolecular NMR Laboratory, Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan.,Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo 102-0076, Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan.,Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo 102-0076, Japan
| | - István Molnár
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, Tucson, Arizona 85739, USA
| | - Yuquan Xu
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, Tucson, Arizona 85739, USA.,Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Timothy P Devarenne
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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