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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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Zhang M, Zhou Z, Zhang J, Yu Y, Sun L, Lu T, Qian H. Metagenomic ecotoxicity assessment of trace difenoconazole on freshwater microbial community. CHEMOSPHERE 2022; 294:133742. [PMID: 35090847 DOI: 10.1016/j.chemosphere.2022.133742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Difenoconazole, a typical triazole fungicide, inhibits the activity of cytochrome P450 enzyme in fungi, and is extensively used in protecting fruits, vegetables, and cereal crops. However, reports elucidating the effects of difenoconazole on aquatic microbial communities are limited. Our study showed that difenoconazole promoted microalgae growth at concentrations ranging from 0.1 to 5 μg/L, which was similar with its environmental residual concentrations. Metagenomic analysis revealed that the aquatic microbial structure could self-regulate to cope with difenoconazole-induced stress by accumulating bacteria exhibiting pollutant degrading abilities. In the short-term, several functional pathways related to xenobiotic biodegradation and analysis were upregulated to provide ability for aquatic microbial community to process xenobiotic stress. Moreover, most disturbed ecological functions were recovered due to the redundancy of microbial communities after prolonged exposure. Furthermore, the risks associated with the dissemination of antibiotic resistance genes were enhanced by difenoconazole in the short-term. Overall, our study contributes to a comprehensive understanding of the difenoconazole-induced ecological impacts and the behavior of aquatic microbial communities that are coping with xenobiotic stress.
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Affiliation(s)
- Mengwei Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China; Department of Jianhu, Zhejiang Industry Polytechnic College, Shaoxing, 312000, PR China
| | - Zhigao Zhou
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Jinfeng Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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Yu Y, Wang H, Tang B, Liang J, Zhang L, Wang H, Bian X, Li YZ, Zhang Y, Zhao GP, Ding X. Reassembly of the Biosynthetic Gene Cluster Enables High Epothilone Yield in Engineered Schlegelella brevitalea. ACS Synth Biol 2020; 9:2009-2022. [PMID: 32603592 DOI: 10.1021/acssynbio.0c00100] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Epothilones, as a new class of microtubule-stabilizing anticancer drugs, exhibit strong bioactivity against taxane-resistant cells and show clinical activity for the treatment of advanced breast cancer. Additionally, they also show great potential for a central nervous system injury and Alzheimer's disease. However, due to the long fermentation period of the original producer and challenges of genetic engineering of nonribosomal peptide/polyketide (NRP/PK) megasynthase genes, the application of epothilones is severely limited. Here, we addressed these problems by reassembling a novel 56-kb epothilone biosynthetic gene cluster, optimizing the promoter of each gene based on RNA-seq profiling, and completing precursor synthetic pathways in engineered Schlegella brevitalea. Furthermore, we debottlenecked the cell autolysis by optimizing culture conditions. Finally, the yield of epothilones in shake flasks was improved to 82 mg/L in six-day fermentation. Overall, we not only constructed epothilone overproducers for further drug development but also provided a rational strategy for high-level NRP/PK compound production.
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Affiliation(s)
- Yucong Yu
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
| | - Huimin Wang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
| | - Biao Tang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, People’s Republic of China
| | - Junheng Liang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
| | - Lin Zhang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
| | - Hongkuan Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
| | - Xiaoying Bian
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Yue-zhong Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Guo-ping Zhao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People’s Republic of China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
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4
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Long R, Yang W, Huang G. Preparation and separation of epothilones with anticancer activity. Chem Biol Drug Des 2020; 96:785-789. [DOI: 10.1111/cbdd.13687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/20/2019] [Accepted: 03/13/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Rong Long
- Active Carbohydrate Research Institute Chongqing Key Laboratory of Green Synthesis and Application College of Chemistry Chongqing Normal University Chongqing China
| | - Wenjian Yang
- Active Carbohydrate Research Institute Chongqing Key Laboratory of Green Synthesis and Application College of Chemistry Chongqing Normal University Chongqing China
| | - Gangliang Huang
- Active Carbohydrate Research Institute Chongqing Key Laboratory of Green Synthesis and Application College of Chemistry Chongqing Normal University Chongqing China
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Dukunde A, Schneider D, Schmidt M, Veldkamp E, Daniel R. Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests. Front Microbiol 2019; 10:1519. [PMID: 31338079 PMCID: PMC6629791 DOI: 10.3389/fmicb.2019.01519] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/18/2019] [Indexed: 01/23/2023] Open
Abstract
Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.
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Affiliation(s)
- Amélie Dukunde
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Marcus Schmidt
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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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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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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Berleman JE, Allen S, Danielewicz MA, Remis JP, Gorur A, Cunha J, Hadi MZ, Zusman DR, Northen TR, Witkowska HE, Auer M. The lethal cargo of Myxococcus xanthus outer membrane vesicles. Front Microbiol 2014; 5:474. [PMID: 25250022 PMCID: PMC4158809 DOI: 10.3389/fmicb.2014.00474] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/22/2014] [Indexed: 11/13/2022] Open
Abstract
Myxococcus xanthus is a bacterial micro-predator known for hunting other microbes in a wolf pack-like manner. Outer membrane vesicles (OMVs) are produced in large quantities by M. xanthus and have a highly organized structure in the extracellular milieu, sometimes occurring in chains that link neighboring cells within a biofilm. OMVs may be a vehicle for mediating wolf pack activity by delivering hydrolytic enzymes and antibiotics aimed at killing prey microbes. Here, both the protein and small molecule cargo of the OMV and membrane fractions of M. xanthus were characterized and compared. Our analysis indicates a number of proteins that are OMV-specific or OMV-enriched, including several with putative hydrolytic function. Secondary metabolite profiling of OMVs identifies 16 molecules, many associated with antibiotic activities. Several hydrolytic enzyme homologs were identified, including the protein encoded by MXAN_3564 (mepA), an M36 protease homolog. Genetic disruption of mepA leads to a significant reduction in extracellular protease activity suggesting MepA is part of the long-predicted (yet to date undetermined) extracellular protease suite of M. xanthus.
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Affiliation(s)
- James E Berleman
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA ; School of Biology, St. Mary's College Moraga, CA, USA
| | - Simon Allen
- Department of Obstetrics, Gynecology and Reproductive Science, UCSF Sandler-Moore Mass Spectrometry Core Facility San Francisco, CA, USA
| | - Megan A Danielewicz
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jonathan P Remis
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Amita Gorur
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jack Cunha
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Masood Z Hadi
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Space Biosciences Division, Synthetic Biology Program, NASA Ames Research Center Moffett Field, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - David R Zusman
- Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
| | - Trent R Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - H Ewa Witkowska
- Department of Obstetrics, Gynecology and Reproductive Science, UCSF Sandler-Moore Mass Spectrometry Core Facility San Francisco, CA, USA
| | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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