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El-Sayed ASA, Shindia A, Ammar H, Seadawy MG, Khashana SA. Bioprocessing of Epothilone B from Aspergillus fumigatus under solid state fermentation: Antiproliferative activity, tubulin polymerization and cell cycle analysis. BMC Microbiol 2024; 24:43. [PMID: 38291363 PMCID: PMC10829302 DOI: 10.1186/s12866-024-03184-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Abstract
Epothilone derivatives have been recognized as one of the most powerful anticancer drugs towards solid tumors, for their unique affinity to bind with β-tubulin microtubule arrays, stabilizing their disassembly, causing cell death. Sornagium cellulosum is the main source for Epothilone, however, the fermentation bioprocessing of this myxobacteria is the main challenge for commercial production of Epothilone. The metabolic biosynthetic potency of epothilone by Aspergillus fumigatus, an endophyte of Catharanthus roseus, raises the hope for commercial epothilone production, for their fast growth rate and feasibility of manipulating their secondary metabolites. Thus, nutritional optimization of A. fumigatus for maximizing their epothilone productivity under solid state fermentation process is the objective. The highest yield of epothilone was obtained by growing A. fumigatus on orange peels under solid state fermentation (2.2 μg/g), bioprocessed by the Plackett-Burman design. The chemical structure of the extracted epothilone was resolved from the HPLC and LC-MS/MS analysis, with molecular mass 507.2 m/z and identical molecular fragmentation pattern of epothilone B of S. cellulosum. The purified A. fumigatus epothilone had a significant activity towards HepG2 (IC50 0.98 μg/ml), Pancl (IC50 1.5 μg/ml), MCF7 (IC50 3.7 μg/ml) and WI38 (IC50 4.6 μg/ml), as well as a strong anti-tubulin polymerization activity (IC50 0.52 μg/ml) compared to Paclitaxel (2.0 μg/ml). The effect of A. fumigatus epothilone on the immigration ability of HepG2 cells was assessed, as revealed from the wound closure of the monolayer cells that was estimated by ~ 63.7 and 72.5%, in response to the sample and doxorubicin, respectively, compared to negative control. From the Annexin V-PI flow cytometry results, a significant shift of the normal cells to the apoptosis was observed in response to A. fumigatus epothilone by ~ 20 folds compared to control cells, with the highest growth arrest of the HepG2 cells at the G0-G1 stage.
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Affiliation(s)
- Ashraf S A El-Sayed
- Enzymology and Fungal Biotechnology lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
| | - Ahmed Shindia
- Enzymology and Fungal Biotechnology lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Hala Ammar
- Enzymology and Fungal Biotechnology lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Mohamed G Seadawy
- Biological Prevention Department, Egyptian Ministry of Defense, Cairo, Egypt
| | - Samar A Khashana
- Enzymology and Fungal Biotechnology lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
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Lartey I, Benucci GMN, Marsh TL, Bonito GM, Melakeberhan H. Characterizing microbial communities associated with northern root-knot nematode ( Meloidogyne hapla) occurrence and soil health. Front Microbiol 2023; 14:1267008. [PMID: 38029134 PMCID: PMC10667709 DOI: 10.3389/fmicb.2023.1267008] [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: 07/25/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.
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Affiliation(s)
- Isaac Lartey
- Agricultural Nematology Laboratory, Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Gian M. N. Benucci
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Terence L. Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gregory M. Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Haddish Melakeberhan
- Agricultural Nematology Laboratory, Department of Horticulture, Michigan State University, East Lansing, MI, United States
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Phillips KE, Akbar S, Stevens DC. Concepts and conjectures concerning predatory performance of myxobacteria. Front Microbiol 2022; 13:1031346. [PMID: 36246230 PMCID: PMC9556981 DOI: 10.3389/fmicb.2022.1031346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/14/2022] [Indexed: 01/28/2023] Open
Abstract
Myxobacteria are excellent model organisms for investigation of predator-prey interactions and predatory shaping of microbial communities. This review covers interdisciplinary topics related to myxobacterial predation and provides current concepts and challenges for determining predatory performance. Discussed topics include the role of specialized metabolites during predation, genetic determinants for predatory performance, challenges associated with methodological differences, discrepancies between sequenced and environmental myxobacteria, and factors that influence predation.
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Affiliation(s)
- Kayleigh E. Phillips
- Department of BioMolecular Sciences, The University of Mississippi, Oxford, MS, United States
| | - Shukria Akbar
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - D. Cole Stevens
- Department of BioMolecular Sciences, The University of Mississippi, Oxford, MS, United States,*Correspondence: D. Cole Stevens,
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Bader CD, Haack PA, Panter F, Krug D, Müller R. Expanding the Scope of Detectable Microbial Natural Products by Complementary Analytical Methods and Cultivation Systems. JOURNAL OF NATURAL PRODUCTS 2021; 84:268-277. [PMID: 33449690 DOI: 10.1021/acs.jnatprod.0c00942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent advances in genome sequencing have unveiled a large discrepancy between the genome-encoded capacity of microorganisms to produce secondary metabolites and the number detected. In this work, a two-platform mass spectrometry analysis for the comprehensive secondary metabolomics characterization of nine myxobacterial strains, focusing on extending the range of detectable secondary metabolites by diversifying analytical methods and cultivation conditions, is presented. Direct infusion measurements of crude extracts on a Fourier transform ion cyclotron resonance mass spectrometer are compared to a time-of-flight device coupled to liquid chromatography measurements. Both methods are successful in detecting known metabolites, whereas statistical analysis of unknowns highlights their complementarity: Strikingly, 82-99% of molecular features detected with one setup were not detectable with the other. Metabolite profile differences from our set of strains grown in liquid culture versus their swarming colonies on agar plates were evaluated. The detection of up to 96% more molecular features when both liquid and plate cultures were analyzed translates into increased chances to identify new secondary metabolites. Discrimination between primary and secondary metabolism in combination with GNPS molecular networking revealed strain Mx3 as particularly promising for the isolation of novel secondary metabolites among the nine strains investigated in this study.
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Affiliation(s)
- Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Patrick A Haack
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Daniel Krug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
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Prokhorova A, Kainuma M, Hiyane R, Boerner S, Goryanin I. Concurrent treatment of raw and aerated swine wastewater using an electrotrophic denitrification system. BIORESOURCE TECHNOLOGY 2021; 322:124508. [PMID: 33341711 DOI: 10.1016/j.biortech.2020.124508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Enhanced nitrate removal in the cathode chamber of bioelectrochemical systems (BES) using aerated swine wastewater under high nitrate levels and low organic carbon was investigated in this study, focusing on the relationship between nitrogen and bacterial communities involved in denitrification pathways. BESs with the anion exchange membrane (AEM) under cathodic applied potentials of -0.6 V vs. AgCl/AgCl reference electrode showed a removal rate of 99 ± 2 mg L-1 d-1. Moreover, organic compounds from the untreated full-strength wastewater were simultaneously eliminated in the anode chamber with a removal rate of 0.46 g COD L-1 d-1 with achieved efficiency of 61.4 ± 0.5% from an initial concentration of around 5 g of COD L-1, measured over the course of 7 days. The highest microbial diversity was detected in BESs under potentials of -0.6 V, which include autotrophic denitrifiers such as Syderoxidans, Gallionela and Thiobacillus.
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Affiliation(s)
- Anna Prokhorova
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Mami Kainuma
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Rie Hiyane
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Susan Boerner
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Igor Goryanin
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan; School of Informatics, University of Edinburgh, Edinburgh, UK
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Secondary Metabolites of Endophytic Actinomycetes: Isolation, Synthesis, Biosynthesis, and Biological Activities. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 108 2019; 108:207-296. [DOI: 10.1007/978-3-030-01099-7_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Gong Y, Zhang Z, Zhou XW, Anwar MN, Hu XZ, Li ZS, Chen XJ, Li YZ. Competitive Interactions Between Incompatible Mutants of the Social Bacterium Myxococcus xanthus DK1622. Front Microbiol 2018; 9:1200. [PMID: 29922269 PMCID: PMC5996272 DOI: 10.3389/fmicb.2018.01200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 05/16/2018] [Indexed: 01/03/2023] Open
Abstract
Due to the high similarity in their requirements for space and food, close bacterial relatives may be each other's strongest competitors. Close bacterial relatives often form visible boundaries to separate their swarming colonies, a phenomenon termed colony-merger incompatibility. While bacterial species are known to have many incompatible strains, it is largely unclear which traits lead to multiple incompatibilities and the interactions between multiple incompatible siblings. To investigate the competitive interactions of closely related incompatible strains, we mutated Myxococcus xanthus DK1622, a predatory bacterium with complex social behavior. From 3392 random transposon mutations, we obtained 11 self-identification (SI) deficient mutants that formed unmerged colony boundaries with the ancestral strain. The mutations were at nine loci with unknown functions and formed nine independent SI mutants. Compared with their ancestral strain, most of the SI mutants showed reduced growth, swarming and development abilities, but some remained unchanged from their monocultures. When pairwise mixed with their ancestral strain for co-cultivation, these mutants exhibited improved, reduced or unchanged competitive abilities compared with the ancestral strain. The sporulation efficiencies were affected by the DK1622 partner, ranging from almost complete inhibition to 360% stimulation. The differences in competitive growth between the SI mutants and DK1622 were highly correlated with the differences in their sporulation efficiencies. However, the competitive efficiencies of the mutants in mixture were inconsistent with their growth or sporulation abilities in monocultures. We propose that the colony-merger incompatibility in M. xanthus is associated with multiple independent genetic loci, and the incompatible strains hold competitive interaction abilities, which probably determine the complex relationships between multiple incompatible M. xanthus strains and their co-existence strategies.
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Affiliation(s)
- Ya Gong
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Xiu-Wen Zhou
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Mian N Anwar
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Xiao-Zhuang Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Ze-Shuo Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Xiao-Jing Chen
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
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8
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Complex molecules, clever solutions – Enzymatic approaches towards natural product and active agent syntheses. Bioorg Med Chem 2018; 26:1285-1303. [DOI: 10.1016/j.bmc.2017.06.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/29/2017] [Accepted: 06/27/2017] [Indexed: 12/31/2022]
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9
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Cao YN, Zheng LL, Wang D, Liang XX, Gao F, Zhou XL. Recent advances in microtubule-stabilizing agents. Eur J Med Chem 2017; 143:806-828. [PMID: 29223097 DOI: 10.1016/j.ejmech.2017.11.062] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/04/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022]
Abstract
Highly dynamic mitotic spindle microtubules are superb therapeutic targets for a group of chemically diverse and clinically successful anticancer drugs. Microtubule-targeted drugs disrupt microtubule dynamics in distinct ways, and they are primarily classified into two groups: microtubule destabilizing agents (MDAs), such as vinblastine, colchicine, and combretastatin-A4, and microtubule stabilizing agents (MSAs), such as paclitaxel and epothilones. Systematic discovery and development of new MSAs have been aided by extensive research on paclitaxel, yielding a large number of promising anticancer compounds. This review focuses on the natural sources, structural features, mechanisms of action, structure-activity relationship (SAR) and chemical synthesis of MSAs. These MSAs mainly include paclitaxel, taccalonolides, epothilones, FR182877 (cyclostreptin), dictyostatin, discodermolide, eleutherobin and sarcodictyins, zampanolide, dactylolide, laulimalides, peloruside and ceratamines from natural sources, as well as small molecular microtubule stabilizers obtained via chemical synthesis. Then we discuss the application prospect and development of these anticancer compounds.
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Affiliation(s)
- Ya-Nan Cao
- Agronomy College, Sichuan Agriculture University, Chengdu 611130, PR China; School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, PR China
| | - Ling-Li Zheng
- Department of Pharmacy, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, PR China
| | - Dan Wang
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Xiao-Xia Liang
- Agronomy College, Sichuan Agriculture University, Chengdu 611130, PR China.
| | - Feng Gao
- Agronomy College, Sichuan Agriculture University, Chengdu 611130, PR China; School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, PR China.
| | - Xian-Li Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, PR China
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Li ZF, Zhu LP, Gu JY, Singh RP, Li YZ. Isolation and characterisation of the epothilone gene cluster with flanks from high alkalotolerant strain Sorangium cellulosum (So0157-2). World J Microbiol Biotechnol 2017; 33:137. [PMID: 28585173 DOI: 10.1007/s11274-017-2301-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/26/2017] [Indexed: 01/12/2023]
Abstract
Epothilones are cytotoxic macrolactones having auspicious anti-tumorous activities, but merely produced by rare Sorangium strains. Here, we have focused on the epothilone gene cluster from special niche bacterial strain, S. cellulosum So0157-2. Therefore, we have isolated a high pH tolerant S. cellulosum strain So0157-2 and characterized the epothilones gene cluster and its flanks by cosmid/fosmid libraries preparation and sequencing. The assembly spanned 94,459 bp and consisted of 56,019 bp core region. Remarkably, the core as well as upstream 420 bp and downstream 315 bp were highly conserved, while further neighboring regions varied extremely. Transposase traces were identified near the core of clusters, supporting that the transposon-mediated transgenesis is a naturally evolved strategy for the cluster's dissemination. A predicted neighboring esterase gene was identified as a potential epothilone-resistance gene preventing self-toxicity. Novel modification or regulatory genes, a multi-position-cyclo releasing gene and their relationship with corresponding analogs were identified in strain So0157-2. These findings open the door to discover additional, naturally evolved epothilone-related genes for significant applications in industrial as well as clinical sector.
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Affiliation(s)
- Zhi-Feng Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Li-Ping Zhu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Jing-Yan Gu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Raghvendra Pratap Singh
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
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Yue XJ, Cui XW, Zhang Z, Peng R, Zhang P, Li ZF, Li YZ. A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis. Microb Cell Fact 2017; 16:92. [PMID: 28535774 PMCID: PMC5442856 DOI: 10.1186/s12934-017-0706-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/15/2017] [Indexed: 12/29/2022] Open
Abstract
Background Microbial secondary metabolism is regulated by a complex and mostly-unknown network of global and pathway-specific regulators. A dozen biosynthetic gene clusters for secondary metabolites have been reported in myxobacteria, but a few regulation factors have been identified. Results We identified a transcription regulator Esi for the biosynthesis of epothilones. Inactivation of esi promoted the epothilone production, while overexpression of the gene suppressed the production. The regulation was determined to be resulted from the transcriptional changes of epothilone genes. Esi was able to bind, probably via the N-terminus of the protein, to an inverted repeat sequence in the promoter of the epothilone biosynthetic gene cluster. The Esi-homologous sequences retrieved from the RefSeq database are all of the Proteobacteria. However, the Esi regulation is not universal in myxobacteria, because the esi gene exists only in a few myxobacterial genomes. Conclusions Esi binds to the epothilone promoter and down-regulates the transcriptional level of the whole gene cluster to affect the biosynthesis of epothilone. This is the first transcription regulator identified for epothilone biosynthesis. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0706-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin-Jing Yue
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Xiao-Wen Cui
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Ran Peng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Zhi-Feng Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
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Zhu LP, Yue XJ, Han K, Li ZF, Zheng LS, Yi XN, Wang HL, Zhang YM, Li YZ. Allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in Myxococcus xanthus. Microb Cell Fact 2015; 14:105. [PMID: 26194479 PMCID: PMC4509775 DOI: 10.1186/s12934-015-0294-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/07/2015] [Indexed: 01/29/2023] Open
Abstract
Background Exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. The influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear. Results We compared the integration and expression efficiencies of single and multiple exotic genes that were inserted into Myxococcus xanthus genome by transposition and attB-site-directed recombination. While the site-directed integration had a rather stable chloramphenicol acetyl transferase (CAT) activity, the transposition produced varied CAT enzyme activities. We attempted to integrate the 56-kb gene cluster for the biosynthesis of antitumor polyketides epothilones into M. xanthus genome by site-direction but failed, which was determined to be due to the insertion size limitation at the attB site. The transposition technique produced many recombinants with varied production capabilities of epothilones, which, however, were not paralleled to the transcriptional characteristics of the local sites where the genes were integrated. Comparative transcriptomics analysis demonstrated that the allopatric integrations caused selective changes of host transcriptomes, leading to varied expressions of epothilone genes in different mutants. Conclusions With the increase of insertion fragment size, transposition is a more practicable integration method for the expression of exotic genes. Allopatric integrations selectively change host transcriptomes, which lead to varied expression efficiencies of exotic genes. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0294-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li-Ping Zhu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Kui Han
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Zhi-Feng Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Lian-Shuai Zheng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Xiu-Nan Yi
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Hai-Long Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - You-Ming Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
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13
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Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Sci Rep 2013; 3:2101. [PMID: 23812535 PMCID: PMC3696898 DOI: 10.1038/srep02101] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 06/13/2013] [Indexed: 01/03/2023] Open
Abstract
Complex environmental conditions can significantly affect bacterial genome size by unknown mechanisms. The So0157-2 strain of Sorangium cellulosum is an alkaline-adaptive epothilone producer that grows across a wide pH range. Here, we show that the genome of this strain is 14,782,125 base pairs, 1.75-megabases larger than the largest bacterial genome from S. cellulosum reported previously. The total 11,599 coding sequences (CDSs) include massive duplications and horizontally transferred genes, regulated by lots of protein kinases, sigma factors and related transcriptional regulation co-factors, providing the So0157-2 strain abundant resources and flexibility for ecological adaptation. The comparative transcriptomics approach, which detected 90.7% of the total CDSs, not only demonstrates complex expression patterns under varying environmental conditions but also suggests an alkaline-improved pathway of the insertion and duplication, which has been genetically testified, in this strain. These results provide insights into and a paradigm for how environmental conditions can affect bacterial genome expansion.
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