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Chen Y, Niu X, Cheng M, Wang L, Sun P, Song H, Cao Y. CRISPR/dCas9-RpoD-Mediated Simultaneous Transcriptional Activation and Repression in Shewanella oneidensis MR-1. ACS Synth Biol 2022; 11:2184-2192. [PMID: 35608070 DOI: 10.1021/acssynbio.2c00149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extracellular electron transfer (EET) of electroactive microorganisms (EAMs) is the dominating factor for versatile applications of bio-electrochemical systems. Shewanella oneidensis MR-1 is one of the model EAMs for the study of EET, which is associated with a variety of cellular activities. However, due to the lack of a transcriptional activation tool, regulation of multiple genes is labor-intensive and time-consuming, which hampers the advancement of improving the EET efficiency in S. oneidensis. In this study, we developed an easily operated and multifunctional regulatory tool, that is, a simultaneous clustered regularly interspaced short palindromic repeats (CRISPR)-mediated transcriptional activation (CRISPRa) and interference (CRISPRi) system, for application in S. oneidensis. First, a large number of activators were screened, and RpoD (σ70) was determined as the optimal activator. Second, the effective activation range was identified to be 190-216 base upstream of the transcriptional start site. Third, up- and downregulation was achieved in concert by two orthogonal single guide RNAs targeting different positions. The activation of the cell division gene (minCDE) and repression of the cytotoxic gene (SO_3166) were concurrently implemented, increasing the power density by 2.5-fold and enhancing the degradation rate of azo dyes by 2.9-fold. The simultaneous CRISPRa and CRISPRi system enables simultaneous multiplex genetic regulation, offering the potential to further advance studies of the EET mechanism and application in S. oneidensis.
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Affiliation(s)
- Yaru Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xiaolong Niu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Meijie Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Luxin Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Panxing Sun
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
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2
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Palanisamy N, Öztürk MA, Akmeriç EB, Di Ventura B. C-terminal eYFP fusion impairs Escherichia coli MinE function. Open Biol 2020; 10:200010. [PMID: 32456552 PMCID: PMC7276532 DOI: 10.1098/rsob.200010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Escherichia coli Min system plays an important role in the proper placement of the septum ring at mid-cell during cell division. MinE forms a pole-to-pole spatial oscillator with the membrane-bound ATPase MinD, resulting in MinD concentration being the lowest at mid-cell. MinC, the direct inhibitor of the septum initiator protein FtsZ, forms a complex with MinD at the membrane, mirroring its polar gradients. Therefore, MinC-mediated FtsZ inhibition occurs away from mid-cell. Min oscillations are often studied in living cells by time-lapse microscopy using fluorescently labelled Min proteins. Here, we show that, despite permitting oscillations to occur in a range of protein concentrations, the enhanced yellow fluorescent protein (eYFP) C-terminally fused to MinE impairs its function. Combining in vivo, in vitro and in silico approaches, we demonstrate that eYFP compromises the ability of MinE to displace MinC from MinD, to stimulate MinD ATPase activity and to directly bind to the membrane. Moreover, we reveal that MinE-eYFP is prone to aggregation. In silico analyses predict that other fluorescent proteins are also likely to compromise several functionalities of MinE, suggesting that the results presented here are not specific to eYFP.
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Affiliation(s)
- Navaneethan Palanisamy
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Mehmet Ali Öztürk
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Emir Bora Akmeriç
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Barbara Di Ventura
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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Ramm B, Heermann T, Schwille P. The E. coli MinCDE system in the regulation of protein patterns and gradients. Cell Mol Life Sci 2019; 76:4245-4273. [PMID: 31317204 PMCID: PMC6803595 DOI: 10.1007/s00018-019-03218-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
Molecular self-organziation, also regarded as pattern formation, is crucial for the correct distribution of cellular content. The processes leading to spatiotemporal patterns often involve a multitude of molecules interacting in complex networks, so that only very few cellular pattern-forming systems can be regarded as well understood. Due to its compositional simplicity, the Escherichia coli MinCDE system has, thus, become a paradigm for protein pattern formation. This biological reaction diffusion system spatiotemporally positions the division machinery in E. coli and is closely related to ParA-type ATPases involved in most aspects of spatiotemporal organization in bacteria. The ATPase MinD and the ATPase-activating protein MinE self-organize on the membrane as a reaction matrix. In vivo, these two proteins typically oscillate from pole-to-pole, while in vitro they can form a variety of distinct patterns. MinC is a passenger protein supposedly operating as a downstream cue of the system, coupling it to the division machinery. The MinCDE system has helped to extract not only the principles underlying intracellular patterns, but also how they are shaped by cellular boundaries. Moreover, it serves as a model to investigate how patterns can confer information through specific and non-specific interactions with other molecules. Here, we review how the three Min proteins self-organize to form patterns, their response to geometric boundaries, and how these patterns can in turn induce patterns of other molecules, focusing primarily on experimental approaches and developments.
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Affiliation(s)
- Beatrice Ramm
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tamara Heermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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Szewczak‐Harris A, Wagstaff J, Löwe J. Cryo-EM structure of the MinCD copolymeric filament from Pseudomonas aeruginosa at 3.1 Å resolution. FEBS Lett 2019; 593:1915-1926. [PMID: 31166018 PMCID: PMC6771821 DOI: 10.1002/1873-3468.13471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 11/07/2022]
Abstract
Positioning of the division site in many bacterial species relies on the MinCDE system, which prevents the cytokinetic Z-ring from assembling anywhere but the mid-cell, through an oscillatory diffusion-reaction mechanism. MinD dimers bind to membranes and, via their partner MinC, inhibit the polymerization of cell division protein FtsZ into the Z-ring. MinC and MinD form polymeric assemblies in solution and on cell membranes. Here, we report the high-resolution cryo-EM structure of the copolymeric filaments of Pseudomonas aeruginosa MinCD. The filaments consist of three protofilaments made of alternating MinC and MinD dimers. The MinCD protofilaments are almost completely straight and assemble as single protofilaments on lipid membranes, which we also visualized by cryo-EM.
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Affiliation(s)
- Andrzej Szewczak‐Harris
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of CambridgeUK
| | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUK
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MinC N- and C-Domain Interactions Modulate FtsZ Assembly, Division Site Selection, and MinD-Dependent Oscillation in Escherichia coli. J Bacteriol 2019; 201:JB.00374-18. [PMID: 30455283 DOI: 10.1128/jb.00374-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
The Min system in Escherichia coli, consisting of MinC, MinD, and MinE proteins, regulates division site selection by preventing assembly of the FtsZ-ring (Z-ring) and exhibits polar oscillation in vivo MinC antagonizes FtsZ polymerization, and in vivo, the cellular location of MinC is controlled by a direct association with MinD at the membrane. To further understand the interactions of MinC with FtsZ and MinD, we performed a mutagenesis screen to identify substitutions in minC that are associated with defects in cell division. We identified amino acids in both the N- and C-domains of MinC that are important for direct interactions with FtsZ and MinD in vitro, as well as mutations that modify the observed in vivo oscillation of green fluorescent protein (GFP)-MinC. Our results indicate that there are two distinct surface-exposed sites on MinC that are important for direct interactions with FtsZ, one at a cleft on the surface of the N-domain and a second on the C-domain that is adjacent to the MinD interaction site. Mutation of either of these sites leads to slower oscillation of GFP-MinC in vivo, although the MinC mutant proteins are still capable of a direct interaction with MinD in phospholipid recruitment assays. Furthermore, we demonstrate that interactions between FtsZ and both sites of MinC identified here are important for assembly of FtsZ-MinC-MinD complexes and that the conserved C-terminal end of FtsZ is not required for MinC-MinD complex formation with GTP-dependent FtsZ polymers.IMPORTANCE Bacterial cell division proceeds through the coordinated assembly of the FtsZ-ring, or Z-ring, at the site of division. Assembly of the Z-ring requires polymerization of FtsZ, which is regulated by several proteins in the cell. In Escherichia coli, the Min system, which contains MinC, MinD, and MinE proteins, exhibits polar oscillation and inhibits the assembly of FtsZ at nonseptal locations. Here, we identify regions on the surface of MinC that are important for contacting FtsZ and destabilizing FtsZ polymers.
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Ke L, Cao LJ, Geng MT, Wang CC, Yao Y, Xiao Y, Huang W, Li RM, Min Y, Guo JC. Identification and expression analysis of MinD gene involved in plastid division in cassava. Biosci Biotechnol Biochem 2018; 83:76-86. [PMID: 30286695 DOI: 10.1080/09168451.2018.1520075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Cassava is a tropical crop known for its starchy root and excellent properties. Considering that starch biosynthesis in the amyloplast is affected by its division, it appears conceivable that the regulation of plastid division plays an important role in starch accumulation. As a member of the Min system genes, MinD participated in the spatial regulation of the position of the plastid division site.In our studies, sequence analysis and phylogenetic analysis showed that MeMinD has been highly conserved during the evolutionary process. Subcellular localisation indicated that MeMinD carries a chloroplast transit peptide and was localised in the chloroplast. Overexpression of MeMinD resulted in division site misplacement and filamentous formation in E. coli, indicating that MeMinD protein was functional across species. MeMinD exhibited different spatial and temporal expression patterns which was highly expressed in the source compared to that in the sink organ.
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Affiliation(s)
- Lei Ke
- a Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource , Institute of Tropical Agriculture and Forestry, Hainan University , Haikou , China
| | - Liang-Jing Cao
- b Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou , China
| | - Meng-Ting Geng
- a Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource , Institute of Tropical Agriculture and Forestry, Hainan University , Haikou , China
| | - Cong-Cong Wang
- a Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource , Institute of Tropical Agriculture and Forestry, Hainan University , Haikou , China
| | - Yuan Yao
- b Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou , China
| | - Yu Xiao
- a Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource , Institute of Tropical Agriculture and Forestry, Hainan University , Haikou , China
| | - Wu Huang
- a Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource , Institute of Tropical Agriculture and Forestry, Hainan University , Haikou , China
| | - Rui-Mei Li
- b Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou , China
| | - Yi Min
- a Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource , Institute of Tropical Agriculture and Forestry, Hainan University , Haikou , China
| | - Jian-Chun Guo
- b Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou , China
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