1
|
Grundmann CO, Guzman J, Vilcinskas A, Pupo MT. The insect microbiome is a vast source of bioactive small molecules. Nat Prod Rep 2024; 41:935-967. [PMID: 38411238 DOI: 10.1039/d3np00054k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: September 1964 to June 2023Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.
Collapse
Affiliation(s)
| | - Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Giessen, Germany
| | - Mônica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| |
Collapse
|
2
|
Yang C, Halitschke R, O'Connor SE. OXIDOSQUALENE CYCLASE 1 and 2 influence triterpene biosynthesis and defense in Nicotiana attenuata. PLANT PHYSIOLOGY 2024; 194:2580-2599. [PMID: 38101922 PMCID: PMC10980520 DOI: 10.1093/plphys/kiad643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023]
Abstract
Triterpenes are a class of bioactive compounds with diverse biological functions, playing pivotal roles in plant defense against biotic stressors. Oxidosqualene cyclases (OSCs) serve as gatekeepers in the biosynthesis of triterpenes. In this study, we utilized a Nicotiana benthamiana heterologous expression system to characterize NaOSC1 from Nicotiana attenuata as a multifunctional enzyme capable of synthesizing lupeol, dammarenediol II, 3-alpha,20-lupanediol, and 7 other triterpene scaffolds. We also demonstrated that NaOSC2 is, in contrast, a selective enzyme, producing only the β-amyrin scaffold. Through virus-induced gene silencing and in vitro toxicity assays, we elucidated the roles of NaOSC1 and NaOSC2 in the defense of N. attenuata against Manduca sexta larvae. Metabolomic and feature-based molecular network analyses of leaves with silenced NaOSC1 and NaOSC2 unveiled 3 potential triterpene glycoside metabolite clusters. Interestingly, features identified as triterpenes within these clusters displayed a significant negative correlation with larval mass. Our study highlights the pivotal roles of NaOSC1 and NaOSC2 from N. attenuata in the initial steps of triterpene biosynthesis, subsequently influencing defense against M. sexta through the modulation of downstream triterpene glycoside compounds.
Collapse
Affiliation(s)
- Caiqiong Yang
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena D-07745, Germany
| | - Rayko Halitschke
- Mass Spectrometry and Metabolomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena D-07745, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena D-07745, Germany
| |
Collapse
|
3
|
Abstract
Covering: up to July 2023Terpene cyclases (TCs) catalyze some of the most complicated reactions in nature and are responsible for creating the skeletons of more than 95 000 terpenoid natural products. The canonical TCs are divided into two classes according to their structures, functions, and mechanisms. The class II TCs mediate acid-base-initiated cyclization reactions of isoprenoid diphosphates, terpenes without diphosphates (e.g., squalene or oxidosqualene), and prenyl moieties on meroterpenes. The past twenty years witnessed the emergence of many class II TCs, their reactions and their roles in biosynthesis. Class II TCs often act as one of the first steps in the biosynthesis of biologically active natural products including the gibberellin family of phytohormones and fungal meroterpenoids. Due to their mechanisms and biocatalytic potential, TCs elicit fervent attention in the biosynthetic and organic communities and provide great enthusiasm for enzyme engineering to construct novel and bioactive molecules. To engineer and expand the structural diversities of terpenoids, it is imperative to fully understand how these enzymes generate, precisely control, and quench the reactive carbocation intermediates. In this review, we summarize class II TCs from nature, including sesquiterpene, diterpene, triterpene, and meroterpenoid cyclases as well as noncanonical class II TCs and inspect their sequences, structures, mechanisms, and structure-guided engineering studies.
Collapse
Affiliation(s)
- Xingming Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, USA.
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| |
Collapse
|
4
|
Xu H, Xiao Q, Dai Y, Chen D, Zhang C, Jiang Y, Xie J. Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data. MICROBIAL ECOLOGY 2023; 86:3043-3056. [PMID: 37831075 DOI: 10.1007/s00248-023-02307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.
Collapse
Affiliation(s)
- Hongxiang Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiong Xiao
- Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China
| | - Yongdong Dai
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Dexin Chen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Cheng Zhang
- Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China.
| | - Yongjun Jiang
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
5
|
Sraphet S, Javadi B. Computational analysis of carboxylesterase genes and proteins in non-pathogenic food bacterium Alicyclobacillus acidocaldarius: insights from proteogenomics. World J Microbiol Biotechnol 2023; 39:348. [PMID: 37855845 DOI: 10.1007/s11274-023-03805-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
Over recent years, Alicyclobacillus acidocaldarius, a Gram-positive nonpathogenic rod-shaped thermo-acid-tolerant bacterium, has posed numerous challenges for the fruit juice industry. However, the bacterium's unique characteristics, particularly its nonpathogenic and thermophilic capabilities, offer significant opportunities for genetic exploration by biotechnologists. This study presents the computational proteogenomics report on the carboxylesterase (CE) enzyme in A. acidocaldarius, shedding light on structural and evolutional of CEs from this bacterium. Our analysis revealed that the average molecular weight of CEs in A. acidocaldarius was 41 kDa, with an isoelectric point around 5. The amino acid composition favored negative amino acids over positive ones. The aliphatic index and hydropathicity were approximately 88 and - 0.15, respectively. While the protein sequence showed no disulfide bonds in the CEs' structure, the presence of Cys amino acids was observed in the structure of CEs. Phylogenetic analysis presented more than 99% similarity between CEs, indicating their close evolutionary relationship. By applying homology modeling, the 3-dimensional structural models of the carboxylesterase were constructed, which with the help of structural conservation and solvent accessibility analysis highlighted key residues and regions responsible for enzyme stability and conformation. The specific patterns presented the total solvent accessibility of less than 25 (Å2) was in considerable position as well as Gly residues were noticeably have high accessibility to solvent in all structures. Ala was the more frequent amino acids in the conserved-SASA of carboxylesterases. Furthermore, unsupervised agglomerative hierarchical clustering based on solvent accessibility feature successfully clustered and even distinguished this enzyme from proteases from the same genome. These findings contribute to a deeper understanding of the nonpathogenic A. acidocaldarius carboxylesterase and its potential applications in biotechnology. Additionally, structural analysis of CEs would help to address potential solutions in fruit juice industry with utilization of computational structural biology.
Collapse
Affiliation(s)
- Supajit Sraphet
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Bagher Javadi
- Department of Sciences, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand.
| |
Collapse
|
6
|
Nair IM, Kochupurackal J. Squalene hopene cyclases and oxido squalene cyclases: potential targets for regulating cyclisation reactions. Biotechnol Lett 2023; 45:573-588. [PMID: 37055654 DOI: 10.1007/s10529-023-03366-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 04/15/2023]
Abstract
Squalene hopene cyclases (SHC) convert squalene, the linear triterpene to fused ring product hopanoid by the cationic cyclization mechanism. The main function of hopanoids, a class of pentacyclic triterpenoids in bacteria involves the maintenance of membrane fluidity and stability. 2, 3-oxido squalene cyclases are functional analogues of SHC in eukaryotes and both these enzymes have fascinated researchers for the high stereo selectivity, complexity, and efficiency they possess. The peculiar property of the enzyme squalene hopene cyclase to accommodate substrates other than its natural substrate can be exploited for the use of these enzymes in an industrial perspective. Here, we present an extensive overview of the enzyme squalene hopene cyclase with emphasis on the cloning and overexpression strategies. An attempt has been made to explore recent research trends around squalene cyclase mediated cyclization reactions of flavour and pharmaceutical significance by using non-natural molecules as substrates.
Collapse
Affiliation(s)
- Indu Muraleedharan Nair
- School of Biosciences, Mahatma Gandhi University, Athirampuzha, Kottayam, 686560, India
- Department of Physiology, School of Medicine, University College Cork, Cork, T12 XF62, Ireland
| | | |
Collapse
|
7
|
Eichhorn E, Schroeder F. From Ambergris to (-)-Ambrox: Chemistry Meets Biocatalysis for Sustainable (-)-Ambrox Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5042-5052. [PMID: 36961824 DOI: 10.1021/acs.jafc.2c09010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
(-)-Ambrox, the most prominent olfactive component of ambergris is one of the most widely used biodegradable fragrance ingredients. Traditionally it is produced from the diterpene sclareol, modified and cyclized into (-)-ambrox by classical chemistry steps. The availability of the new feedstock (E)-β-farnesene produced by fermentation opened new pathways to (E,E)-homofarnesol as a precursor to (-)-ambrox. Combining chemical transformation of (E)-β-farnesene to (E,E)-homofarnesol and its enzymatic cyclization at the industrial scale to (-)-ambrox with an engineered squalene hopene cyclase illustrates the potential of biotechnology for a more sustainable process, thus meeting the increasing consumers' demand for sustainably produced high quality perfumery and consumer goods. This review traces back to the origin of ambergris and the search for the source of its mysterious odor, leading to the discovery of (-)-ambrox as its main olfactive principle. It discusses the plethora of ways explored for its synthesis from diverse starting materials and presents the development of a process with significantly improved carbon efficiency for the industrial production of (-)-ambrox as 100% renewable Ambrofix.
Collapse
Affiliation(s)
- Eric Eichhorn
- Fragrances S&T, Ingredients Research, Givaudan Schweiz AG, Kemptpark 50, CH-8310 Kemptthal, Switzerland
| | - Fridtjof Schroeder
- Fragrances S&T, Ingredients Research, Givaudan Schweiz AG, Kemptpark 50, CH-8310 Kemptthal, Switzerland
| |
Collapse
|
8
|
Schell K, Li H, Lauterbach L, Taizoumbe KA, Dickschat JS, Hauer B. Alternative Active Site Confinement in Squalene–Hopene Cyclase Enforces Substrate Preorganization for Cyclization. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
|
9
|
Rodrigues JS, Bourgade B, Galle KR, Lindberg P. Mapping competitive pathways to terpenoid biosynthesis in Synechocystis sp. PCC 6803 using an antisense RNA synthetic tool. Microb Cell Fact 2023; 22:35. [PMID: 36823631 PMCID: PMC9951418 DOI: 10.1186/s12934-023-02040-2] [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: 11/24/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Synechocystis sp. PCC 6803 utilizes pyruvate and glyceraldehyde 3-phosphate via the methylerythritol 4-phosphate (MEP) pathway for the biosynthesis of terpenoids. Considering the deep connection of the MEP pathway to the central carbon metabolism, and the low carbon partitioning towards terpenoid biosynthesis, significant changes in the metabolic network are required to increase cyanobacterial production of terpenoids. RESULTS We used the Hfq-MicC antisense RNA regulatory tool, under control of the nickel-inducible PnrsB promoter, to target 12 different genes involved in terpenoid biosynthesis, central carbon metabolism, amino acid biosynthesis and ATP production, and evaluated the changes in the performance of an isoprene-producing cyanobacterial strain. Six candidate targets showed a positive effect on isoprene production: three genes involved in terpenoid biosynthesis (crtE, chlP and thiG), two involved in amino acid biosynthesis (ilvG and ccmA) and one involved in sugar catabolism (gpi). The same strategy was applied to interfere with different parts of the terpenoid biosynthetic pathway in a bisabolene-producing strain. Increased bisabolene production was observed not only when interfering with chlorophyll a biosynthesis, but also with carotenogenesis. CONCLUSIONS We demonstrated that the Hfq-MicC synthetic tool can be used to evaluate the effects of gene knockdown on heterologous terpenoid production, despite the need for further optimization of the technique. Possible targets for future engineering of Synechocystis aiming at improved terpenoid microbial production were identified.
Collapse
Affiliation(s)
- João S. Rodrigues
- grid.8993.b0000 0004 1936 9457Department of Chemistry – Ångström, Uppsala University, Uppsala, Sweden
| | - Barbara Bourgade
- grid.8993.b0000 0004 1936 9457Department of Chemistry – Ångström, Uppsala University, Uppsala, Sweden
| | - Karen R. Galle
- grid.8993.b0000 0004 1936 9457Department of Chemistry – Ångström, Uppsala University, Uppsala, Sweden ,grid.5808.50000 0001 1503 7226Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pia Lindberg
- Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
10
|
Santoscoy MC, Jarboe LR. Production of cholesterol-like molecules impacts Escherichia coli robustness, production capacity, and vesicle trafficking. Metab Eng 2022; 73:134-143. [PMID: 35842218 DOI: 10.1016/j.ymben.2022.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/26/2022] [Accepted: 07/03/2022] [Indexed: 10/17/2022]
Abstract
The economic viability of bioprocesses is constrained by the limited range of operating conditions that can be tolerated by the cell factory. Engineering of the microbial cell membrane is one strategy that can increase robustness and thus alter this range. In this work, we targeted cellular components that contribute to maintenance of appropriate membrane function, such as: flotillin-like proteins, membrane structural proteins, and membrane lipids. Specifically, we exploited the promiscuity of squalene hopene cyclase (SHC) to produce polycyclic terpenoids with properties analogous to cholesterol. Strains producing these cholesterol-like molecules were visualized by AFM and height features were observed. Production of these cholesterol-like molecules was associated with increased tolerance towards a diversity of chemicals, particularly alcohols, and membrane trafficking processes such as lipid droplet accumulation and production of extracellular vesicles. This engineering approach improved the production titers for wax-esters and ethanol by 80- and 10-fold, respectively. Expression of SHC resulted in the production of steroids. Strains engineered to also express truncated squalene synthase (tERG9) produced diplopterol and generally did not perform as well. Increased expression of several membrane-associated proteins, such as YqiK, was observed to impact vesicle trafficking and further improve tolerance relative to SHC alone, but did not improve bio-production. Deletion of YbbJ increased lipid droplet accumulation as well as production of intracellular wax esters. This work serves as a proof of concept for engineering strategies targeting membrane physiology and trafficking to expand the production capacity of microbial cell factories.
Collapse
Affiliation(s)
- Miguel C Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.
| |
Collapse
|
11
|
He C, Liu J, Wang R, Li Y, Zheng Q, Jiao F, He C, Shi Q, Xu Y, Zhang R, Thomas H, Batt J, Hill P, Lewis M, Maclntyre H, Lu L, Zhang Q, Tu Q, Shi T, Chen F, Jiao N. Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment. WATER RESEARCH 2022; 216:118281. [PMID: 35316680 DOI: 10.1016/j.watres.2022.118281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (IDEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as IDEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3‑hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.
Collapse
Affiliation(s)
- Changfei He
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou 510000, China.
| | - Rui Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Qiang Zheng
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Fanglue Jiao
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Rui Zhang
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Helmuth Thomas
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada; Helmholtz-Center Geesthacht, Institute for Coastal Research, Max-Planck-Strasse 1, Geesthacht d-21502, Germany
| | - John Batt
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Paul Hill
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Marlon Lewis
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Hugh Maclntyre
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Longfei Lu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, Shandong, China
| | - Qinghua Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Marine Equipment Inspection & Testing Co. Ltd, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Tuo Shi
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Feng Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Environmental Research Center, University of Maryland at Baltimore, United States
| | - Nianzhi Jiao
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou 510000, China
| |
Collapse
|
12
|
Sangster JJ, Marshall JR, Turner NJ, Mangas‐Sanchez J. New Trends and Future Opportunities in the Enzymatic Formation of C-C, C-N, and C-O bonds. Chembiochem 2022; 23:e202100464. [PMID: 34726813 PMCID: PMC9401909 DOI: 10.1002/cbic.202100464] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/29/2021] [Indexed: 01/04/2023]
Abstract
Organic chemistry provides society with fundamental products we use daily. Concerns about the impact that the chemical industry has over the environment is propelling major changes in the way we manufacture chemicals. Biocatalysis offers an alternative to other synthetic approaches as it employs enzymes, Nature's catalysts, to carry out chemical transformations. Enzymes are biodegradable, come from renewable sources, operate under mild reaction conditions, and display high selectivities in the processes they catalyse. As a highly multidisciplinary field, biocatalysis benefits from advances in different areas, and developments in the fields of molecular biology, bioinformatics, and chemical engineering have accelerated the extension of the range of available transformations (E. L. Bell et al., Nat. Rev. Meth. Prim. 2021, 1, 1-21). Recently, we surveyed advances in the expansion of the scope of biocatalysis via enzyme discovery and protein engineering (J. R. Marshall et al., Tetrahedron 2021, 82, 131926). Herein, we focus on novel enzymes currently available to the broad synthetic community for the construction of new C-C, C-N and C-O bonds, with the purpose of providing the non-specialist with new and alternative tools for chiral and sustainable chemical synthesis.
Collapse
Affiliation(s)
- Jack J. Sangster
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - James R. Marshall
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Nicholas J. Turner
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Juan Mangas‐Sanchez
- Institute of Chemical Synthesis and Homogeneous CatalysisSpanish National Research Council (CSIC)Pedro Cerbuna 1250009ZaragozaSpain
- ARAID FoundationZaragozaSpain
| |
Collapse
|
13
|
Hwang S, Lee N, Choe D, Lee Y, Kim W, Kim JH, Kim G, Kim H, Ahn NH, Lee BH, Palsson BO, Cho BK. System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus. Front Bioeng Biotechnol 2022; 10:844200. [PMID: 35284422 PMCID: PMC8914203 DOI: 10.3389/fbioe.2022.844200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteria belonging to Streptomyces have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative growth terminates. Despite considerable effort to understand the regulatory elements governing gene expression related to primary and secondary metabolism in Streptomyces, system-level information remains limited. In this study, we integrated four multi-omics datasets from Streptomyces griseus NBRC 13350: RNA-seq, ribosome profiling, dRNA-seq, and Term-Seq, to analyze the regulatory elements of transcription and translation of differentially expressed genes during cell growth. With the functional enrichment of gene expression in different growth phases, one sigma factor regulon and four transcription factor regulons governing differential gene transcription patterns were found. In addition, the regulatory elements of transcription termination and post-transcriptional processing at transcript 3'-end positions were elucidated, including their conserved motifs, stem-loop RNA structures, and non-terminal locations within the polycistronic operons, and the potential regulatory elements of translation initiation and elongation such as 5'-UTR length, RNA structures at ribosome-bound sites, and codon usage were investigated. This comprehensive genetic information provides a foundational genetic resource for strain engineering to enhance secondary metabolite production in Streptomyces.
Collapse
Affiliation(s)
- Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Gahyeon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Hyeseong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Neung-Ho Ahn
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Byoung-Hee Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| |
Collapse
|
14
|
Eichenberger M, Hüppi S, Patsch D, Aeberli N, Berweger R, Dossenbach S, Eichhorn E, Flachsmann F, Hortencio L, Voirol F, Vollenweider S, Bornscheuer UT, Buller R. Asymmetric Cation-Olefin Monocyclization by Engineered Squalene-Hopene Cyclases. Angew Chem Int Ed Engl 2021; 60:26080-26086. [PMID: 34346556 PMCID: PMC9290348 DOI: 10.1002/anie.202108037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/09/2021] [Indexed: 12/31/2022]
Abstract
Squalene-hopene cyclases (SHCs) have great potential for the industrial synthesis of enantiopure cyclic terpenoids. A limitation of SHC catalysis has been the enzymes' strict (S)-enantioselectivity at the stereocenter formed after the first cyclization step. To gain enantio-complementary access to valuable monocyclic terpenoids, an SHC-wild-type library including 18 novel homologs was set up. A previously not described SHC (AciSHC) was found to synthesize small amounts of monocyclic (R)-γ-dihydroionone from (E/Z)-geranylacetone. Using enzyme and process optimization, the conversion to the desired product was increased to 79 %. Notably, analyzed AciSHC variants could finely differentiate between the geometric geranylacetone isomers: While the (Z)-isomer yielded the desired monocyclic (R)-γ-dihydroionone (>99 % ee), the (E)-isomer was converted to the (S,S)-bicyclic ether (>95 % ee). Applying the knowledge gained from the observed stereodivergent and enantioselective transformations to an additional SHC-substrate pair, access to the complementary (S)-γ-dihydroionone (>99.9 % ee) could be obtained.
Collapse
Affiliation(s)
- Michael Eichenberger
- Zurich University of Applied SciencesLife Sciences and Facility ManagementEinsiedlerstrasse 318820WädenswilSwitzerland
| | - Sean Hüppi
- Zurich University of Applied SciencesLife Sciences and Facility ManagementEinsiedlerstrasse 318820WädenswilSwitzerland
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - David Patsch
- Zurich University of Applied SciencesLife Sciences and Facility ManagementEinsiedlerstrasse 318820WädenswilSwitzerland
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Natalie Aeberli
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Raphael Berweger
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Sandro Dossenbach
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Eric Eichhorn
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Felix Flachsmann
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Lucas Hortencio
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Francis Voirol
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Sabine Vollenweider
- Science & TechnologyGivaudan International SAKemptpark 508310KemptthalSwitzerland
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Rebecca Buller
- Zurich University of Applied SciencesLife Sciences and Facility ManagementEinsiedlerstrasse 318820WädenswilSwitzerland
| |
Collapse
|
15
|
Eichenberger M, Hüppi S, Patsch D, Aeberli N, Berweger R, Dossenbach S, Eichhorn E, Flachsmann F, Hortencio L, Voirol F, Vollenweider S, Bornscheuer UT, Buller R. Asymmetric Cation‐Olefin Monocyclization by Engineered Squalene–Hopene Cyclases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Eichenberger
- Zurich University of Applied Sciences Life Sciences and Facility Management Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Sean Hüppi
- Zurich University of Applied Sciences Life Sciences and Facility Management Einsiedlerstrasse 31 8820 Wädenswil Switzerland
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - David Patsch
- Zurich University of Applied Sciences Life Sciences and Facility Management Einsiedlerstrasse 31 8820 Wädenswil Switzerland
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis Greifswald University Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Natalie Aeberli
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Raphael Berweger
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Sandro Dossenbach
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Eric Eichhorn
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Felix Flachsmann
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Lucas Hortencio
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Francis Voirol
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Sabine Vollenweider
- Science & Technology Givaudan International SA Kemptpark 50 8310 Kemptthal Switzerland
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis Greifswald University Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Rebecca Buller
- Zurich University of Applied Sciences Life Sciences and Facility Management Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| |
Collapse
|
16
|
Almeida OGG, Gimenez MP, De Martinis ECP. Comparative pangenomic analyses and biotechnological potential of cocoa-related Acetobacter senegalensis strains. Antonie van Leeuwenhoek 2021; 115:111-123. [PMID: 34817761 DOI: 10.1007/s10482-021-01684-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/06/2021] [Indexed: 10/19/2022]
Abstract
Acetobacter senegalensis belongs to the group of acetic acid bacteria (AAB) that present potential biotechnological applications, for production of D-gluconate, cellulose and acetic acid. AAB can overcome heat and acid stresses by using strategies involving the overexpression of heat-shock proteins and enzymes from the complex pyrroquinoline-ADH, besides alcohol dehydrogenases (ADH). Nonetheless, the isolation of A. senegalensis and other AAB from food may be challenging due to presence of viable but non-culturable (VBNC) cells and due to uncertainties about nutritional requirements. To contribute for a better understanding of the ecology of AAB, this paper reports on the pangenome analysis of five strains of A. senegalensis recently isolated from a Brazilian spontaneous cocoa fermentation. The results showed biosynthetic clusters exclusively found in some cocoa-related AAB, such as those related to terpene pathways, which are important for flavour development. Genes related to oxidative stress were conserved in all the genomes, with multiple clusters. Moreover, there were genes coding for ADH and putative ABC transporters distributed in core, shell and cloud genomes, while chaperonin-encoding genes were present only in the core and soft-core genomes. Regarding quorum sensing, a response regulator gene was in the shell genome, and the gene encoding for acyl-homoserine lactone efflux protein was in the soft-core genome. There were quorum quenching-related genes, mainly encoding for lactonases, but also for acylases. Moreover, A. senegalensis did not have determinants of virulence or antibiotic resistance, which are good traits for strains intended to be applied in food fermentation.
Collapse
Affiliation(s)
- O G G Almeida
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - M P Gimenez
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - E C P De Martinis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil.
| |
Collapse
|
17
|
Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites. Antonie van Leeuwenhoek 2021; 115:41-58. [PMID: 34761294 PMCID: PMC8776678 DOI: 10.1007/s10482-021-01676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022]
Abstract
Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 141 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~ 6.3 and ~ 3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis. Our in silico analysis indicated that the family Acetobacteraceae is a potential source of many undiscovered bacterial metabolites and deserves more detailed experimental exploration.
Collapse
|
18
|
Abstract
The Pd-catalyzed carbon-carbon bond formation pioneered by Heck in 1969 has dominated medicinal chemistry development for the ensuing fifty years. As the demand for more complex three-dimensional active pharmaceuticals continues to increase, preparative enzyme-mediated assembly, by virtue of its exquisite selectivity and sustainable nature, is poised to provide a practical and affordable alternative for accessing such compounds. In this minireview, we summarize recent state-of-the-art developments in practical enzyme-mediated assembly of carbocycles. When appropriate, background information on the enzymatic transformation is provided and challenges and/or limitations are also highlighted.
Collapse
Affiliation(s)
- Weijin Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Douglass F Taber
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| |
Collapse
|
19
|
Henche S, Nestl BM, Hauer B. Enzymatic Friedel‐Crafts Alkylation Using Squalene‐Hopene Cyclases. ChemCatChem 2021. [DOI: 10.1002/cctc.202100452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sabrina Henche
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry Universitaet Stuttgart Allmandring 31 70569 Stuttgart Germany
| | | | - Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry Universitaet Stuttgart Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
20
|
Huang ZY, Ye RY, Yu HL, Li AT, Xu JH. Mining methods and typical structural mechanisms of terpene cyclases. BIORESOUR BIOPROCESS 2021; 8:66. [PMID: 38650244 PMCID: PMC10992375 DOI: 10.1186/s40643-021-00421-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/24/2021] [Indexed: 12/13/2022] Open
Abstract
Terpenoids, formed by cyclization and/or permutation of isoprenes, are the most diverse and abundant class of natural products with a broad range of significant functions. One family of the critical enzymes involved in terpenoid biosynthesis is terpene cyclases (TCs), also known as terpene synthases (TSs), which are responsible for forming the ring structure as a backbone of functionally diverse terpenoids. With the recent advances in biotechnology, the researches on terpene cyclases have gradually shifted from the genomic mining of novel enzyme resources to the analysis of their structures and mechanisms. In this review, we summarize both the new methods for genomic mining and the structural mechanisms of some typical terpene cyclases, which are helpful for the discovery, engineering and application of more and new TCs.
Collapse
Affiliation(s)
- Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Ru-Yi Ye
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Ai-Tao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China.
| |
Collapse
|
21
|
Zhao J, Sun C, Shi F, Ma S, Zheng J, Du X, Zhang L. Comparative transcriptome analysis reveals sesquiterpenoid biosynthesis among 1-, 2- and 3-year old Atractylodes chinensis. BMC PLANT BIOLOGY 2021; 21:354. [PMID: 34315414 PMCID: PMC8314494 DOI: 10.1186/s12870-021-03131-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Atractylodes chinensis (DC.) Koidz is a well-known medicinal plant containing the major bioactive compound, atractylodin, a sesquiterpenoid. High-performance liquid chromatography (HPLC) analysis demonstrated that atractylodin was most abundant in 3-year old A. chinensis rhizome, compared with those from 1- and 2-year old rhizomes, however, the molecular mechanisms underlying accumulation of atractylodin in rhizomes are poorly understood. RESULTS In this study, we characterized the transcriptomes from rhizomes of 1-, 2- and 3-year old (Y1, Y2 and Y3, respectively) A. chinensis, to identify differentially expressed genes (DEGs). We identified 240, 169 and 131 unigenes encoding the enzyme genes in the mevalonate (MVA), methylerythritol phosphate (MEP), sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. To confirm the reliability of the RNA sequencing analysis, eleven key gene encoding factors involved in the sesquiterpenoid and triterpenoid biosynthetic pathway, as well as in pigment, amino acid, hormone and transcription factor functions, were selected for quantitative real time PCR (qRT-PCR) analysis. The results demonstrated similar expression patterns to those determined by RNA sequencing, with a Pearson's correlation coefficient of 0.9 between qRT-PCR and RNA-seq data. Differential gene expression analysis of rhizomes from different ages revealed 52 genes related to sesquiterpenoid and triterpenoid biosynthesis. Among these, seven DEGs were identified in Y1 vs Y2, Y1 vs Y3 and Y2 vs Y3, of which five encoded four key enzymes, squalene/phytoene synthase (SS), squalene-hopene cyclase (SHC), squalene epoxidase (SE) and dammarenediol II synthase (DS). These four enzymes directly related to squalene biosynthesis and subsequent catalytic action. To validate the result of these seven DEGs, qRT-PCR was performed and indicated most of them displayed lower relative expression in 3-year old rhizome, similar to transcriptomic analysis. CONCLUSION The enzymes SS, SHC, SE and DS down-regulated expression in 3-year old rhizome. This data corresponded to the higher content of sesquiterpenoid in 3-year old rhizome, and confirmed by qRT-PCR. The results of comparative transcriptome analysis and identified key enzyme genes laid a solid foundation for investigation of production sesquiterpenoid in A. chinensis.
Collapse
Affiliation(s)
- Jianhua Zhao
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei, China
| | - Chengzhen Sun
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei, China
| | - Fengyu Shi
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei, China
| | - Shanshan Ma
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei, China
| | - Jinshuang Zheng
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei, China.
| | - Xin Du
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei, China
| | - Liping Zhang
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei, China
| |
Collapse
|
22
|
Tookmanian EM, Belin BJ, Sáenz JP, Newman DK. The role of hopanoids in fortifying rhizobia against a changing climate. Environ Microbiol 2021; 23:2906-2918. [PMID: 33989442 DOI: 10.1111/1462-2920.15594] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022]
Abstract
Bacteria are a globally sustainable source of fixed nitrogen, which is essential for life and crucial for modern agriculture. Many nitrogen-fixing bacteria are agriculturally important, including bacteria known as rhizobia that participate in growth-promoting symbioses with legume plants throughout the world. To be effective symbionts, rhizobia must overcome multiple environmental challenges: from surviving in the soil, to transitioning to the plant environment, to maintaining high metabolic activity within root nodules. Climate change threatens to exacerbate these challenges, especially through fluctuations in soil water potential. Understanding how rhizobia cope with environmental stress is crucial for maintaining agricultural yields in the coming century. The bacterial outer membrane is the first line of defence against physical and chemical environmental stresses, and lipids play a crucial role in determining the robustness of the outer membrane. In particular, structural remodelling of lipid A and sterol-analogues known as hopanoids are instrumental in stress acclimation. Here, we discuss how the unique outer membrane lipid composition of rhizobia may underpin their resilience in the face of increasing osmotic stress expected due to climate change, illustrating the importance of studying microbial membranes and highlighting potential avenues towards more sustainable soil additives.
Collapse
Affiliation(s)
- Elise M Tookmanian
- Division of Chemistry & Chemical Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Brittany J Belin
- Department of Embryology, The Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - James P Sáenz
- B CUBE Center for Molecular Bioengineering, Tatzberg 41, Technische Universität Dresden, Dresden, 01307, Germany
| | - Dianne K Newman
- Division of Biology & Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
- Division of Geology & Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| |
Collapse
|
23
|
Zhu LP, Song SZ, Yang S. Gene repression using synthetic small regulatory RNA in Methylorubrum extorquens. J Appl Microbiol 2021; 131:2861-2875. [PMID: 34021964 DOI: 10.1111/jam.15159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022]
Abstract
AIM Genetic tools are a prerequisite for engineering cell factories for synthetic biology and biotechnology. Methylorubrum extorquens is an important platform for a future one-carbon (C1) bioeconomy, but its application is currently limited by the availability of genetic tools. Small regulatory RNA (sRNA) is an important regulatory factor in bacteria and has been applied for gene repression in several strains. This study aimed to construct a synthetic sRNA system based on the MicC scaffold and the chaperone Hfq to control gene expression in M. extorquens. METHODS AND RESULTS Initially, the exogenous lacZ gene was transposed into the M. extorquens chromosome as a reporter, and corresponding β-galactosidase was measured to assess the knockdown efficiency of lacZ. A synthetic sRNA containing a 24-nt antisense RNA targeting lacZ and an Escherichia coli MicC scaffold were constructed, and different Hfqs from E. coli, M. extorquens AM1 and PA1 were further identified. The results showed that the expression of endogenous hfqs from the chromosome in M. extorquens strains was inadequate, and only when it was overexpressed via the plasmid did the colonies show a colour change and a corresponding decrease in β-galactosidase expression. More specifically, M. extorquens strains with overexpressing their own Hfq showed the best gene repression efficiency. Furthermore, this E. coli MicC scaffold and AM1 Hfq system were combined to knock down crtI gene expression in AM1, leading to an 86% decrease in carotenoid production (0·09 mg g-1 ) compared to that (0·65 mg g-1 ) in the wild-type strain. CONCLUSION A functional synthetic sRNA system combined with E. coli MicC and endogenous Hfq was constructed in M. extorquens strains, which was able to interfere with the target crtI gene and reduce carotenoid production. SIGNIFICANCE AND IMPACT OF THE STUDY The synthetic sRNA system reported in this study provides a genetic tool for the manipulation of M. extorquens. The present findings might be helpful for achieving high-throughput gene knockdown expression.
Collapse
Affiliation(s)
- L-P Zhu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - S-Z Song
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - S Yang
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| |
Collapse
|
24
|
Hernández J, Gabrielli M, Costa J, Uttaro AD. Phagocytic and pinocytic uptake of cholesterol in Tetrahymena thermophila impact differently on gene regulation for sterol homeostasis. Sci Rep 2021; 11:9067. [PMID: 33907281 PMCID: PMC8079401 DOI: 10.1038/s41598-021-88737-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 04/15/2021] [Indexed: 01/02/2023] Open
Abstract
The ciliate Tetrahymena thermophila can either synthesize tetrahymanol or when available, assimilate and modify sterols from its diet. This metabolic shift is mainly driven by transcriptional regulation of genes for tetrahymanol synthesis (TS) and sterol bioconversion (SB). The mechanistic details of sterol uptake, intracellular trafficking and the associated gene expression changes are unknown. By following cholesterol incorporation over time in a conditional phagocytosis-deficient mutant, we found that although phagocytosis is the main sterol intake route, a secondary endocytic pathway exists. Different expression patterns for TS and SB genes were associated with these entry mechanisms. Squalene synthase was down-regulated by a massive cholesterol intake only attainable by phagocytosis-proficient cells, whereas C22-sterol desaturase required ten times less cholesterol and was up-regulated in both wild-type and mutant cells. These patterns are suggestive of at least two different signaling pathways. Sterol trafficking beyond phagosomes and esterification was impaired by the NPC1 inhibitor U18666A. NPC1 is a protein that mediates cholesterol export from late endosomes/lysosomes in mammalian cells. U18666A also produced a delay in the transcriptional response to cholesterol, suggesting that the regulatory signals are triggered between lysosomes and the endoplasmic reticulum. These findings could hint at partial conservation of sterol homeostasis between eukaryote lineages.
Collapse
Affiliation(s)
- Josefina Hernández
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2000FHQ, Ocampo y Esmeralda, Rosario, Argentina
| | - Matías Gabrielli
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2000FHQ, Ocampo y Esmeralda, Rosario, Argentina
| | - Joaquín Costa
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2000FHQ, Ocampo y Esmeralda, Rosario, Argentina
| | - Antonio D Uttaro
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2000FHQ, Ocampo y Esmeralda, Rosario, Argentina.
| |
Collapse
|
25
|
Francoeur CB, Khadempour L, Moreira-Soto RD, Gotting K, Book AJ, Pinto-Tomás AA, Keefover-Ring K, Currie CR. Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System. mBio 2020; 11:e02146-20. [PMID: 32934088 PMCID: PMC7492740 DOI: 10.1128/mbio.02146-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Herbivores must overcome a variety of plant defenses, including coping with plant secondary compounds (PSCs). To help detoxify these defensive chemicals, several insect herbivores are known to harbor gut microbiota with the metabolic capacity to degrade PSCs. Leaf-cutter ants are generalist herbivores, obtaining sustenance from specialized fungus gardens that act as external digestive systems and which degrade the diverse collection of plants foraged by the ants. There is in vitro evidence that certain PSCs harm Leucoagaricus gongylophorus, the fungal cultivar of leaf-cutter ants, suggesting a role for the Proteobacteria-dominant bacterial community present within fungus gardens. In this study, we investigated the ability of symbiotic bacteria present within fungus gardens of leaf-cutter ants to degrade PSCs. We cultured fungus garden bacteria, sequenced the genomes of 42 isolates, and identified genes involved in PSC degradation, including genes encoding cytochrome P450 enzymes and genes in geraniol, cumate, cinnamate, and α-pinene/limonene degradation pathways. Using metatranscriptomic analysis, we showed that some of these degradation genes are expressed in situ Most of the bacterial isolates grew unhindered in the presence of PSCs and, using gas chromatography-mass spectrometry (GC-MS), we determined that isolates from the genera Bacillus, Burkholderia, Enterobacter, Klebsiella, and Pseudomonas degrade α-pinene, β-caryophyllene, or linalool. Using a headspace sampler, we show that subcolonies of fungus gardens reduced α-pinene and linalool over a 36-h period, while L. gongylophorus strains alone reduced only linalool. Overall, our results reveal that the bacterial communities in fungus gardens play a pivotal role in alleviating the effect of PSCs on the leaf-cutter ant system.IMPORTANCE Leaf-cutter ants are dominant neotropical herbivores capable of deriving energy from a wide range of plant substrates. The success of leaf-cutter ants is largely due to their external gut, composed of key microbial symbionts, specifically, the fungal mutualist L. gongylophorus and a consistent bacterial community. Both symbionts are known to have critical roles in extracting energy from plant material, yet comparatively little is known about their roles in the detoxification of plant secondary compounds. In this study, we assessed if the bacterial communities associated with leaf-cutter ant fungus gardens can degrade harmful plant chemicals. We identify plant secondary compound detoxification in leaf-cutter ant gardens as a process that depends on the degradative potential of both the bacterial community and L. gongylophorus Our findings suggest that the fungus garden and its associated microbial community influence the generalist foraging abilities of the ants, underscoring the importance of microbial symbionts in plant substrate suitability for herbivores.
Collapse
Affiliation(s)
- Charlotte B Francoeur
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lily Khadempour
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rolando D Moreira-Soto
- Sección de Entomología Medica, Departamento de Parasitología, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Kirsten Gotting
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adam J Book
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica
- Departamento de Bioquímica, Facultad de Medicina, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
26
|
Zetzsche LE, Narayan ARH. Broadening the scope of biocatalytic C-C bond formation. Nat Rev Chem 2020; 4:334-346. [PMID: 34430708 PMCID: PMC8382263 DOI: 10.1038/s41570-020-0191-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2020] [Indexed: 12/18/2022]
Abstract
The impeccable control over chemo-, site-, and stereoselectivity possible in enzymatic reactions has led to a surge in the development of new biocatalytic methods. Despite carbon-carbon (C-C) bonds providing the central framework for organic molecules, development of biocatalytic methods for their formation has been largely confined to the use of a select few lyases over the last several decades, limiting the types of C-C bond-forming transformations possible through biocatalytic methods. This Review provides an update on the suite of enzymes available for highly selective biocatalytic C-C bond formation. Examples will be discussed in reference to the (1) native activity of enzymes, (2) alteration of activity through protein or substrate engineering for broader applicability, and (3) utility of the biocatalyst for abiotic synthesis.
Collapse
Affiliation(s)
- Lara E. Zetzsche
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alison R. H. Narayan
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
27
|
Liu Z, Zhang Y, Sun J, Huang WC, Xue C, Mao X. A Novel Soluble Squalene-Hopene Cyclase and Its Application in Efficient Synthesis of Hopene. Front Bioeng Biotechnol 2020; 8:426. [PMID: 32478051 PMCID: PMC7232578 DOI: 10.3389/fbioe.2020.00426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/14/2020] [Indexed: 11/13/2022] Open
Abstract
Hopene is an important precursor for synthesizing bioactive hopanoids with great commercial value. However, the chemical methods for synthesizing hopene are not efficient to date. Hopene is commonly obtained by extracting from plants or bacteria like other terpenoids, but the complicated extraction process is inefficient and unfriendly to the environment. Hopene can be biological synthesized by squalene-hopene cyclase (SHC) from squalene. However, hopene production by SHC remained at a low level until now. In this work, we found a novel SHC named OUC-SaSHC from Streptomyces albolongus ATCC 27414. An easy procedure for expression and purification of OUC-SaSHC was established. The conditions for OUC-SaSHC to convert squalene into hopene are optimized as in 100 mM sodium phosphate buffer (pH 7.0) containing 0.5% Tween 80, 20 mM squalene and 0.14 mg/mL OUC-SaSHC at 30°C. In the scale-up reaction with the final volume of 100 mL, the yield of squalene could be up to 99% at 36 h, and 8.07 mg/mL hopene was produced. Our work showed a great potential of OUC-SaSHC as biocatalyst on scale-up production of hopene, hence improves the SHC-catalyzing enzyme synthesis of hopene from laboratory level to application level.
Collapse
Affiliation(s)
- Zhen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yinan Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Wen-Can Huang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
28
|
Shinozaki J, Ohtake M, Sato M, Ono K, Kamiyama S. Molecular basis of triterpene-based chemophenetics in ferns. PLANTA 2020; 251:78. [PMID: 32157441 DOI: 10.1007/s00425-020-03369-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
A hypothesis that squalene cyclase genes are widely distributed throughout ferns was proposed. We successfully isolated a squalene cyclase pseudogene from a fern from which no triterpene hydrocarbons were detected Ferns are the most primitive vascular plants, with their locations ranging from tropical to cold temperate regions and from lowland to alpine zones. The triterpene hydrocarbons and their derivatives are characteristic fern metabolites, and are also chemophenetic markers. Recently, our biosynthetic study into fern squalene cyclases (SCs), the enzymes responsible for triterpene synthesis, gave an unexpected inconsistency between genotype (enzyme function) and chemotype (triterpene profile). This finding prompted us to propose a hypothesis that SC genes are widely distributed throughout ferns and lycophytes whether or not they produce triterpene hydrocarbons. To test this hypothesis, we employed a multifaceted approach based on phytochemical, biochemical, and phylogenetic analyses. As anticipated, we successfully isolated two SC pseudogenes from a fern from in which no or only one triterpene hydrocarbon was detected. Subsequent mutagenesis experiments resulted in the functional conversion of these pseudogenes into active SC genes. Given an auxiliary hypothesis regarding the inherent limit of the degenerate polymerase chain reaction (PCR) method, the overall dataset supported our hypothesis, although correction was required with respect to plant coverage. Not only did the corrected hypothesis outline the distribution of SC genes throughout ferns, it provided insight into the molecular basis of the triterpene-based chemophenetics in ferns, which is also discussed.
Collapse
Affiliation(s)
- Junichi Shinozaki
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan.
| | - Mizuki Ohtake
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Mami Sato
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Keisuke Ono
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Shigeki Kamiyama
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| |
Collapse
|
29
|
Introduction of a green algal squalene synthase enhances squalene accumulation in a strain of Synechocystis sp. PCC 6803. Metab Eng Commun 2020; 10:e00125. [PMID: 32123662 PMCID: PMC7038009 DOI: 10.1016/j.mec.2020.e00125] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/28/2019] [Accepted: 02/03/2020] [Indexed: 11/21/2022] Open
Abstract
Squalene is a triterpene which is produced as a precursor for a wide range of terpenoid compounds in many organisms. It has commercial use in food and cosmetics but could also be used as a feedstock for production of chemicals and fuels, if generated sustainably on a large scale. We have engineered a cyanobacterium, Synechocystis sp. PCC 6803, for production of squalene from CO2. In this organism, squalene is produced via the methylerythritol-phosphate (MEP) pathway for terpenoid biosynthesis, and consumed by the enzyme squalene hopene cyclase (Shc) for generation of hopanoids. The gene encoding Shc in Synechocystis was inactivated (Δshc) by insertion of a gene encoding a squalene synthase from the green alga Botryococcus braunii, under control of an inducible promoter. We could demonstrate elevated squalene generation in cells where the algal enzyme was induced. Heterologous overexpression of genes upstream in the MEP pathway further enhanced the production of squalene, to a level three times higher than the Δshc background strain. During growth in flat panel bioreactors, a squalene titer of 5.1 mg/L of culture was reached.
Collapse
|
30
|
Wickell DA, Li FW. On the evolutionary significance of horizontal gene transfers in plants. THE NEW PHYTOLOGIST 2020; 225:113-117. [PMID: 31347197 DOI: 10.1111/nph.16022] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/04/2019] [Indexed: 05/05/2023]
Abstract
Horizontal gene transfer (HGT) has long been seen as a crucial process in the evolution of prokaryotic species, but until recently it was thought to have little, if any, effect on the evolution of eukaryotic life forms. Detecting and describing HGT events in eukaryotes is difficult, making this phenomenon at times controversial. However, modern advances in genomics and bioinformatics have radically altered our view of HGT in eukaryotes, especially in plants. It now appears that HGT to and from plant lineages is more common than previously suspected. Importantly, the transfer of functional nuclear genes with adaptive significance has been reported in numerous taxa. Here we review several recent studies that have found evidence of the horizontal transfer of nuclear genes, and argue that HGT has undoubtedly had profound impacts on plant evolution as a whole.
Collapse
Affiliation(s)
- David A Wickell
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, Cornell University, New York, NY, 14853, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, Cornell University, New York, NY, 14853, USA
| |
Collapse
|
31
|
Heinsch SC, Hsu SY, Otto-Hanson L, Kinkel L, Smanski MJ. Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils. BMC Genomics 2019; 20:994. [PMID: 31856709 PMCID: PMC6923854 DOI: 10.1186/s12864-019-6279-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Background Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces spp. have been implicated as important members of naturally disease-suppressive soils. To shine more light on the ecology and evolution of disease-suppressive microbial communities, we have sequenced the genome of three Streptomyces strains isolated from disease-suppressive soils and compared them to previously sequenced isolates. Strains selected for sequencing had previously showed strong phenotypes in competition or signaling assays. Results Here we present the de novo sequencing of three strains of the genus Streptomyces isolated from disease-suppressive soils to produce high-quality complete genomes. Streptomyces sp. GS93–23, Streptomyces sp. 3211–3, and Streptomyces sp. S3–4 were found to have linear chromosomes of 8.24 Mb, 8.23 Mb, and greater than 7.5 Mb, respectively. In addition, two of the strains were found to have large, linear plasmids. Each strain harbors between 26 and 38 natural product biosynthetic gene clusters, on par with previously sequenced Streptomyces spp. We compared these newly sequenced genomes with those of previously sequenced organisms. We see substantial natural product biosynthetic diversity between closely related strains, with the gain/loss of episomal DNA elements being a primary driver of genome evolution. Conclusions Long read sequencing data facilitates large contig assembly for high-GC Streptomyces genomes. While the sample number is too small for a definitive conclusion, we do not see evidence that disease suppressive soil isolates are particularly privileged in terms of numbers of biosynthetic gene clusters. The strong sequence similarity between GS93–23 and previously isolated Streptomyces lydicus suggests that species recruitment may contribute to the evolution of disease-suppressive microbial communities.
Collapse
Affiliation(s)
- Stephen C Heinsch
- Bioinformatics and Computational Biology, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA.,BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA
| | - Szu-Yi Hsu
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA
| | - Lindsey Otto-Hanson
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA.,Department of Plant Pathology, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA
| | - Linda Kinkel
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA.,Department of Plant Pathology, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA
| | - Michael J Smanski
- Bioinformatics and Computational Biology, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA. .,BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA. .,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin-Cities, Saint Paul, MN, 55108, USA.
| |
Collapse
|
32
|
Nair IM, Kochupurakal J. In silico characterization and over-expression of squalene hopene cyclase from Pseudomonas mendocina. 3 Biotech 2019; 9:381. [PMID: 31588405 DOI: 10.1007/s13205-019-1901-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/16/2019] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas mendocina was identified as a novel endophytic isolate of Murraya koenigii with squalene cyclase activity. The PCR amplification of squalene hopene cyclase (shc) gene from the isolate Pseudomonas mendocina with the primers PA1/PA2 showed a band at 1980 bp specific for the enzyme squalene hopene cyclase. The in silico translation of the squalene hopene cyclase gene showed 96% sequence similarity with squalene hopene cyclase of Pseudomonas agarici (WP-060782422). Docking studies of the template and the modeled protein with the ligand squalene showed that the main interacting residues were Asp376 and Asp377. Squalene hopene cyclase template 1 sqc.1A sequence from Alicyclobacillus acidocaldaruis was used as the template for docking experiments. The gene coding for squalene hopene cyclase from Pseudomonas mendocina has been cloned in pET-28a vector to produce recombinant vector and was expressed in E.coli BL21 (DE3) expression system. Squalene hopene cyclase enzyme was isolated, purified and the molecular weight was confirmed by SDS-PAGE as 75 KDa.
Collapse
Affiliation(s)
- Indu M Nair
- School of Biosciences, Mahatma Gandhi University Kottayam, Kottayam, Kerala 686560 India
| | | |
Collapse
|
33
|
Suzuki A, Aikawa Y, Ito R, Hoshino T. Oryza sativa
Parkeol Cyclase: Changes in the Substrate‐Folding Conformation and the Deprotonation Sites on Mutation at Tyr257: Importance of the Hydroxy Group and Steric Bulk. Chembiochem 2019; 20:2862-2875. [DOI: 10.1002/cbic.201900314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Asuka Suzuki
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Yuko Aikawa
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Ryousuke Ito
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| |
Collapse
|
34
|
Welander PV. Deciphering the evolutionary history of microbial cyclic triterpenoids. Free Radic Biol Med 2019; 140:270-278. [PMID: 31071437 DOI: 10.1016/j.freeradbiomed.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 11/26/2022]
Abstract
Cyclic triterpenoids are a class of lipids that have fascinated chemists, biologist, and geologist alike for many years. These molecules have diverse physiological roles in a variety of bacterial and eukaryotic organisms and a shared evolutionary ancestry that is reflected in the elegant biochemistry required for their synthesis. Cyclic triterpenoids are also quite recalcitrant and are preserved in sedimentary rocks where they are utilized as "molecular fossils" or biomarkers that can physically link microbial taxa and their metabolisms to a specific time or event in Earth's history. However, a proper interpretation of cyclic triterpenoid biosignatures requires a robust understanding of their function in extant organisms and in the evolutionary history of their biosynthetic pathways. Here, I review two potential cyclic triterpenoid evolutionary scenarios and the recent genetic and biochemical studies that are providing experimental evidence to distinguish between these hypotheses. The study of cyclic triterpenoids will continue to provide a wealth of information that can significantly impact the interpretation of lipid biosignatures in the rock record and provides a compelling model of how two natural repositories of evolutionary history available on Earth, the geologic record in sedimentary rocks and the molecular record in living organisms, can be linked.
Collapse
Affiliation(s)
- Paula V Welander
- Department of Earth System Science, Stanford University, 473 Via Ortega, Rm 140, Stanford, CA, 94305, USA.
| |
Collapse
|
35
|
Peters C, Buller R. Linear enzyme cascade for the production of (-)-iso-isopulegol. ACTA ACUST UNITED AC 2019; 74:63-70. [PMID: 30645192 DOI: 10.1515/znc-2018-0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/09/2018] [Indexed: 01/31/2023]
Abstract
Biocatalysis has developed enormously in the last decade and now offers solutions for the sustainable production of chiral and highly functionalised asset molecules. Products generated by enzymatic transformations are already being used in the food, feed, chemical, pharmaceutical and cosmetic industry, and the accessible compound panoply is expected to expand even further. In particular, the combination of stereo-selective enzymes in linear cascade reactions is an elegant strategy toward enantiomeric pure compounds, as it reduces the number of isolation and purification steps and avoids accumulation of potentially unstable intermediates. Here, we present the set-up of an enzyme cascade to selectively convert citral to (-)-iso-isopulegol by combining an ene reductase and a squalene hopene cyclase. In the initial reaction step, the ene reductase YqjM from Bacillus subtilis selectively transforms citral to (S)-citronellal, which is subsequently cyclised exclusively to (-)-iso-isopulegol by a mutant of the squalene hopene cyclase from Alicyclobacillus acidocaldarius (AacSHC). With this approach, we can convert citral to an enantiopure precursor for isomenthol derivatives.
Collapse
Affiliation(s)
- Christin Peters
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Rebecca Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| |
Collapse
|
36
|
Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
Collapse
Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
37
|
Berni R, Hoque MZ, Legay S, Cai G, Siddiqui KS, Hausman JF, Andre CM, Guerriero G. Tuscan Varieties of Sweet Cherry Are Rich Sources of Ursolic and Oleanolic Acid: Protein Modeling Coupled to Targeted Gene Expression and Metabolite Analyses. Molecules 2019; 24:E1590. [PMID: 31013661 PMCID: PMC6515059 DOI: 10.3390/molecules24081590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/20/2019] [Accepted: 04/20/2019] [Indexed: 11/16/2022] Open
Abstract
The potential of six ancient Tuscan sweet cherry (Prunus avium L.) varieties as a source of health-promoting pentacyclic triterpenes is here evaluated by means of a targeted gene expression and metabolite analysis. By using a sequence homology criterion, we identify five oxidosqualene cyclase genes (OSCs) and three cytochrome P450s (CYP85s) that are putatively involved in the triterpene production pathway in sweet cherries. We performed 3D structure prediction and induced-fit docking using cation intermediates and reaction products for some OSCs to predict their function. We show that the Tuscan varieties have different amounts of ursolic and oleanolic acids and that these variations are related to different gene expression profiles. This study stresses the interest of valorizing ancient fruits as alternative sources of functional molecules with nutraceutical value. It also provides information on sweet cherry triterpene biosynthetic genes, which could be the object of follow-up functional studies.
Collapse
Affiliation(s)
- Roberto Berni
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, 53100 Siena, Italy.
- Trees and Timber Institute, National Research Council of Italy (CNR-IVALSA), via Aurelia 49, 58022 Follonica (GR), Italy.
| | - Mubasher Zahir Hoque
- Bio-Bio-1 Research Foundation, Sangskriti Bikash Kendra Bhaban, 1/E/1 Poribagh, Dhaka 1000, Bangladesh.
- Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
| | - Sylvain Legay
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, 53100 Siena, Italy.
| | - Khawar Sohail Siddiqui
- Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
| | - Jean-Francois Hausman
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Christelle M Andre
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| |
Collapse
|
38
|
Pütter KM, van Deenen N, Müller B, Fuchs L, Vorwerk K, Unland K, Bröker JN, Scherer E, Huber C, Eisenreich W, Prüfer D, Schulze Gronover C. The enzymes OSC1 and CYP716A263 produce a high variety of triterpenoids in the latex of Taraxacum koksaghyz. Sci Rep 2019; 9:5942. [PMID: 30976052 PMCID: PMC6459903 DOI: 10.1038/s41598-019-42381-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/28/2019] [Indexed: 01/01/2023] Open
Abstract
Only very little is known about the resin composition of natural rubber from the dandelion species Taraxacum koksaghyz, thus its full characterization could provide new insights into how the isoprenoid end-products influence the physical properties of natural rubber, and this resin might be a good source of highly diverse triterpenoids. Here, we present a comprehensive analysis of the triterpenoid composition in an acetone extract and identified 13 triterpenes and triterpenoids also including the so far unknown pentacyclic compounds lup-19(21)-en-3-ol (1) and its ketone lup-19(21)-en-3-one (2). We purified single triterpenes from the acetone extract by developing a two-step HPLC system that is adapted to the structural differences of the described triterpenoids. Furthermore, we isolated six different oxidosqualene cyclases (OSCs) and two P450 enzymes, and we functionally characterized TkOSC1 and CYP716A263 in Nicotiana benthamiana and Saccharomyces cerevisiae in detail. TkOSC1 is a multifunctional OSC that was capable of synthesizing at least four of the latex-predominant pentacyclic triterpenes (taraxasterol, α-, β-amyrin and lup-19(21)-en-3-ol) while CYP716A263 oxidized pentacyclic triterpenes at the C-3 position. The identified enzymes responsible for biosynthesis and modification of pentacyclic triterpenes in T. koksaghyz latex may represent excellent tools for bioengineering approaches to produce pentacyclic triterpenes heterologously.
Collapse
Affiliation(s)
- Katharina M Pütter
- University of Muenster, Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143, Muenster, Germany
| | - Nicole van Deenen
- University of Muenster, Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143, Muenster, Germany
| | - Boje Müller
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143, Muenster, Germany
| | - Lea Fuchs
- University of Muenster, Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143, Muenster, Germany
| | - Kirsten Vorwerk
- University of Muenster, Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143, Muenster, Germany
| | - Kristina Unland
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143, Muenster, Germany
| | - Jan Niklas Bröker
- University of Muenster, Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143, Muenster, Germany
| | - Emely Scherer
- Technische Universität München, Chair of Biochemistry, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Claudia Huber
- Technische Universität München, Chair of Biochemistry, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Wolfgang Eisenreich
- Technische Universität München, Chair of Biochemistry, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Dirk Prüfer
- University of Muenster, Institute of Plant Biology and Biotechnology, Schlossplatz 8, 48143, Muenster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143, Muenster, Germany
| | - Christian Schulze Gronover
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143, Muenster, Germany.
| |
Collapse
|
39
|
Fukuda Y, Watanabe T, Hoshino T. Mutated variants of squalene-hopene cyclase: enzymatic syntheses of triterpenes bearing oxygen-bridged monocycles and a new 6,6,6,6,6-fusded pentacyclic scaffold, named neogammacerane, from 2,3-oxidosqualene. Org Biomol Chem 2019; 16:8365-8378. [PMID: 30209480 DOI: 10.1039/c8ob02009d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Squalene-hopene cyclase (SHC) catalyzes the conversion of acyclic squalene molecule into a 6,6,6,6,5-fused pentacyclic hopene and hopanol. SHC is also able to convert (3S)-2,3-oxidosqualene into 3β-hydroxyhopene and 3β-hydroxyhopanol and can generate 3α-hydroxyhopene and 3α-hydroxyhopanol from (3R)-2,3-oxidosqualene. Functional analyses of active site residues toward the squalene cyclization reaction have been extensively reported, but investigations of the cyclization reactions of (3R,S)-oxidosqualene by SHC have rarely been reported. The cyclization reactions of oxidosqualene with W169X, G600F/F601G and F601G/P602F were examined. The variants of the W169L generated new triterpene skeletons possessing a 7-oxabicyclo[2.2.1]heptane moiety (oxygen-bridged monocycle) with (1S,2S,4R)- and (1R,2S,4S)-stereochemistry, which were produced from (3R)- and (3S)-oxidosqualenes, respectively. The F601G/P602F double mutant also furnished a novel triterpene, named neogammacer-21(22)-en-3β-ol, consisting of a 6,6,6,6,6-fused pentacyclic system, in which Me-29 at C-22 of the gammacerane skeleton migrated to C-21. We propose to name this novel scaffold neogammacerane. The formation mechanisms of the enzymatic products from 2,3-oxidosqualene are discussed.
Collapse
Affiliation(s)
- Yoriyuki Fukuda
- Graduate School of Science and Technology and Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.
| | | | | |
Collapse
|
40
|
Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H)Stanford University Stanford CA 94305 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
| |
Collapse
|
41
|
Nakano C, Watanabe T, Minamino M, Hoshino T. Enzymatic syntheses of novel carbocyclic scaffolds with a 6,5 + 5,5 ring system by squalene-hopene cyclase. Org Biomol Chem 2019; 17:9375-9389. [DOI: 10.1039/c9ob01941c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel scaffold with a 6,5 + 5, 5 ring system (allodammarane) was synthesized from 27-norsqualene (13a), 3R-(18) and 3S-27-noroxidosqualenes (19).
Collapse
Affiliation(s)
- Chiaki Nakano
- Department of Applied Biological Chemistry
- Faculty of Agriculture
- and Graduate School of Science and Technology
- Niigata University
- Niigata
| | - Takumi Watanabe
- Department of Applied Biological Chemistry
- Faculty of Agriculture
- and Graduate School of Science and Technology
- Niigata University
- Niigata
| | - Mai Minamino
- Department of Applied Biological Chemistry
- Faculty of Agriculture
- and Graduate School of Science and Technology
- Niigata University
- Niigata
| | - Tsutomu Hoshino
- Department of Applied Biological Chemistry
- Faculty of Agriculture
- and Graduate School of Science and Technology
- Niigata University
- Niigata
| |
Collapse
|
42
|
Ideno N, Umeyama S, Watanabe T, Nakajima M, Sato T, Hoshino T. Alicyclobacillus acidocaldarius
Squalene‐Hopene Cyclase: The Critical Role of Steric Bulk at Ala306 and the First Enzymatic Synthesis of Epoxydammarane from 2,3‐Oxidosqualene. Chembiochem 2018; 19:1873-1886. [DOI: 10.1002/cbic.201800281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Natsumi Ideno
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Shikou Umeyama
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Takashi Watanabe
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Mami Nakajima
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Sato
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| |
Collapse
|
43
|
Kaneko I, Terasawa Y, Hoshino T. Squalene-Hopene Cyclase: Mechanistic Insights into the Polycyclization Cascades of Squalene Analogs Bearing Ethyl and Hydroxymethyl Groups at the C-2 and C-23 Positions. Chemistry 2018; 24:11139-11157. [DOI: 10.1002/chem.201801668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Ikki Kaneko
- Graduate School of Science and Technology and Department of Applied Biological Chemistry, Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Yuri Terasawa
- Graduate School of Science and Technology and Department of Applied Biological Chemistry, Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology and Department of Applied Biological Chemistry, Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| |
Collapse
|
44
|
Engleder M, Pichler H. On the current role of hydratases in biocatalysis. Appl Microbiol Biotechnol 2018; 102:5841-5858. [PMID: 29785499 PMCID: PMC6013536 DOI: 10.1007/s00253-018-9065-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 11/06/2022]
Abstract
Water addition to carbon-carbon double bonds provides access to value-added products from inexpensive organic feedstock. This interesting but relatively little-studied reaction is catalysed by hydratases in a highly regio- and enantiospecific fashion with excellent atom economy. Considering that asymmetric hydration of (non-activated) carbon-carbon double bonds is virtually impossible with current organic chemistry, enzymatic hydration reactions are highly attractive for industrial applications. Hydratases have been known for several decades but their biocatalytic potential has only been explored over the past 15 years. As a result, a considerable amount of information on this enzyme group has become available, enabling their development for practical applications. This review focuses on hydratases catalysing water addition to non-activated carbon-carbon double bonds, and examines hydratases from a biochemical, structural and mechanistic angle. Current challenges and opportunities in hydration biocatalysis are discussed, and, ultimately, their potential for organic synthesis is highlighted.
Collapse
Affiliation(s)
- Matthias Engleder
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 8010, Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria.
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 8010, Graz, Austria.
| |
Collapse
|
45
|
Eichhorn E, Locher E, Guillemer S, Wahler D, Fourage L, Schilling B. Biocatalytic Process for (−)-Ambrox Production Using Squalene Hopene Cyclase. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800132] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Eric Eichhorn
- Givaudan Schweiz AG; Ueberlandstrasse 138 8600 Dübendorf Switzerland
| | - Esther Locher
- Givaudan Schweiz AG; Ueberlandstrasse 138 8600 Dübendorf Switzerland
| | - Sabrina Guillemer
- Protéus SA; 70, allée Graham Bell, Parc Georges Besse 30035 Nîmes Cedex 1 France
- PCAS; 2-8 rue de Rouen 78440 Porcheville France
| | - Denis Wahler
- Protéus SA; 70, allée Graham Bell, Parc Georges Besse 30035 Nîmes Cedex 1 France
- Givaudan France SAS; 3 rue des Satellites 31400 Toulouse France
| | - Laurent Fourage
- Protéus SA; 70, allée Graham Bell, Parc Georges Besse 30035 Nîmes Cedex 1 France
- Total RC Stratégie Développement Recherche; 2 Place Jean Millier 92078 Paris La Défense France
| | - Boris Schilling
- Givaudan Schweiz AG; Ueberlandstrasse 138 8600 Dübendorf Switzerland
| |
Collapse
|
46
|
Takahashi K, Sasaki Y, Hoshino T. Squalene-Hopene Cyclase: On the Polycyclization Reactions of Squalene Analogues Bearing Ethyl Groups at Positions C-6, C-10, C-15, and C-19. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kazunari Takahashi
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 950-2181 Nishi-ku, Niigata Japan
| | - Yusuke Sasaki
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 950-2181 Nishi-ku, Niigata Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 950-2181 Nishi-ku, Niigata Japan
| |
Collapse
|
47
|
Aiba Y, Watanabe T, Terasawa Y, Nakano C, Hoshino T. Strictly Conserved Residues in Euphorbia tirucalli
β-Amyrin Cyclase: Trp612 Stabilizes Transient Cation through Cation-π Interaction and CH-π Interaction of Tyr736 with Leu734 Confers Robust Local Protein Architecture. Chembiochem 2018; 19:486-495. [DOI: 10.1002/cbic.201700572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Yukari Aiba
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Takumi Watanabe
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Yuri Terasawa
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Chiaki Nakano
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| |
Collapse
|
48
|
Ivarsson M, Bengtson S, Drake H, Francis W. Fungi in Deep Subsurface Environments. ADVANCES IN APPLIED MICROBIOLOGY 2018; 102:83-116. [PMID: 29680127 DOI: 10.1016/bs.aambs.2017.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The igneous crust of the oceans and the continents represents the major part of Earth's lithosphere and has recently been recognized as a substantial, yet underexplored, microbial habitat. While prokaryotes have been the focus of most investigations, microeukaryotes have been surprisingly neglected. However, recent work acknowledges eukaryotes, and in particular fungi, as common inhabitants of the deep biosphere, including the deep igneous provinces. The fossil record of the subseafloor igneous crust, and to some extent the continental bedrock, establishes fungi or fungus-like organisms as inhabitants of deep rock since at least the Paleoproterozoic, which challenges the present notion of early fungal evolution. Additionally, deep fungi have been shown to play an important ecological role engaging in symbiosis-like relationships with prokaryotes, decomposing organic matter, and being responsible for mineral weathering and formation, thus mediating mobilization of biogeochemically important elements. In this review, we aim at covering the abundance and diversity of fungi in the various igneous rock provinces on Earth as well as describing the ecological impact of deep fungi. We further discuss what consequences recent findings might have for the understanding of the fungal distribution in extensive anoxic environments and for early fungal evolution.
Collapse
Affiliation(s)
- Magnus Ivarsson
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark; Swedish Museum of Natural History, Stockholm, Sweden.
| | | | | | - Warren Francis
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
49
|
The complex resistomes of Paenibacillaceae reflect diverse antibiotic chemical ecologies. ISME JOURNAL 2017; 12:885-897. [PMID: 29259290 DOI: 10.1038/s41396-017-0017-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/17/2017] [Accepted: 11/05/2017] [Indexed: 12/31/2022]
Abstract
The ecology of antibiotic resistance involves the interplay of a long natural history of antibiotic production in the environment, and the modern selection of resistance in pathogens through human use of these drugs. Important components of the resistome are intrinsic resistance genes of environmental bacteria, evolved and acquired over millennia, and their mobilization, which drives dissemination in pathogens. Understanding the dynamics and evolution of resistance across bacterial taxa is essential to address the current crisis in drug-resistant infections. Here we report the exploration of antibiotic resistance in the Paenibacillaceae prompted by our discovery of an ancient intrinsic resistome in Paenibacillus sp. LC231, recovered from the isolated Lechuguilla cave environment. Using biochemical and gene expression analysis, we have mined the resistome of the second member of the Paenibacillaceae family, Brevibacillus brevis VM4, which produces several antimicrobial secondary metabolites. Using phylogenomics, we show that Paenibacillaceae resistomes are in flux, evolve mostly independent of secondary metabolite biosynthetic diversity, and are characterized by cryptic, redundant, pseudoparalogous, and orthologous genes. We find that in contrast to pathogens, mobile genetic elements are not significantly responsible for resistome remodeling. This offers divergent modes of resistome development in pathogens and environmental bacteria.
Collapse
|
50
|
Hoshino T, Nakagawa K, Aiba Y, Itoh D, Nakada C, Masukawa Y. Euphorbia tirucalli
β-Amyrin Synthase: Critical Roles of Steric Sizes at Val483 and Met729 and the CH-π Interaction between Val483 and Trp534 for Catalytic Action. Chembiochem 2017; 18:2145-2155. [DOI: 10.1002/cbic.201700368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Tsutomu Hoshino
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Kazuya Nakagawa
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Yukari Aiba
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Daichi Itoh
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Chika Nakada
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Yukari Masukawa
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| |
Collapse
|