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Cheng H, Chen D, Li X, Al-Sheikh U, Duan D, Fan Y, Zhu L, Zeng W, Hu Z, Tong X, Zhao G, Zhang Y, Zou W, Duan S, Kang L. Phasic/tonic glial GABA differentially transduce for olfactory adaptation and neuronal aging. Neuron 2024; 112:1473-1486.e6. [PMID: 38447577 DOI: 10.1016/j.neuron.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/11/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Phasic (fast) and tonic (sustained) inhibition of γ-aminobutyric acid (GABA) are fundamental for regulating day-to-day activities, neuronal excitability, and plasticity. However, the mechanisms and physiological functions of glial GABA transductions remain poorly understood. Here, we report that the AMsh glia in Caenorhabditis elegans exhibit both phasic and tonic GABAergic signaling, which distinctively regulate olfactory adaptation and neuronal aging. Through genetic screening, we find that GABA permeates through bestrophin-9/-13/-14 anion channels from AMsh glia, which primarily activate the metabolic GABAB receptor GBB-1 in the neighboring ASH sensory neurons. This tonic action of glial GABA regulates the age-associated changes of ASH neurons and olfactory responses via a conserved signaling pathway, inducing neuroprotection. In addition, the calcium-evoked, vesicular glial GABA release acts upon the ionotropic GABAA receptor LGC-38 in ASH neurons to regulate olfactory adaptation. These findings underscore the fundamental significance of glial GABA in maintaining healthy aging and neuronal stability.
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Affiliation(s)
- Hankui Cheng
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Du Chen
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Xiao Li
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Umar Al-Sheikh
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Duo Duan
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Yuedan Fan
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Linhui Zhu
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Wanxin Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhitao Hu
- Department of Neuroscience, City University of Hong Kong, Kowloon, China
| | - Xiajing Tong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guohua Zhao
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Yongming Zhang
- Department of Ophthalmology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Wenjuan Zou
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Shumin Duan
- MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Lijun Kang
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China.
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Martin-Pascual M, Batianis C, Bruinsma L, Asin-Garcia E, Garcia-Morales L, Weusthuis RA, van Kranenburg R, Martins Dos Santos VAP. A navigation guide of synthetic biology tools for Pseudomonas putida. Biotechnol Adv 2021; 49:107732. [PMID: 33785373 DOI: 10.1016/j.biotechadv.2021.107732] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
Pseudomonas putida is a microbial chassis of huge potential for industrial and environmental biotechnology, owing to its remarkable metabolic versatility and ability to sustain difficult redox reactions and operational stresses, among other attractive characteristics. A wealth of genetic and in silico tools have been developed to enable the unravelling of its physiology and improvement of its performance. However, the rise of this microbe as a promising platform for biotechnological applications has resulted in diversification of tools and methods rather than standardization and convergence. As a consequence, multiple tools for the same purpose have been generated, whilst most of them have not been embraced by the scientific community, which has led to compartmentalization and inefficient use of resources. Inspired by this and by the substantial increase in popularity of P. putida, we aim herein to bring together and assess all currently available (wet and dry) synthetic biology tools specific for this microbe, focusing on the last 5 years. We provide information on the principles, functionality, advantages and limitations, with special focus on their use in metabolic engineering. Additionally, we compare the tool portfolio for P. putida with those for other bacterial chassis and discuss potential future directions for tool development. Therefore, this review is intended as a reference guide for experts and new 'users' of this promising chassis.
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Affiliation(s)
- Maria Martin-Pascual
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Luis Garcia-Morales
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem 4206 AC, The Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen 6708 WE, the Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands; LifeGlimmer GmbH, Berlin 12163, Germany.
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3
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Duan D, Zhang H, Yue X, Fan Y, Xue Y, Shao J, Ding G, Chen D, Li S, Cheng H, Zhang X, Zou W, Liu J, Zhao J, Wang L, Zhao B, Wang Z, Xu S, Wen Q, Liu J, Duan S, Kang L. Sensory Glia Detect Repulsive Odorants and Drive Olfactory Adaptation. Neuron 2020; 108:707-721.e8. [PMID: 32970991 DOI: 10.1016/j.neuron.2020.08.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/25/2020] [Accepted: 08/26/2020] [Indexed: 12/18/2022]
Abstract
Glia are typically considered as supporting cells for neural development and synaptic transmission. Here, we report an active role of a glia in olfactory transduction. As a polymodal sensory neuron in C. elegans, the ASH neuron is previously known to detect multiple aversive odorants. We reveal that the AMsh glia, a sheath for multiple sensory neurons including ASH, cell-autonomously respond to aversive odorants via G-protein-coupled receptors (GPCRs) distinct from those in ASH. Upon activation, the AMsh glia suppress aversive odorant-triggered avoidance and promote olfactory adaptation by inhibiting the ASH neuron via GABA signaling. Thus, we propose a novel two-receptor model where the glia and sensory neuron jointly mediate adaptive olfaction. Our study reveals a non-canonical function of glial cells in olfactory transduction, which may provide new insights into the glia-like supporting cells in mammalian sensory procession.
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Affiliation(s)
- Duo Duan
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China; Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Hu Zhang
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Xiaomin Yue
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Yuedan Fan
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Yadan Xue
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Jiajie Shao
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Gang Ding
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Du Chen
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Shitian Li
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Hankui Cheng
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Xiaoyan Zhang
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Wenjuan Zou
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Jia Liu
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Jian Zhao
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Linmei Wang
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Bingzhen Zhao
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhiping Wang
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China
| | - Suhong Xu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Quan Wen
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jie Liu
- Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Shumin Duan
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China; Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China.
| | - Lijun Kang
- Department of Neurobiology and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310053, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China.
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4
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Bu QT, Li YP, Xie H, Wang J, Li ZY, Chen XA, Mao XM, Li YQ. Comprehensive dissection of dispensable genomic regions in Streptomyces based on comparative analysis approach. Microb Cell Fact 2020; 19:99. [PMID: 32375781 PMCID: PMC7204314 DOI: 10.1186/s12934-020-01359-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/29/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Large-scale genome reduction has been performed to significantly improve the performance of microbial chassis. Identification of the essential or dispensable genes is pivotal for genome reduction to avoid synthetic lethality. Here, taking Streptomyces as an example, we developed a combinatorial strategy for systematic identification of large and dispensable genomic regions in Streptomyces based on multi-omics approaches. RESULTS Phylogenetic tree analysis revealed that the model strains including S. coelicolor A3(2), S. albus J1074 and S. avermitilis MA-4680 were preferred reference for comparative analysis of candidate genomes. Multiple genome alignment suggested that the Streptomyces genomes embodied highly conserved core region and variable sub-telomeric regions, and may present symmetric or asymmetric structure. Pan-genome and functional genome analyses showed that most conserved genes responsible for the fundamental functions of cell viability were concentrated in the core region and the vast majority of abundant genes were dispersed in the sub-telomeric regions. These results suggested that large-scale deletion can be performed in sub-telomeric regions to greatly streamline the Streptomyces genomes for developing versatile chassis. CONCLUSIONS The integrative approach of comparative genomics, functional genomics and pan-genomics can not only be applied to perform a multi-tiered dissection for Streptomyces genomes, but also work as a universal method for systematic analysis of removable regions in other microbial hosts in order to generate more miscellaneous and versatile chassis with minimized genome for drug discovery.
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Affiliation(s)
- Qing-Ting Bu
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Yue-Ping Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
| | - Huang Xie
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Jue Wang
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Zi-Yue Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
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5
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Choi KR, Lee SY. Protocols for RecET-based markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida. Microb Biotechnol 2019; 13:199-209. [PMID: 30761747 PMCID: PMC6922525 DOI: 10.1111/1751-7915.13374] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/19/2019] [Accepted: 01/19/2019] [Indexed: 11/27/2022] Open
Abstract
Pseudomonas putida has emerged as a promising host for the production of chemicals and materials thanks to its metabolic versatility and cellular robustness. In particular, P. putida KT2440 has been officially classified as a generally recognized as safe (GRAS) strain, which makes it suitable for the production of compounds that humans directly consume, including secondary metabolites of high importance. Although various tools and strategies have been developed to facilitate metabolic engineering of P. putida, modification of large genes/clusters essential for heterologous expression of natural products with large biosynthetic gene clusters (BGCs) has not been straightforward. Recently, we reported a RecET-based markerless recombineering system for engineering P. putida and demonstrated deletion of multiple regions as large as 101.7 kb throughout the chromosome by single rounds of recombineering. In addition, development of a donor plasmid system allowed successful markerless integration of heterologous BGCs to P. putida chromosome using the recombineering system with examples of - but not limited to - integrating multiple heterologous BGCs as large as 7.4 kb to the chromosome of P. putida KT2440. In response to the increasing interest in our markerless recombineering system, here we provide detailed protocols for markerless gene knockout and integration for the genome engineering of P. putida and related species of high industrial importance.
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Affiliation(s)
- Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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6
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Markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida. Metab Eng 2018; 47:463-474. [PMID: 29751103 DOI: 10.1016/j.ymben.2018.05.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/05/2018] [Accepted: 05/06/2018] [Indexed: 11/22/2022]
Abstract
Pseudomonas putida has gained much interest among metabolic engineers as a workhorse for producing valuable natural products. While a few gene knockout tools for P. putida have been reported, integration of heterologous genes into the chromosome of P. putida, an essential strategy to develop stable industrial strains producing heterologous bioproducts, requires development of a more efficient method. Current methods rely on time-consuming homologous recombination techniques and transposon-mediated random insertions. Here we report a RecET recombineering system for markerless integration of heterologous genes into the P. putida chromosome. The efficiency and capacity of the recombineering system were first demonstrated by knocking out various genetic loci on the P. putida chromosome with knockout lengths widely spanning 0.6-101.7 kb. The RecET recombineering system developed here allowed successful integration of biosynthetic gene clusters for four proof-of-concept bioproducts, including protein, polyketide, isoprenoid, and amino acid derivative, into the target genetic locus of P. putida chromosome. The markerless recombineering system was completed by combining Cre/lox system and developing efficient plasmid curing systems, generating final strains free of antibiotic markers and plasmids. This markerless recombineering system for efficient gene knockout and integration will expedite metabolic engineering of P. putida, a bacterial host strain of increasing academic and industrial interest.
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Martínez-García E, de Lorenzo V. Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas. Curr Opin Biotechnol 2017; 47:120-132. [DOI: 10.1016/j.copbio.2017.06.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/19/2017] [Indexed: 11/26/2022]
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8
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Mol M, Kabra R, Singh S. Genome modularity and synthetic biology: Engineering systems. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 132:43-51. [PMID: 28801037 DOI: 10.1016/j.pbiomolbio.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/05/2017] [Indexed: 12/15/2022]
Abstract
Whole genome sequencing projects running in various laboratories around the world has generated immense data. A systematic phylogenetic analysis of this data shows that genome complexity goes on decreasing as it evolves, due to its modular nature. This modularity can be harnessed to minimize the genome further to reduce it with the bare minimum essential genes. A reduced modular genome, can fuel progress in the area of synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health.
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Affiliation(s)
- Milsee Mol
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India
| | - Ritika Kabra
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India.
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9
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Martínez-García E, de Lorenzo V. The quest for the minimal bacterial genome. Curr Opin Biotechnol 2016; 42:216-224. [DOI: 10.1016/j.copbio.2016.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 01/09/2023]
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10
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Belda E, van Heck RGA, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins dos Santos VAP, de Lorenzo V, Danchin A, Médigue C. The revisited genome ofPseudomonas putidaKT2440 enlightens its value as a robust metabolicchassis. Environ Microbiol 2016; 18:3403-3424. [DOI: 10.1111/1462-2920.13230] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/16/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Eugeni Belda
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasitology and Mycology; 28, rue du Dr. Roux, Paris, Cedex 15 75724 France
| | - Ruben G. A. van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Maria José Lopez-Sanchez
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Stéphane Cruveiller
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Valérie Barbe
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute, National Sequencing Center; 2 rue Gaston Crémieux 91057 Evry France
| | - Claire Fraser
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore MD USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
- School of Biology, Newcastle University; Newcastle upon Tyne NE1 7RU UK
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Anne Morgat
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics; Geneva CH-1206 Switzerland
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - David Vallenet
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Zoé Rouy
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Claudine Médigue
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
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Leprince A, de Lorenzo V, Völler P, van Passel MWJ, Martins dos Santos VAP. Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol 2012; 14:1444-53. [PMID: 22429517 PMCID: PMC3429869 DOI: 10.1111/j.1462-2920.2012.02730.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Cumulative site-directed mutagenesis is of limited suitability for the global analysis of the gene functions in the microbe's cellular network. In order to simplify and stabilize the genome of the soil bacterium Pseudomonas putida, we developed a recyclable three-step excision method based on the combination of customized mini-transposons and the FLP-FRT site-specific recombination system. To demonstrate the powerful potential of these tools, we first established insertion mutant libraries that allow users to study gene functions with respect either to phenotypic characteristics (single insertions) or to their involvement in predicted networks (double insertions). Based on these libraries, we generated as a proof-of-principle, single-deletion mutants lacking ∼ 4.1% of the genome (∼ 3.7% of the gene repertoire). A cyclical application of the method generated four double-deletion mutants of which a maximum of ∼ 7.4% of the chromosome (∼ 6.9% of the gene count) was excised. This procedure demonstrates a new strategy for rapid genome streamlining and gain of new insights into the molecular interactions and regulations.
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Affiliation(s)
- Audrey Leprince
- Systems and Synthetic Biology Group, Helmholtz-Centre for Infection Research, Braunschweig, Germany
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Programmable bacterial catalysis - designing cells for biosynthesis of value-added compounds. FEBS Lett 2012; 586:2184-90. [DOI: 10.1016/j.febslet.2012.02.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 12/26/2022]
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Poblete-Castro I, Becker J, Dohnt K, dos Santos VM, Wittmann C. Industrial biotechnology of Pseudomonas putida and related species. Appl Microbiol Biotechnol 2012; 93:2279-90. [DOI: 10.1007/s00253-012-3928-0] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/29/2022]
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